Diff for /imach/src/imach.c between versions 1.46 and 1.282

version 1.46, 2002/05/30 17:44:35 version 1.282, 2018/02/27 22:50:02
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.282  2018/02/27 22:50:02  brouard
      *** empty log message ***
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.281  2018/02/27 19:25:23  brouard
   first survey ("cross") where individuals from different ages are    Summary: Adding second argument for quitting
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.280  2018/02/21 07:58:13  brouard
   second wave of interviews ("longitudinal") which measure each change    Summary: 0.99r15
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.279  2017/07/20 13:35:01  brouard
   simplest model is the multinomial logistic model where pij is the    Summary: temporary working
   probability to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.278  2017/07/19 14:09:02  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Summary: Bug for mobil_average=0 and prevforecast fixed(?)
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    Revision 1.277  2017/07/17 08:53:49  brouard
   where the markup *Covariates have to be included here again* invites    Summary: BOM files can be read now
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.276  2017/06/30 15:48:31  brouard
     Summary: Graphs improvements
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.275  2017/06/30 13:39:33  brouard
   identical for each individual. Also, if a individual missed an    Summary: Saito's color
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.274  2017/06/29 09:47:08  brouard
     Summary: Version 0.99r14
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    Revision 1.273  2017/06/27 11:06:02  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    Summary: More documentation on projections
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.272  2017/06/27 10:22:40  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    Summary: Color of backprojection changed from 6 to 5(yellow)
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Revision 1.271  2017/06/27 10:17:50  brouard
     Summary: Some bug with rint
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.270  2017/05/24 05:45:29  brouard
      *** empty log message ***
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.269  2017/05/23 08:39:25  brouard
   This software have been partly granted by Euro-REVES, a concerted action    Summary: Code into subroutine, cleanings
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.268  2017/05/18 20:09:32  brouard
   software can be distributed freely for non commercial use. Latest version    Summary: backprojection and confidence intervals of backprevalence
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.267  2017/05/13 10:25:05  brouard
      Summary: temporary save for backprojection
 #include <math.h>  
 #include <stdio.h>    Revision 1.266  2017/05/13 07:26:12  brouard
 #include <stdlib.h>    Summary: Version 0.99r13 (improvements and bugs fixed)
 #include <unistd.h>  
     Revision 1.265  2017/04/26 16:22:11  brouard
 #define MAXLINE 256    Summary: imach 0.99r13 Some bugs fixed
 #define GNUPLOTPROGRAM "gnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.264  2017/04/26 06:01:29  brouard
 #define FILENAMELENGTH 80    Summary: Labels in graphs
 /*#define DEBUG*/  
 #define windows    Revision 1.263  2017/04/24 15:23:15  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Summary: to save
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.262  2017/04/18 16:48:12  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    *** empty log message ***
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.261  2017/04/05 10:14:09  brouard
 #define NINTERVMAX 8    Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.260  2017/04/04 17:46:59  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    Summary: Gnuplot indexations fixed (humm)
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.259  2017/04/04 13:01:16  brouard
 #define AGESUP 130    Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
 #define AGEBASE 40  
     Revision 1.258  2017/04/03 10:17:47  brouard
     Summary: Version 0.99r12
 int erreur; /* Error number */  
 int nvar;    Some cleanings, conformed with updated documentation.
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.257  2017/03/29 16:53:30  brouard
 int nlstate=2; /* Number of live states */    Summary: Temp
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.256  2017/03/27 05:50:23  brouard
 int popbased=0;    Summary: Temporary
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.255  2017/03/08 16:02:28  brouard
 int maxwav; /* Maxim number of waves */    Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.254  2017/03/08 07:13:00  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Summary: Fixing data parameter line
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Revision 1.253  2016/12/15 11:59:41  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Summary: 0.99 in progress
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Revision 1.252  2016/09/15 21:15:37  brouard
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    *** empty log message ***
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.251  2016/09/15 15:01:13  brouard
  FILE  *ficresvij;    Summary: not working
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.250  2016/09/08 16:07:27  brouard
   char fileresvpl[FILENAMELENGTH];    Summary: continue
   
 #define NR_END 1    Revision 1.249  2016/09/07 17:14:18  brouard
 #define FREE_ARG char*    Summary: Starting values from frequencies
 #define FTOL 1.0e-10  
     Revision 1.248  2016/09/07 14:10:18  brouard
 #define NRANSI    *** empty log message ***
 #define ITMAX 200  
     Revision 1.247  2016/09/02 11:11:21  brouard
 #define TOL 2.0e-4    *** empty log message ***
   
 #define CGOLD 0.3819660    Revision 1.246  2016/09/02 08:49:22  brouard
 #define ZEPS 1.0e-10    *** empty log message ***
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.245  2016/09/02 07:25:01  brouard
 #define GOLD 1.618034    *** empty log message ***
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.244  2016/09/02 07:17:34  brouard
     *** empty log message ***
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.243  2016/09/02 06:45:35  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    *** empty log message ***
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.242  2016/08/30 15:01:20  brouard
 #define rint(a) floor(a+0.5)    Summary: Fixing a lots
   
 static double sqrarg;    Revision 1.241  2016/08/29 17:17:25  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Summary: gnuplot problem in Back projection to fix
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.240  2016/08/29 07:53:18  brouard
 int imx;    Summary: Better
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.239  2016/08/26 15:51:03  brouard
     Summary: Improvement in Powell output in order to copy and paste
 int estepm;  
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    Author:
   
 int m,nb;    Revision 1.238  2016/08/26 14:23:35  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Summary: Starting tests of 0.99
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.237  2016/08/26 09:20:19  brouard
 double dateintmean=0;    Summary: to valgrind
   
 double *weight;    Revision 1.236  2016/08/25 10:50:18  brouard
 int **s; /* Status */    *** empty log message ***
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.235  2016/08/25 06:59:23  brouard
     *** empty log message ***
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.234  2016/08/23 16:51:20  brouard
     *** empty log message ***
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Revision 1.233  2016/08/23 07:40:50  brouard
 {    Summary: not working
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Revision 1.232  2016/08/22 14:20:21  brouard
     Summary: not working
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.231  2016/08/22 07:17:15  brouard
 #ifdef windows    Summary: not working
    s = strrchr( path, '\\' );           /* find last / */  
 #else    Revision 1.230  2016/08/22 06:55:53  brouard
    s = strrchr( path, '/' );            /* find last / */    Summary: Not working
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */    Revision 1.229  2016/07/23 09:45:53  brouard
 #if     defined(__bsd__)                /* get current working directory */    Summary: Completing for func too
       extern char       *getwd( );  
     Revision 1.228  2016/07/22 17:45:30  brouard
       if ( getwd( dirc ) == NULL ) {    Summary: Fixing some arrays, still debugging
 #else  
       extern char       *getcwd( );    Revision 1.226  2016/07/12 18:42:34  brouard
     Summary: temp
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.225  2016/07/12 08:40:03  brouard
          return( GLOCK_ERROR_GETCWD );    Summary: saving but not running
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.224  2016/07/01 13:16:01  brouard
    } else {                             /* strip direcotry from path */    Summary: Fixes
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    Revision 1.223  2016/02/19 09:23:35  brouard
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Summary: temporary
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Revision 1.222  2016/02/17 08:14:50  brouard
       dirc[l1-l2] = 0;                  /* add zero */    Summary: Probably last 0.98 stable version 0.98r6
    }  
    l1 = strlen( dirc );                 /* length of directory */    Revision 1.221  2016/02/15 23:35:36  brouard
 #ifdef windows    Summary: minor bug
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else    Revision 1.219  2016/02/15 00:48:12  brouard
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    *** empty log message ***
 #endif  
    s = strrchr( name, '.' );            /* find last / */    Revision 1.218  2016/02/12 11:29:23  brouard
    s++;    Summary: 0.99 Back projections
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);    Revision 1.217  2015/12/23 17:18:31  brouard
    l2= strlen( s)+1;    Summary: Experimental backcast
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    Revision 1.216  2015/12/18 17:32:11  brouard
    return( 0 );                         /* we're done */    Summary: 0.98r4 Warning and status=-2
 }  
     Version 0.98r4 is now:
      - displaying an error when status is -1, date of interview unknown and date of death known;
 /******************************************/     - permitting a status -2 when the vital status is unknown at a known date of right truncation.
     Older changes concerning s=-2, dating from 2005 have been supersed.
 void replace(char *s, char*t)  
 {    Revision 1.215  2015/12/16 08:52:24  brouard
   int i;    Summary: 0.98r4 working
   int lg=20;  
   i=0;    Revision 1.214  2015/12/16 06:57:54  brouard
   lg=strlen(t);    Summary: temporary not working
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.213  2015/12/11 18:22:17  brouard
     if (t[i]== '\\') s[i]='/';    Summary: 0.98r4
   }  
 }    Revision 1.212  2015/11/21 12:47:24  brouard
     Summary: minor typo
 int nbocc(char *s, char occ)  
 {    Revision 1.211  2015/11/21 12:41:11  brouard
   int i,j=0;    Summary: 0.98r3 with some graph of projected cross-sectional
   int lg=20;  
   i=0;    Author: Nicolas Brouard
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.210  2015/11/18 17:41:20  brouard
   if  (s[i] == occ ) j++;    Summary: Start working on projected prevalences  Revision 1.209  2015/11/17 22:12:03  brouard
   }    Summary: Adding ftolpl parameter
   return j;    Author: N Brouard
 }  
     We had difficulties to get smoothed confidence intervals. It was due
 void cutv(char *u,char *v, char*t, char occ)    to the period prevalence which wasn't computed accurately. The inner
 {    parameter ftolpl is now an outer parameter of the .imach parameter
   int i,lg,j,p=0;    file after estepm. If ftolpl is small 1.e-4 and estepm too,
   i=0;    computation are long.
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Revision 1.208  2015/11/17 14:31:57  brouard
   }    Summary: temporary
   
   lg=strlen(t);    Revision 1.207  2015/10/27 17:36:57  brouard
   for(j=0; j<p; j++) {    *** empty log message ***
     (u[j] = t[j]);  
   }    Revision 1.206  2015/10/24 07:14:11  brouard
      u[p]='\0';    *** empty log message ***
   
    for(j=0; j<= lg; j++) {    Revision 1.205  2015/10/23 15:50:53  brouard
     if (j>=(p+1))(v[j-p-1] = t[j]);    Summary: 0.98r3 some clarification for graphs on likelihood contributions
   }  
 }    Revision 1.204  2015/10/01 16:20:26  brouard
     Summary: Some new graphs of contribution to likelihood
 /********************** nrerror ********************/  
     Revision 1.203  2015/09/30 17:45:14  brouard
 void nrerror(char error_text[])    Summary: looking at better estimation of the hessian
 {  
   fprintf(stderr,"ERREUR ...\n");    Also a better criteria for convergence to the period prevalence And
   fprintf(stderr,"%s\n",error_text);    therefore adding the number of years needed to converge. (The
   exit(1);    prevalence in any alive state shold sum to one
 }  
 /*********************** vector *******************/    Revision 1.202  2015/09/22 19:45:16  brouard
 double *vector(int nl, int nh)    Summary: Adding some overall graph on contribution to likelihood. Might change
 {  
   double *v;    Revision 1.201  2015/09/15 17:34:58  brouard
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Summary: 0.98r0
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    - Some new graphs like suvival functions
 }    - Some bugs fixed like model=1+age+V2.
   
 /************************ free vector ******************/    Revision 1.200  2015/09/09 16:53:55  brouard
 void free_vector(double*v, int nl, int nh)    Summary: Big bug thanks to Flavia
 {  
   free((FREE_ARG)(v+nl-NR_END));    Even model=1+age+V2. did not work anymore
 }  
     Revision 1.199  2015/09/07 14:09:23  brouard
 /************************ivector *******************************/    Summary: 0.98q6 changing default small png format for graph to vectorized svg.
 int *ivector(long nl,long nh)  
 {    Revision 1.198  2015/09/03 07:14:39  brouard
   int *v;    Summary: 0.98q5 Flavia
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");    Revision 1.197  2015/09/01 18:24:39  brouard
   return v-nl+NR_END;    *** empty log message ***
 }  
     Revision 1.196  2015/08/18 23:17:52  brouard
 /******************free ivector **************************/    Summary: 0.98q5
 void free_ivector(int *v, long nl, long nh)  
 {    Revision 1.195  2015/08/18 16:28:39  brouard
   free((FREE_ARG)(v+nl-NR_END));    Summary: Adding a hack for testing purpose
 }  
     After reading the title, ftol and model lines, if the comment line has
 /******************* imatrix *******************************/    a q, starting with #q, the answer at the end of the run is quit. It
 int **imatrix(long nrl, long nrh, long ncl, long nch)    permits to run test files in batch with ctest. The former workaround was
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    $ echo q | imach foo.imach
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Revision 1.194  2015/08/18 13:32:00  brouard
   int **m;    Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
    
   /* allocate pointers to rows */    Revision 1.193  2015/08/04 07:17:42  brouard
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    Summary: 0.98q4
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.192  2015/07/16 16:49:02  brouard
   m -= nrl;    Summary: Fixing some outputs
    
      Revision 1.191  2015/07/14 10:00:33  brouard
   /* allocate rows and set pointers to them */    Summary: Some fixes
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.190  2015/05/05 08:51:13  brouard
   m[nrl] += NR_END;    Summary: Adding digits in output parameters (7 digits instead of 6)
   m[nrl] -= ncl;  
      Fix 1+age+.
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
      Revision 1.189  2015/04/30 14:45:16  brouard
   /* return pointer to array of pointers to rows */    Summary: 0.98q2
   return m;  
 }    Revision 1.188  2015/04/30 08:27:53  brouard
     *** empty log message ***
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)    Revision 1.187  2015/04/29 09:11:15  brouard
       int **m;    *** empty log message ***
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */    Revision 1.186  2015/04/23 12:01:52  brouard
 {    Summary: V1*age is working now, version 0.98q1
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));    Some codes had been disabled in order to simplify and Vn*age was
 }    working in the optimization phase, ie, giving correct MLE parameters,
     but, as usual, outputs were not correct and program core dumped.
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    Revision 1.185  2015/03/11 13:26:42  brouard
 {    Summary: Inclusion of compile and links command line for Intel Compiler
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Revision 1.184  2015/03/11 11:52:39  brouard
     Summary: Back from Windows 8. Intel Compiler
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.183  2015/03/10 20:34:32  brouard
   m += NR_END;    Summary: 0.98q0, trying with directest, mnbrak fixed
   m -= nrl;  
     We use directest instead of original Powell test; probably no
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    incidence on the results, but better justifications;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    We fixed Numerical Recipes mnbrak routine which was wrong and gave
   m[nrl] += NR_END;    wrong results.
   m[nrl] -= ncl;  
     Revision 1.182  2015/02/12 08:19:57  brouard
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Summary: Trying to keep directest which seems simpler and more general
   return m;    Author: Nicolas Brouard
 }  
     Revision 1.181  2015/02/11 23:22:24  brouard
 /*************************free matrix ************************/    Summary: Comments on Powell added
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {    Author:
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    Revision 1.180  2015/02/11 17:33:45  brouard
 }    Summary: Finishing move from main to function (hpijx and prevalence_limit)
   
 /******************* ma3x *******************************/    Revision 1.179  2015/01/04 09:57:06  brouard
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    Summary: back to OS/X
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    Revision 1.178  2015/01/04 09:35:48  brouard
   double ***m;    *** empty log message ***
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Revision 1.177  2015/01/03 18:40:56  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    Summary: Still testing ilc32 on OSX
   m += NR_END;  
   m -= nrl;    Revision 1.176  2015/01/03 16:45:04  brouard
     *** empty log message ***
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.175  2015/01/03 16:33:42  brouard
   m[nrl] += NR_END;    *** empty log message ***
   m[nrl] -= ncl;  
     Revision 1.174  2015/01/03 16:15:49  brouard
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Summary: Still in cross-compilation
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    Revision 1.173  2015/01/03 12:06:26  brouard
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    Summary: trying to detect cross-compilation
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;    Revision 1.172  2014/12/27 12:07:47  brouard
   for (j=ncl+1; j<=nch; j++)    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
     m[nrl][j]=m[nrl][j-1]+nlay;  
      Revision 1.171  2014/12/23 13:26:59  brouard
   for (i=nrl+1; i<=nrh; i++) {    Summary: Back from Visual C
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)    Still problem with utsname.h on Windows
       m[i][j]=m[i][j-1]+nlay;  
   }    Revision 1.170  2014/12/23 11:17:12  brouard
   return m;    Summary: Cleaning some \%% back to %%
 }  
     The escape was mandatory for a specific compiler (which one?), but too many warnings.
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    Revision 1.169  2014/12/22 23:08:31  brouard
 {    Summary: 0.98p
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Outputs some informations on compiler used, OS etc. Testing on different platforms.
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Revision 1.168  2014/12/22 15:17:42  brouard
     Summary: update
 /***************** f1dim *************************/  
 extern int ncom;    Revision 1.167  2014/12/22 13:50:56  brouard
 extern double *pcom,*xicom;    Summary: Testing uname and compiler version and if compiled 32 or 64
 extern double (*nrfunc)(double []);  
      Testing on Linux 64
 double f1dim(double x)  
 {    Revision 1.166  2014/12/22 11:40:47  brouard
   int j;    *** empty log message ***
   double f;  
   double *xt;    Revision 1.165  2014/12/16 11:20:36  brouard
      Summary: After compiling on Visual C
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    * imach.c (Module): Merging 1.61 to 1.162
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);    Revision 1.164  2014/12/16 10:52:11  brouard
   return f;    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 }  
     * imach.c (Module): Merging 1.61 to 1.162
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    Revision 1.163  2014/12/16 10:30:11  brouard
 {    * imach.c (Module): Merging 1.61 to 1.162
   int iter;  
   double a,b,d,etemp;    Revision 1.162  2014/09/25 11:43:39  brouard
   double fu,fv,fw,fx;    Summary: temporary backup 0.99!
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;    Revision 1.1  2014/09/16 11:06:58  brouard
   double e=0.0;    Summary: With some code (wrong) for nlopt
    
   a=(ax < cx ? ax : cx);    Author:
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    Revision 1.161  2014/09/15 20:41:41  brouard
   fw=fv=fx=(*f)(x);    Summary: Problem with macro SQR on Intel compiler
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);    Revision 1.160  2014/09/02 09:24:05  brouard
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    *** empty log message ***
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);    Revision 1.159  2014/09/01 10:34:10  brouard
 #ifdef DEBUG    Summary: WIN32
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    Author: Brouard
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif    Revision 1.158  2014/08/27 17:11:51  brouard
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    *** empty log message ***
       *xmin=x;  
       return fx;    Revision 1.157  2014/08/27 16:26:55  brouard
     }    Summary: Preparing windows Visual studio version
     ftemp=fu;    Author: Brouard
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);    In order to compile on Visual studio, time.h is now correct and time_t
       q=(x-v)*(fx-fw);    and tm struct should be used. difftime should be used but sometimes I
       p=(x-v)*q-(x-w)*r;    just make the differences in raw time format (time(&now).
       q=2.0*(q-r);    Trying to suppress #ifdef LINUX
       if (q > 0.0) p = -p;    Add xdg-open for __linux in order to open default browser.
       q=fabs(q);  
       etemp=e;    Revision 1.156  2014/08/25 20:10:10  brouard
       e=d;    *** empty log message ***
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    Revision 1.155  2014/08/25 18:32:34  brouard
       else {    Summary: New compile, minor changes
         d=p/q;    Author: Brouard
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)    Revision 1.154  2014/06/20 17:32:08  brouard
           d=SIGN(tol1,xm-x);    Summary: Outputs now all graphs of convergence to period prevalence
       }  
     } else {    Revision 1.153  2014/06/20 16:45:46  brouard
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    Summary: If 3 live state, convergence to period prevalence on same graph
     }    Author: Brouard
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);    Revision 1.152  2014/06/18 17:54:09  brouard
     if (fu <= fx) {    Summary: open browser, use gnuplot on same dir than imach if not found in the path
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)    Revision 1.151  2014/06/18 16:43:30  brouard
         SHFT(fv,fw,fx,fu)    *** empty log message ***
         } else {  
           if (u < x) a=u; else b=u;    Revision 1.150  2014/06/18 16:42:35  brouard
           if (fu <= fw || w == x) {    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
             v=w;    Author: brouard
             w=u;  
             fv=fw;    Revision 1.149  2014/06/18 15:51:14  brouard
             fw=fu;    Summary: Some fixes in parameter files errors
           } else if (fu <= fv || v == x || v == w) {    Author: Nicolas Brouard
             v=u;  
             fv=fu;    Revision 1.148  2014/06/17 17:38:48  brouard
           }    Summary: Nothing new
         }    Author: Brouard
   }  
   nrerror("Too many iterations in brent");    Just a new packaging for OS/X version 0.98nS
   *xmin=x;  
   return fx;    Revision 1.147  2014/06/16 10:33:11  brouard
 }    *** empty log message ***
   
 /****************** mnbrak ***********************/    Revision 1.146  2014/06/16 10:20:28  brouard
     Summary: Merge
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    Author: Brouard
             double (*func)(double))  
 {    Merge, before building revised version.
   double ulim,u,r,q, dum;  
   double fu;    Revision 1.145  2014/06/10 21:23:15  brouard
      Summary: Debugging with valgrind
   *fa=(*func)(*ax);    Author: Nicolas Brouard
   *fb=(*func)(*bx);  
   if (*fb > *fa) {    Lot of changes in order to output the results with some covariates
     SHFT(dum,*ax,*bx,dum)    After the Edimburgh REVES conference 2014, it seems mandatory to
       SHFT(dum,*fb,*fa,dum)    improve the code.
       }    No more memory valgrind error but a lot has to be done in order to
   *cx=(*bx)+GOLD*(*bx-*ax);    continue the work of splitting the code into subroutines.
   *fc=(*func)(*cx);    Also, decodemodel has been improved. Tricode is still not
   while (*fb > *fc) {    optimal. nbcode should be improved. Documentation has been added in
     r=(*bx-*ax)*(*fb-*fc);    the source code.
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    Revision 1.143  2014/01/26 09:45:38  brouard
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
       fu=(*func)(u);    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);    Revision 1.142  2014/01/26 03:57:36  brouard
       if (fu < *fc) {    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    Revision 1.141  2014/01/26 02:42:01  brouard
       u=ulim;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
       fu=(*func)(u);  
     } else {    Revision 1.140  2011/09/02 10:37:54  brouard
       u=(*cx)+GOLD*(*cx-*bx);    Summary: times.h is ok with mingw32 now.
       fu=(*func)(u);  
     }    Revision 1.139  2010/06/14 07:50:17  brouard
     SHFT(*ax,*bx,*cx,u)    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
       SHFT(*fa,*fb,*fc,fu)    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
       }  
 }    Revision 1.138  2010/04/30 18:19:40  brouard
     *** empty log message ***
 /*************** linmin ************************/  
     Revision 1.137  2010/04/29 18:11:38  brouard
 int ncom;    (Module): Checking covariates for more complex models
 double *pcom,*xicom;    than V1+V2. A lot of change to be done. Unstable.
 double (*nrfunc)(double []);  
      Revision 1.136  2010/04/26 20:30:53  brouard
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    (Module): merging some libgsl code. Fixing computation
 {    of likelione (using inter/intrapolation if mle = 0) in order to
   double brent(double ax, double bx, double cx,    get same likelihood as if mle=1.
                double (*f)(double), double tol, double *xmin);    Some cleaning of code and comments added.
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    Revision 1.135  2009/10/29 15:33:14  brouard
               double *fc, double (*func)(double));    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   int j;  
   double xx,xmin,bx,ax;    Revision 1.134  2009/10/29 13:18:53  brouard
   double fx,fb,fa;    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
    
   ncom=n;    Revision 1.133  2009/07/06 10:21:25  brouard
   pcom=vector(1,n);    just nforces
   xicom=vector(1,n);  
   nrfunc=func;    Revision 1.132  2009/07/06 08:22:05  brouard
   for (j=1;j<=n;j++) {    Many tings
     pcom[j]=p[j];  
     xicom[j]=xi[j];    Revision 1.131  2009/06/20 16:22:47  brouard
   }    Some dimensions resccaled
   ax=0.0;  
   xx=1.0;    Revision 1.130  2009/05/26 06:44:34  brouard
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    (Module): Max Covariate is now set to 20 instead of 8. A
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    lot of cleaning with variables initialized to 0. Trying to make
 #ifdef DEBUG    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif    Revision 1.129  2007/08/31 13:49:27  lievre
   for (j=1;j<=n;j++) {    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
     xi[j] *= xmin;  
     p[j] += xi[j];    Revision 1.128  2006/06/30 13:02:05  brouard
   }    (Module): Clarifications on computing e.j
   free_vector(xicom,1,n);  
   free_vector(pcom,1,n);    Revision 1.127  2006/04/28 18:11:50  brouard
 }    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
 /*************** powell ************************/    loop. Now we define nhstepma in the age loop.
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    (Module): In order to speed up (in case of numerous covariates) we
             double (*func)(double []))    compute health expectancies (without variances) in a first step
 {    and then all the health expectancies with variances or standard
   void linmin(double p[], double xi[], int n, double *fret,    deviation (needs data from the Hessian matrices) which slows the
               double (*func)(double []));    computation.
   int i,ibig,j;    In the future we should be able to stop the program is only health
   double del,t,*pt,*ptt,*xit;    expectancies and graph are needed without standard deviations.
   double fp,fptt;  
   double *xits;    Revision 1.126  2006/04/28 17:23:28  brouard
   pt=vector(1,n);    (Module): Yes the sum of survivors was wrong since
   ptt=vector(1,n);    imach-114 because nhstepm was no more computed in the age
   xit=vector(1,n);    loop. Now we define nhstepma in the age loop.
   xits=vector(1,n);    Version 0.98h
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];    Revision 1.125  2006/04/04 15:20:31  lievre
   for (*iter=1;;++(*iter)) {    Errors in calculation of health expectancies. Age was not initialized.
     fp=(*fret);    Forecasting file added.
     ibig=0;  
     del=0.0;    Revision 1.124  2006/03/22 17:13:53  lievre
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    Parameters are printed with %lf instead of %f (more numbers after the comma).
     for (i=1;i<=n;i++)    The log-likelihood is printed in the log file
       printf(" %d %.12f",i, p[i]);  
     printf("\n");    Revision 1.123  2006/03/20 10:52:43  brouard
     for (i=1;i<=n;i++) {    * imach.c (Module): <title> changed, corresponds to .htm file
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    name. <head> headers where missing.
       fptt=(*fret);  
 #ifdef DEBUG    * imach.c (Module): Weights can have a decimal point as for
       printf("fret=%lf \n",*fret);    English (a comma might work with a correct LC_NUMERIC environment,
 #endif    otherwise the weight is truncated).
       printf("%d",i);fflush(stdout);    Modification of warning when the covariates values are not 0 or
       linmin(p,xit,n,fret,func);    1.
       if (fabs(fptt-(*fret)) > del) {    Version 0.98g
         del=fabs(fptt-(*fret));  
         ibig=i;    Revision 1.122  2006/03/20 09:45:41  brouard
       }    (Module): Weights can have a decimal point as for
 #ifdef DEBUG    English (a comma might work with a correct LC_NUMERIC environment,
       printf("%d %.12e",i,(*fret));    otherwise the weight is truncated).
       for (j=1;j<=n;j++) {    Modification of warning when the covariates values are not 0 or
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    1.
         printf(" x(%d)=%.12e",j,xit[j]);    Version 0.98g
       }  
       for(j=1;j<=n;j++)    Revision 1.121  2006/03/16 17:45:01  lievre
         printf(" p=%.12e",p[j]);    * imach.c (Module): Comments concerning covariates added
       printf("\n");  
 #endif    * imach.c (Module): refinements in the computation of lli if
     }    status=-2 in order to have more reliable computation if stepm is
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    not 1 month. Version 0.98f
 #ifdef DEBUG  
       int k[2],l;    Revision 1.120  2006/03/16 15:10:38  lievre
       k[0]=1;    (Module): refinements in the computation of lli if
       k[1]=-1;    status=-2 in order to have more reliable computation if stepm is
       printf("Max: %.12e",(*func)(p));    not 1 month. Version 0.98f
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);    Revision 1.119  2006/03/15 17:42:26  brouard
       printf("\n");    (Module): Bug if status = -2, the loglikelihood was
       for(l=0;l<=1;l++) {    computed as likelihood omitting the logarithm. Version O.98e
         for (j=1;j<=n;j++) {  
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    Revision 1.118  2006/03/14 18:20:07  brouard
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    (Module): varevsij Comments added explaining the second
         }    table of variances if popbased=1 .
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
       }    (Module): Function pstamp added
 #endif    (Module): Version 0.98d
   
     Revision 1.117  2006/03/14 17:16:22  brouard
       free_vector(xit,1,n);    (Module): varevsij Comments added explaining the second
       free_vector(xits,1,n);    table of variances if popbased=1 .
       free_vector(ptt,1,n);    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
       free_vector(pt,1,n);    (Module): Function pstamp added
       return;    (Module): Version 0.98d
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    Revision 1.116  2006/03/06 10:29:27  brouard
     for (j=1;j<=n;j++) {    (Module): Variance-covariance wrong links and
       ptt[j]=2.0*p[j]-pt[j];    varian-covariance of ej. is needed (Saito).
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];    Revision 1.115  2006/02/27 12:17:45  brouard
     }    (Module): One freematrix added in mlikeli! 0.98c
     fptt=(*func)(ptt);  
     if (fptt < fp) {    Revision 1.114  2006/02/26 12:57:58  brouard
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    (Module): Some improvements in processing parameter
       if (t < 0.0) {    filename with strsep.
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {    Revision 1.113  2006/02/24 14:20:24  brouard
           xi[j][ibig]=xi[j][n];    (Module): Memory leaks checks with valgrind and:
           xi[j][n]=xit[j];    datafile was not closed, some imatrix were not freed and on matrix
         }    allocation too.
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    Revision 1.112  2006/01/30 09:55:26  brouard
         for(j=1;j<=n;j++)    (Module): Back to gnuplot.exe instead of wgnuplot.exe
           printf(" %.12e",xit[j]);  
         printf("\n");    Revision 1.111  2006/01/25 20:38:18  brouard
 #endif    (Module): Lots of cleaning and bugs added (Gompertz)
       }    (Module): Comments can be added in data file. Missing date values
     }    can be a simple dot '.'.
   }  
 }    Revision 1.110  2006/01/25 00:51:50  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 /**** Prevalence limit ****************/  
     Revision 1.109  2006/01/24 19:37:15  brouard
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    (Module): Comments (lines starting with a #) are allowed in data.
 {  
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    Revision 1.108  2006/01/19 18:05:42  lievre
      matrix by transitions matrix until convergence is reached */    Gnuplot problem appeared...
     To be fixed
   int i, ii,j,k;  
   double min, max, maxmin, maxmax,sumnew=0.;    Revision 1.107  2006/01/19 16:20:37  brouard
   double **matprod2();    Test existence of gnuplot in imach path
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;    Revision 1.106  2006/01/19 13:24:36  brouard
   double agefin, delaymax=50 ; /* Max number of years to converge */    Some cleaning and links added in html output
   
   for (ii=1;ii<=nlstate+ndeath;ii++)    Revision 1.105  2006/01/05 20:23:19  lievre
     for (j=1;j<=nlstate+ndeath;j++){    *** empty log message ***
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
     }    Revision 1.104  2005/09/30 16:11:43  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
    cov[1]=1.;    (Module): If the status is missing at the last wave but we know
      that the person is alive, then we can code his/her status as -2
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    (instead of missing=-1 in earlier versions) and his/her
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    contributions to the likelihood is 1 - Prob of dying from last
     newm=savm;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
     /* Covariates have to be included here again */    the healthy state at last known wave). Version is 0.98
      cov[2]=agefin;  
      Revision 1.103  2005/09/30 15:54:49  lievre
       for (k=1; k<=cptcovn;k++) {    (Module): sump fixed, loop imx fixed, and simplifications.
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/    Revision 1.102  2004/09/15 17:31:30  brouard
       }    Add the possibility to read data file including tab characters.
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)    Revision 1.101  2004/09/15 10:38:38  brouard
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    Fix on curr_time
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    Revision 1.100  2004/07/12 18:29:06  brouard
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    Add version for Mac OS X. Just define UNIX in Makefile
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
     savm=oldm;  
     oldm=newm;    Revision 1.98  2004/05/16 15:05:56  brouard
     maxmax=0.;    New version 0.97 . First attempt to estimate force of mortality
     for(j=1;j<=nlstate;j++){    directly from the data i.e. without the need of knowing the health
       min=1.;    state at each age, but using a Gompertz model: log u =a + b*age .
       max=0.;    This is the basic analysis of mortality and should be done before any
       for(i=1; i<=nlstate; i++) {    other analysis, in order to test if the mortality estimated from the
         sumnew=0;    cross-longitudinal survey is different from the mortality estimated
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    from other sources like vital statistic data.
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);    The same imach parameter file can be used but the option for mle should be -3.
         min=FMIN(min,prlim[i][j]);  
       }    Agnès, who wrote this part of the code, tried to keep most of the
       maxmin=max-min;    former routines in order to include the new code within the former code.
       maxmax=FMAX(maxmax,maxmin);  
     }    The output is very simple: only an estimate of the intercept and of
     if(maxmax < ftolpl){    the slope with 95% confident intervals.
       return prlim;  
     }    Current limitations:
   }    A) Even if you enter covariates, i.e. with the
 }    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
     B) There is no computation of Life Expectancy nor Life Table.
 /*************** transition probabilities ***************/  
     Revision 1.97  2004/02/20 13:25:42  lievre
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    Version 0.96d. Population forecasting command line is (temporarily)
 {    suppressed.
   double s1, s2;  
   /*double t34;*/    Revision 1.96  2003/07/15 15:38:55  brouard
   int i,j,j1, nc, ii, jj;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     rewritten within the same printf. Workaround: many printfs.
     for(i=1; i<= nlstate; i++){  
     for(j=1; j<i;j++){    Revision 1.95  2003/07/08 07:54:34  brouard
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    * imach.c (Repository):
         /*s2 += param[i][j][nc]*cov[nc];*/    (Repository): Using imachwizard code to output a more meaningful covariance
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    matrix (cov(a12,c31) instead of numbers.
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }    Revision 1.94  2003/06/27 13:00:02  brouard
       ps[i][j]=s2;    Just cleaning
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }    Revision 1.93  2003/06/25 16:33:55  brouard
     for(j=i+1; j<=nlstate+ndeath;j++){    (Module): On windows (cygwin) function asctime_r doesn't
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    exist so I changed back to asctime which exists.
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    (Module): Version 0.96b
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  
       }    Revision 1.92  2003/06/25 16:30:45  brouard
       ps[i][j]=s2;    (Module): On windows (cygwin) function asctime_r doesn't
     }    exist so I changed back to asctime which exists.
   }  
     /*ps[3][2]=1;*/    Revision 1.91  2003/06/25 15:30:29  brouard
     * imach.c (Repository): Duplicated warning errors corrected.
   for(i=1; i<= nlstate; i++){    (Repository): Elapsed time after each iteration is now output. It
      s1=0;    helps to forecast when convergence will be reached. Elapsed time
     for(j=1; j<i; j++)    is stamped in powell.  We created a new html file for the graphs
       s1+=exp(ps[i][j]);    concerning matrix of covariance. It has extension -cov.htm.
     for(j=i+1; j<=nlstate+ndeath; j++)  
       s1+=exp(ps[i][j]);    Revision 1.90  2003/06/24 12:34:15  brouard
     ps[i][i]=1./(s1+1.);    (Module): Some bugs corrected for windows. Also, when
     for(j=1; j<i; j++)    mle=-1 a template is output in file "or"mypar.txt with the design
       ps[i][j]= exp(ps[i][j])*ps[i][i];    of the covariance matrix to be input.
     for(j=i+1; j<=nlstate+ndeath; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];    Revision 1.89  2003/06/24 12:30:52  brouard
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    (Module): Some bugs corrected for windows. Also, when
   } /* end i */    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){    Revision 1.88  2003/06/23 17:54:56  brouard
       ps[ii][jj]=0;    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
       ps[ii][ii]=1;  
     }    Revision 1.87  2003/06/18 12:26:01  brouard
   }    Version 0.96
   
     Revision 1.86  2003/06/17 20:04:08  brouard
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    (Module): Change position of html and gnuplot routines and added
     for(jj=1; jj<= nlstate+ndeath; jj++){    routine fileappend.
      printf("%lf ",ps[ii][jj]);  
    }    Revision 1.85  2003/06/17 13:12:43  brouard
     printf("\n ");    * imach.c (Repository): Check when date of death was earlier that
     }    current date of interview. It may happen when the death was just
     printf("\n ");printf("%lf ",cov[2]);*/    prior to the death. In this case, dh was negative and likelihood
 /*    was wrong (infinity). We still send an "Error" but patch by
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    assuming that the date of death was just one stepm after the
   goto end;*/    interview.
     return ps;    (Repository): Because some people have very long ID (first column)
 }    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
 /**************** Product of 2 matrices ******************/    truncation)
     (Repository): No more line truncation errors.
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  
 {    Revision 1.84  2003/06/13 21:44:43  brouard
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    * imach.c (Repository): Replace "freqsummary" at a correct
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    place. It differs from routine "prevalence" which may be called
   /* in, b, out are matrice of pointers which should have been initialized    many times. Probs is memory consuming and must be used with
      before: only the contents of out is modified. The function returns    parcimony.
      a pointer to pointers identical to out */    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)    Revision 1.83  2003/06/10 13:39:11  lievre
     for(k=ncolol; k<=ncoloh; k++)    *** empty log message ***
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];    Revision 1.82  2003/06/05 15:57:20  brouard
     Add log in  imach.c and  fullversion number is now printed.
   return out;  
 }  */
   /*
      Interpolated Markov Chain
 /************* Higher Matrix Product ***************/  
     Short summary of the programme:
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    
 {    This program computes Healthy Life Expectancies or State-specific
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    (if states aren't health statuses) Expectancies from
      duration (i.e. until    cross-longitudinal data. Cross-longitudinal data consist in: 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    -1- a first survey ("cross") where individuals from different ages
      (typically every 2 years instead of every month which is too big).    are interviewed on their health status or degree of disability (in
      Model is determined by parameters x and covariates have to be    the case of a health survey which is our main interest)
      included manually here.  
     -2- at least a second wave of interviews ("longitudinal") which
      */    measure each change (if any) in individual health status.  Health
     expectancies are computed from the time spent in each health state
   int i, j, d, h, k;    according to a model. More health states you consider, more time is
   double **out, cov[NCOVMAX];    necessary to reach the Maximum Likelihood of the parameters involved
   double **newm;    in the model.  The simplest model is the multinomial logistic model
     where pij is the probability to be observed in state j at the second
   /* Hstepm could be zero and should return the unit matrix */    wave conditional to be observed in state i at the first
   for (i=1;i<=nlstate+ndeath;i++)    wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
     for (j=1;j<=nlstate+ndeath;j++){    etc , where 'age' is age and 'sex' is a covariate. If you want to
       oldm[i][j]=(i==j ? 1.0 : 0.0);    have a more complex model than "constant and age", you should modify
       po[i][j][0]=(i==j ? 1.0 : 0.0);    the program where the markup *Covariates have to be included here
     }    again* invites you to do it.  More covariates you add, slower the
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    convergence.
   for(h=1; h <=nhstepm; h++){  
     for(d=1; d <=hstepm; d++){    The advantage of this computer programme, compared to a simple
       newm=savm;    multinomial logistic model, is clear when the delay between waves is not
       /* Covariates have to be included here again */    identical for each individual. Also, if a individual missed an
       cov[1]=1.;    intermediate interview, the information is lost, but taken into
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    account using an interpolation or extrapolation.  
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
       for (k=1; k<=cptcovage;k++)    hPijx is the probability to be observed in state i at age x+h
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    conditional to the observed state i at age x. The delay 'h' can be
       for (k=1; k<=cptcovprod;k++)    split into an exact number (nh*stepm) of unobserved intermediate
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    states. This elementary transition (by month, quarter,
     semester or year) is modelled as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    and the contribution of each individual to the likelihood is simply
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    hPijx.
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    Also this programme outputs the covariance matrix of the parameters but also
       savm=oldm;    of the life expectancies. It also computes the period (stable) prevalence.
       oldm=newm;  
     }  Back prevalence and projections:
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {   - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
         po[i][j][h]=newm[i][j];     double agemaxpar, double ftolpl, int *ncvyearp, double
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);     dateprev1,double dateprev2, int firstpass, int lastpass, int
          */     mobilavproj)
       }  
   } /* end h */      Computes the back prevalence limit for any combination of
   return po;      covariate values k at any age between ageminpar and agemaxpar and
 }      returns it in **bprlim. In the loops,
   
      - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
 /*************** log-likelihood *************/         **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
 double func( double *x)  
 {     - hBijx Back Probability to be in state i at age x-h being in j at x
   int i, ii, j, k, mi, d, kk;     Computes for any combination of covariates k and any age between bage and fage 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double **out;                          oldm=oldms;savm=savms;
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */     - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
   long ipmx;       Computes the transition matrix starting at age 'age' over
   /*extern weight */       'nhstepm*hstepm*stepm' months (i.e. until
   /* We are differentiating ll according to initial status */       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/       nhstepm*hstepm matrices. 
   /*for(i=1;i<imx;i++)  
     printf(" %d\n",s[4][i]);       Returns p3mat[i][j][h] after calling
   */       p3mat[i][j][h]=matprod2(newm,
   cov[1]=1.;       bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
        dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
   for(k=1; k<=nlstate; k++) ll[k]=0.;       oldm);
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  Important routines
     for(mi=1; mi<= wav[i]-1; mi++){  
       for (ii=1;ii<=nlstate+ndeath;ii++)  - func (or funcone), computes logit (pij) distinguishing
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    o fixed variables (single or product dummies or quantitative);
       for(d=0; d<dh[mi][i]; d++){    o varying variables by:
         newm=savm;     (1) wave (single, product dummies, quantitative), 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;     (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
         for (kk=1; kk<=cptcovage;kk++) {         % fixed dummy (treated) or quantitative (not done because time-consuming);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];         % varying dummy (not done) or quantitative (not done);
         }  - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
            and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
         savm=oldm;      race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
         oldm=newm;  
          
            
       } /* end mult */    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
                   Institut national d'études démographiques, Paris.
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    This software have been partly granted by Euro-REVES, a concerted action
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    from the European Union.
       ipmx +=1;    It is copyrighted identically to a GNU software product, ie programme and
       sw += weight[i];    software can be distributed freely for non commercial use. Latest version
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    can be accessed at http://euroreves.ined.fr/imach .
     } /* end of wave */  
   } /* end of individual */    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    **********************************************************************/
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  /*
   return -l;    main
 }    read parameterfile
     read datafile
     concatwav
 /*********** Maximum Likelihood Estimation ***************/    freqsummary
     if (mle >= 1)
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      mlikeli
 {    print results files
   int i,j, iter;    if mle==1 
   double **xi,*delti;       computes hessian
   double fret;    read end of parameter file: agemin, agemax, bage, fage, estepm
   xi=matrix(1,npar,1,npar);        begin-prev-date,...
   for (i=1;i<=npar;i++)    open gnuplot file
     for (j=1;j<=npar;j++)    open html file
       xi[i][j]=(i==j ? 1.0 : 0.0);    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
   printf("Powell\n");     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
   powell(p,xi,npar,ftol,&iter,&fret,func);                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
       freexexit2 possible for memory heap.
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    h Pij x                         | pij_nom  ficrestpij
      # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
 }         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
          1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
 {         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
   double  **a,**y,*x,pd;    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   double **hess;     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
   int i, j,jk;     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   int *indx;  
     forecasting if prevfcast==1 prevforecast call prevalence()
   double hessii(double p[], double delta, int theta, double delti[]);    health expectancies
   double hessij(double p[], double delti[], int i, int j);    Variance-covariance of DFLE
   void lubksb(double **a, int npar, int *indx, double b[]) ;    prevalence()
   void ludcmp(double **a, int npar, int *indx, double *d) ;     movingaverage()
     varevsij() 
   hess=matrix(1,npar,1,npar);    if popbased==1 varevsij(,popbased)
     total life expectancies
   printf("\nCalculation of the hessian matrix. Wait...\n");    Variance of period (stable) prevalence
   for (i=1;i<=npar;i++){   end
     printf("%d",i);fflush(stdout);  */
     hess[i][i]=hessii(p,ftolhess,i,delti);  
     /*printf(" %f ",p[i]);*/  /* #define DEBUG */
     /*printf(" %lf ",hess[i][i]);*/  /* #define DEBUGBRENT */
   }  /* #define DEBUGLINMIN */
    /* #define DEBUGHESS */
   for (i=1;i<=npar;i++) {  #define DEBUGHESSIJ
     for (j=1;j<=npar;j++)  {  /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan) *\/ */
       if (j>i) {  #define POWELL /* Instead of NLOPT */
         printf(".%d%d",i,j);fflush(stdout);  #define POWELLNOF3INFF1TEST /* Skip test */
         hess[i][j]=hessij(p,delti,i,j);  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
         hess[j][i]=hess[i][j];      /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
         /*printf(" %lf ",hess[i][j]);*/  
       }  #include <math.h>
     }  #include <stdio.h>
   }  #include <stdlib.h>
   printf("\n");  #include <string.h>
   #include <ctype.h>
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  
    #ifdef _WIN32
   a=matrix(1,npar,1,npar);  #include <io.h>
   y=matrix(1,npar,1,npar);  #include <windows.h>
   x=vector(1,npar);  #include <tchar.h>
   indx=ivector(1,npar);  #else
   for (i=1;i<=npar;i++)  #include <unistd.h>
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  #endif
   ludcmp(a,npar,indx,&pd);  
   #include <limits.h>
   for (j=1;j<=npar;j++) {  #include <sys/types.h>
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  #if defined(__GNUC__)
     lubksb(a,npar,indx,x);  #include <sys/utsname.h> /* Doesn't work on Windows */
     for (i=1;i<=npar;i++){  #endif
       matcov[i][j]=x[i];  
     }  #include <sys/stat.h>
   }  #include <errno.h>
   /* extern int errno; */
   printf("\n#Hessian matrix#\n");  
   for (i=1;i<=npar;i++) {  /* #ifdef LINUX */
     for (j=1;j<=npar;j++) {  /* #include <time.h> */
       printf("%.3e ",hess[i][j]);  /* #include "timeval.h" */
     }  /* #else */
     printf("\n");  /* #include <sys/time.h> */
   }  /* #endif */
   
   /* Recompute Inverse */  #include <time.h>
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  #ifdef GSL
   ludcmp(a,npar,indx,&pd);  #include <gsl/gsl_errno.h>
   #include <gsl/gsl_multimin.h>
   /*  printf("\n#Hessian matrix recomputed#\n");  #endif
   
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  #ifdef NLOPT
     x[j]=1;  #include <nlopt.h>
     lubksb(a,npar,indx,x);  typedef struct {
     for (i=1;i<=npar;i++){    double (* function)(double [] );
       y[i][j]=x[i];  } myfunc_data ;
       printf("%.3e ",y[i][j]);  #endif
     }  
     printf("\n");  /* #include <libintl.h> */
   }  /* #define _(String) gettext (String) */
   */  
   #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   free_matrix(a,1,npar,1,npar);  
   free_matrix(y,1,npar,1,npar);  #define GNUPLOTPROGRAM "gnuplot"
   free_vector(x,1,npar);  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   free_ivector(indx,1,npar);  #define FILENAMELENGTH 132
   free_matrix(hess,1,npar,1,npar);  
   #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 }  
   #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
 /*************** hessian matrix ****************/  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
 double hessii( double x[], double delta, int theta, double delti[])  
 {  #define NINTERVMAX 8
   int i;  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
   int l=1, lmax=20;  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
   double k1,k2;  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
   double p2[NPARMAX+1];  #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
   double res;  /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1 
   double fx;  #define MAXN 20000
   int k=0,kmax=10;  #define YEARM 12. /**< Number of months per year */
   double l1;  /* #define AGESUP 130 */
   #define AGESUP 150
   fx=func(x);  #define AGEINF 0
   for (i=1;i<=npar;i++) p2[i]=x[i];  #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
   for(l=0 ; l <=lmax; l++){  #define AGEBASE 40
     l1=pow(10,l);  #define AGEOVERFLOW 1.e20
     delts=delt;  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
     for(k=1 ; k <kmax; k=k+1){  #ifdef _WIN32
       delt = delta*(l1*k);  #define DIRSEPARATOR '\\'
       p2[theta]=x[theta] +delt;  #define CHARSEPARATOR "\\"
       k1=func(p2)-fx;  #define ODIRSEPARATOR '/'
       p2[theta]=x[theta]-delt;  #else
       k2=func(p2)-fx;  #define DIRSEPARATOR '/'
       /*res= (k1-2.0*fx+k2)/delt/delt; */  #define CHARSEPARATOR "/"
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  #define ODIRSEPARATOR '\\'
        #endif
 #ifdef DEBUG  
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  /* $Id$ */
 #endif  /* $State$ */
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  #include "version.h"
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  char version[]=__IMACH_VERSION__;
         k=kmax;  char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
       }  char fullversion[]="$Revision$ $Date$"; 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  char strstart[80];
         k=kmax; l=lmax*10.;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
       }  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
         delts=delt;  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
       }  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
     }  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
   }  int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
   delti[theta]=delts;  int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
   return res;  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
    int cptcovprodnoage=0; /**< Number of covariate products without age */   
 }  int cptcoveff=0; /* Total number of covariates to vary for printing results */
   int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
 double hessij( double x[], double delti[], int thetai,int thetaj)  int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
 {  int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
   int i;  int nsd=0; /**< Total number of single dummy variables (output) */
   int l=1, l1, lmax=20;  int nsq=0; /**< Total number of single quantitative variables (output) */
   double k1,k2,k3,k4,res,fx;  int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
   double p2[NPARMAX+1];  int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
   int k;  int ntveff=0; /**< ntveff number of effective time varying variables */
   int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
   fx=func(x);  int cptcov=0; /* Working variable */
   for (k=1; k<=2; k++) {  int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
     for (i=1;i<=npar;i++) p2[i]=x[i];  int npar=NPARMAX;
     p2[thetai]=x[thetai]+delti[thetai]/k;  int nlstate=2; /* Number of live states */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  int ndeath=1; /* Number of dead states */
     k1=func(p2)-fx;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
    int  nqv=0, ntv=0, nqtv=0;    /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */ 
     p2[thetai]=x[thetai]+delti[thetai]/k;  int popbased=0;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k2=func(p2)-fx;  int *wav; /* Number of waves for this individuual 0 is possible */
    int maxwav=0; /* Maxim number of waves */
     p2[thetai]=x[thetai]-delti[thetai]/k;  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
     k3=func(p2)-fx;  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
                       to the likelihood and the sum of weights (done by funcone)*/
     p2[thetai]=x[thetai]-delti[thetai]/k;  int mle=1, weightopt=0;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
     k4=func(p2)-fx;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 #ifdef DEBUG             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  int countcallfunc=0;  /* Count the number of calls to func */
 #endif  int selected(int kvar); /* Is covariate kvar selected for printing results */
   }  
   return res;  double jmean=1; /* Mean space between 2 waves */
 }  double **matprod2(); /* test */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
 /************** Inverse of matrix **************/  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 void ludcmp(double **a, int n, int *indx, double *d)  double   **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
 {  
   int i,imax,j,k;  /*FILE *fic ; */ /* Used in readdata only */
   double big,dum,sum,temp;  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
   double *vv;  FILE *ficlog, *ficrespow;
    int globpr=0; /* Global variable for printing or not */
   vv=vector(1,n);  double fretone; /* Only one call to likelihood */
   *d=1.0;  long ipmx=0; /* Number of contributions */
   for (i=1;i<=n;i++) {  double sw; /* Sum of weights */
     big=0.0;  char filerespow[FILENAMELENGTH];
     for (j=1;j<=n;j++)  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       if ((temp=fabs(a[i][j])) > big) big=temp;  FILE *ficresilk;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     vv[i]=1.0/big;  FILE *ficresprobmorprev;
   }  FILE *fichtm, *fichtmcov; /* Html File */
   for (j=1;j<=n;j++) {  FILE *ficreseij;
     for (i=1;i<j;i++) {  char filerese[FILENAMELENGTH];
       sum=a[i][j];  FILE *ficresstdeij;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  char fileresstde[FILENAMELENGTH];
       a[i][j]=sum;  FILE *ficrescveij;
     }  char filerescve[FILENAMELENGTH];
     big=0.0;  FILE  *ficresvij;
     for (i=j;i<=n;i++) {  char fileresv[FILENAMELENGTH];
       sum=a[i][j];  
       for (k=1;k<j;k++)  char title[MAXLINE];
         sum -= a[i][k]*a[k][j];  char model[MAXLINE]; /**< The model line */
       a[i][j]=sum;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
       if ( (dum=vv[i]*fabs(sum)) >= big) {  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
         big=dum;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
         imax=i;  char command[FILENAMELENGTH];
       }  int  outcmd=0;
     }  
     if (j != imax) {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       for (k=1;k<=n;k++) {  char fileresu[FILENAMELENGTH]; /* fileres without r in front */
         dum=a[imax][k];  char filelog[FILENAMELENGTH]; /* Log file */
         a[imax][k]=a[j][k];  char filerest[FILENAMELENGTH];
         a[j][k]=dum;  char fileregp[FILENAMELENGTH];
       }  char popfile[FILENAMELENGTH];
       *d = -(*d);  
       vv[imax]=vv[j];  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     }  
     indx[j]=imax;  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
     if (a[j][j] == 0.0) a[j][j]=TINY;  /* struct timezone tzp; */
     if (j != n) {  /* extern int gettimeofday(); */
       dum=1.0/(a[j][j]);  struct tm tml, *gmtime(), *localtime();
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }  extern time_t time();
   }  
   free_vector(vv,1,n);  /* Doesn't work */  struct tm start_time, end_time, curr_time, last_time, forecast_time;
 ;  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
 }  struct tm tm;
   
 void lubksb(double **a, int n, int *indx, double b[])  char strcurr[80], strfor[80];
 {  
   int i,ii=0,ip,j;  char *endptr;
   double sum;  long lval;
    double dval;
   for (i=1;i<=n;i++) {  
     ip=indx[i];  #define NR_END 1
     sum=b[ip];  #define FREE_ARG char*
     b[ip]=b[i];  #define FTOL 1.0e-10
     if (ii)  
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  #define NRANSI 
     else if (sum) ii=i;  #define ITMAX 200
     b[i]=sum;  #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */ 
   }  
   for (i=n;i>=1;i--) {  #define TOL 2.0e-4 
     sum=b[i];  
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  #define CGOLD 0.3819660 
     b[i]=sum/a[i][i];  #define ZEPS 1.0e-10 
   }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 }  
   #define GOLD 1.618034 
 /************ Frequencies ********************/  #define GLIMIT 100.0 
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)  #define TINY 1.0e-20 
 {  /* Some frequencies */  
    static double maxarg1,maxarg2;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   double ***freq; /* Frequencies */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   double *pp;    
   double pos, k2, dateintsum=0,k2cpt=0;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   FILE *ficresp;  #define rint(a) floor(a+0.5)
   char fileresp[FILENAMELENGTH];  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
    #define mytinydouble 1.0e-16
   pp=vector(1,nlstate);  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
   strcpy(fileresp,"p");  /* static double dsqrarg; */
   strcat(fileresp,fileres);  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
   if((ficresp=fopen(fileresp,"w"))==NULL) {  static double sqrarg;
     printf("Problem with prevalence resultfile: %s\n", fileresp);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     exit(0);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   }  int agegomp= AGEGOMP;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;  int imx; 
    int stepm=1;
   j=cptcoveff;  /* Stepm, step in month: minimum step interpolation*/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
    int estepm;
   for(k1=1; k1<=j;k1++){  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     for(i1=1; i1<=ncodemax[k1];i1++){  
       j1++;  int m,nb;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  long *num;
         scanf("%d", i);*/  int firstpass=0, lastpass=4,*cod, *cens;
       for (i=-1; i<=nlstate+ndeath; i++)    int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
         for (jk=-1; jk<=nlstate+ndeath; jk++)                       covariate for which somebody answered excluding 
           for(m=agemin; m <= agemax+3; m++)                     undefined. Usually 2: 0 and 1. */
             freq[i][jk][m]=0;  int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
                                     covariate for which somebody answered including 
       dateintsum=0;                               undefined. Usually 3: -1, 0 and 1. */
       k2cpt=0;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       for (i=1; i<=imx; i++) {  double **pmmij, ***probs; /* Global pointer */
         bool=1;  double ***mobaverage, ***mobaverages; /* New global variable */
         if  (cptcovn>0) {  double *ageexmed,*agecens;
           for (z1=1; z1<=cptcoveff; z1++)  double dateintmean=0;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
               bool=0;  double *weight;
         }  int **s; /* Status */
         if (bool==1) {  double *agedc;
           for(m=firstpass; m<=lastpass; m++){  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
             k2=anint[m][i]+(mint[m][i]/12.);                    * covar=matrix(0,NCOVMAX,1,n); 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
               if(agev[m][i]==0) agev[m][i]=agemax+1;  double **coqvar; /* Fixed quantitative covariate nqv */
               if(agev[m][i]==1) agev[m][i]=agemax+2;  double ***cotvar; /* Time varying covariate ntv */
               if (m<lastpass) {  double ***cotqvar; /* Time varying quantitative covariate itqv */
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  double  idx; 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
               }  /*           V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                /*k          1  2   3   4     5    6    7     8    9 */
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  /*Tvar[k]=   5  4   3   6     5    2    7     1    1 */
                 dateintsum=dateintsum+k2;  /* Tndvar[k]    1   2   3               4          5 */
                 k2cpt++;  /*TDvar         4   3   6               7          1 */ /* For outputs only; combination of dummies fixed or varying */
               }  /* Tns[k]    1  2   2              4               5 */ /* Number of single cova */
             }  /* TvarsD[k]    1   2                              3 */ /* Number of single dummy cova */
           }  /* TvarsDind    2   3                              9 */ /* position K of single dummy cova */
         }  /* TvarsQ[k] 1                     2                 */ /* Number of single quantitative cova */
       }  /* TvarsQind 1                     6                 */ /* position K of single quantitative cova */
          /* Tprod[i]=k           4               7            */
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  /* Tage[i]=k                  5               8      */
   /* */
       if  (cptcovn>0) {  /* Type                    */
         fprintf(ficresp, "\n#********** Variable ");  /* V         1  2  3  4  5 */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  /*           F  F  V  V  V */
         fprintf(ficresp, "**********\n#");  /*           D  Q  D  D  Q */
       }  /*                         */
       for(i=1; i<=nlstate;i++)  int *TvarsD;
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  int *TvarsDind;
       fprintf(ficresp, "\n");  int *TvarsQ;
        int *TvarsQind;
       for(i=(int)agemin; i <= (int)agemax+3; i++){  
         if(i==(int)agemax+3)  #define MAXRESULTLINES 10
           printf("Total");  int nresult=0;
         else  int parameterline=0; /* # of the parameter (type) line */
           printf("Age %d", i);  int TKresult[MAXRESULTLINES];
         for(jk=1; jk <=nlstate ; jk++){  int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
             pp[jk] += freq[jk][m][i];  int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
         }  double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
         for(jk=1; jk <=nlstate ; jk++){  double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
           for(m=-1, pos=0; m <=0 ; m++)  int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
             pos += freq[jk][m][i];  
           if(pp[jk]>=1.e-10)  /* int *TDvar; /\**< TDvar[1]=4,  TDvarF[2]=3, TDvar[3]=6  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  int *TvarF; /**< TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
           else  int *TvarFind; /**< TvarFind[1]=6,  TvarFind[2]=7, Tvarind[3]=9  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  int *TvarV; /**< TvarV[1]=Tvar[1]=5, TvarV[2]=Tvar[2]=4  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         }  int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarA; /**< TvarA[1]=Tvar[5]=5, TvarA[2]=Tvar[8]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         for(jk=1; jk <=nlstate ; jk++){  int *TvarAind; /**< TvarindA[1]=5, TvarAind[2]=8  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
             pp[jk] += freq[jk][m][i];  int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         }  int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
   int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
         for(jk=1,pos=0; jk <=nlstate ; jk++)  int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
           pos += pp[jk];  int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
         for(jk=1; jk <=nlstate ; jk++){  int *TvarVQ; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
           if(pos>=1.e-5)  int *TvarVQind; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  
           else  int *Tvarsel; /**< Selected covariates for output */
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  double *Tvalsel; /**< Selected modality value of covariate for output */
           if( i <= (int) agemax){  int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
             if(pos>=1.e-5){  int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */ 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */ 
               probs[i][jk][j1]= pp[jk]/pos;  int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
             }  int *Tage;
             else  int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */ 
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
           }  int *TmodelInvind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/ 
         }  int *TmodelInvQind; /** Tmodelqind[1]=1 for V5(quantitative varying) position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1  */
          int *Ndum; /** Freq of modality (tricode */
         for(jk=-1; jk <=nlstate+ndeath; jk++)  /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
           for(m=-1; m <=nlstate+ndeath; m++)  int **Tvard;
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  int *Tprod;/**< Gives the k position of the k1 product */
         if(i <= (int) agemax)  /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3  */
           fprintf(ficresp,"\n");  int *Tposprod; /**< Gives the k1 product from the k position */
         printf("\n");     /* if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2) */
       }     /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
     }  int cptcovprod, *Tvaraff, *invalidvarcomb;
   }  double *lsurv, *lpop, *tpop;
   dateintmean=dateintsum/k2cpt;  
    #define FD 1; /* Fixed dummy covariate */
   fclose(ficresp);  #define FQ 2; /* Fixed quantitative covariate */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  #define FP 3; /* Fixed product covariate */
   free_vector(pp,1,nlstate);  #define FPDD 7; /* Fixed product dummy*dummy covariate */
    #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
   /* End of Freq */  #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
 }  #define VD 10; /* Varying dummy covariate */
   #define VQ 11; /* Varying quantitative covariate */
 /************ Prevalence ********************/  #define VP 12; /* Varying product covariate */
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)  #define VPDD 13; /* Varying product dummy*dummy covariate */
 {  /* Some frequencies */  #define VPDQ 14; /* Varying product dummy*quantitative covariate */
    #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  #define APFD 16; /* Age product * fixed dummy covariate */
   double ***freq; /* Frequencies */  #define APFQ 17; /* Age product * fixed quantitative covariate */
   double *pp;  #define APVD 18; /* Age product * varying dummy covariate */
   double pos, k2;  #define APVQ 19; /* Age product * varying quantitative covariate */
   
   pp=vector(1,nlstate);  #define FTYPE 1; /* Fixed covariate */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  #define VTYPE 2; /* Varying covariate (loop in wave) */
    #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;  struct kmodel{
            int maintype; /* main type */
   j=cptcoveff;          int subtype; /* subtype */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  };
    struct kmodel modell[NCOVMAX];
   for(k1=1; k1<=j;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
       j1++;  double ftolhess; /**< Tolerance for computing hessian */
        
       for (i=-1; i<=nlstate+ndeath; i++)    /**************** split *************************/
         for (jk=-1; jk<=nlstate+ndeath; jk++)    static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
           for(m=agemin; m <= agemax+3; m++)  {
             freq[i][jk][m]=0;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
             the name of the file (name), its extension only (ext) and its first part of the name (finame)
       for (i=1; i<=imx; i++) {    */ 
         bool=1;    char  *ss;                            /* pointer */
         if  (cptcovn>0) {    int   l1=0, l2=0;                             /* length counters */
           for (z1=1; z1<=cptcoveff; z1++)  
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    l1 = strlen(path );                   /* length of path */
               bool=0;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
         }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
         if (bool==1) {    if ( ss == NULL ) {                   /* no directory, so determine current directory */
           for(m=firstpass; m<=lastpass; m++){      strcpy( name, path );               /* we got the fullname name because no directory */
             k2=anint[m][i]+(mint[m][i]/12.);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
               if(agev[m][i]==0) agev[m][i]=agemax+1;      /* get current working directory */
               if(agev[m][i]==1) agev[m][i]=agemax+2;      /*    extern  char* getcwd ( char *buf , int len);*/
               if (m<lastpass) {  #ifdef WIN32
                 if (calagedate>0)      if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];  #else
                 else          if (getcwd(dirc, FILENAME_MAX) == NULL) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  #endif
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];        return( GLOCK_ERROR_GETCWD );
               }      }
             }      /* got dirc from getcwd*/
           }      printf(" DIRC = %s \n",dirc);
         }    } else {                              /* strip directory from path */
       }      ss++;                               /* after this, the filename */
       for(i=(int)agemin; i <= (int)agemax+3; i++){      l2 = strlen( ss );                  /* length of filename */
         for(jk=1; jk <=nlstate ; jk++){      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      strcpy( name, ss );         /* save file name */
             pp[jk] += freq[jk][m][i];      strncpy( dirc, path, l1 - l2 );     /* now the directory */
         }      dirc[l1-l2] = '\0';                 /* add zero */
         for(jk=1; jk <=nlstate ; jk++){      printf(" DIRC2 = %s \n",dirc);
           for(m=-1, pos=0; m <=0 ; m++)    }
             pos += freq[jk][m][i];    /* We add a separator at the end of dirc if not exists */
         }    l1 = strlen( dirc );                  /* length of directory */
            if( dirc[l1-1] != DIRSEPARATOR ){
         for(jk=1; jk <=nlstate ; jk++){      dirc[l1] =  DIRSEPARATOR;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      dirc[l1+1] = 0; 
             pp[jk] += freq[jk][m][i];      printf(" DIRC3 = %s \n",dirc);
         }    }
            ss = strrchr( name, '.' );            /* find last / */
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    if (ss >0){
              ss++;
         for(jk=1; jk <=nlstate ; jk++){          strcpy(ext,ss);                     /* save extension */
           if( i <= (int) agemax){      l1= strlen( name);
             if(pos>=1.e-5){      l2= strlen(ss)+1;
               probs[i][jk][j1]= pp[jk]/pos;      strncpy( finame, name, l1-l2);
             }      finame[l1-l2]= 0;
           }    }
         }  
            return( 0 );                          /* we're done */
       }  }
     }  
   }  
   /******************************************/
    
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  void replace_back_to_slash(char *s, char*t)
   free_vector(pp,1,nlstate);  {
      int i;
 }  /* End of Freq */    int lg=0;
     i=0;
 /************* Waves Concatenation ***************/    lg=strlen(t);
     for(i=0; i<= lg; i++) {
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      (s[i] = t[i]);
 {      if (t[i]== '\\') s[i]='/';
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    }
      Death is a valid wave (if date is known).  }
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  char *trimbb(char *out, char *in)
      and mw[mi+1][i]. dh depends on stepm.  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
      */    char *s;
     s=out;
   int i, mi, m;    while (*in != '\0'){
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
      double sum=0., jmean=0.;*/        in++;
       }
   int j, k=0,jk, ju, jl;      *out++ = *in++;
   double sum=0.;    }
   jmin=1e+5;    *out='\0';
   jmax=-1;    return s;
   jmean=0.;  }
   for(i=1; i<=imx; i++){  
     mi=0;  /* char *substrchaine(char *out, char *in, char *chain) */
     m=firstpass;  /* { */
     while(s[m][i] <= nlstate){  /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
       if(s[m][i]>=1)  /*   char *s, *t; */
         mw[++mi][i]=m;  /*   t=in;s=out; */
       if(m >=lastpass)  /*   while ((*in != *chain) && (*in != '\0')){ */
         break;  /*     *out++ = *in++; */
       else  /*   } */
         m++;  
     }/* end while */  /*   /\* *in matches *chain *\/ */
     if (s[m][i] > nlstate){  /*   while ((*in++ == *chain++) && (*in != '\0')){ */
       mi++;     /* Death is another wave */  /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
       /* if(mi==0)  never been interviewed correctly before death */  /*   } */
          /* Only death is a correct wave */  /*   in--; chain--; */
       mw[mi][i]=m;  /*   while ( (*in != '\0')){ */
     }  /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   /*     *out++ = *in++; */
     wav[i]=mi;  /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
     if(mi==0)  /*   } */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  /*   *out='\0'; */
   }  /*   out=s; */
   /*   return out; */
   for(i=1; i<=imx; i++){  /* } */
     for(mi=1; mi<wav[i];mi++){  char *substrchaine(char *out, char *in, char *chain)
       if (stepm <=0)  {
         dh[mi][i]=1;    /* Substract chain 'chain' from 'in', return and output 'out' */
       else{    /* in="V1+V1*age+age*age+V2", chain="age*age" */
         if (s[mw[mi+1][i]][i] > nlstate) {  
           if (agedc[i] < 2*AGESUP) {    char *strloc;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  
           if(j==0) j=1;  /* Survives at least one month after exam */    strcpy (out, in); 
           k=k+1;    strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
           if (j >= jmax) jmax=j;    printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
           if (j <= jmin) jmin=j;    if(strloc != NULL){ 
           sum=sum+j;      /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
           }      /* strcpy (strloc, strloc +strlen(chain));*/
         }    }
         else{    printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    return out;
           k=k+1;  }
           if (j >= jmax) jmax=j;  
           else if (j <= jmin)jmin=j;  
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  char *cutl(char *blocc, char *alocc, char *in, char occ)
           sum=sum+j;  {
         }    /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' 
         jk= j/stepm;       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
         jl= j -jk*stepm;       gives blocc="abcdef" and alocc="ghi2j".
         ju= j -(jk+1)*stepm;       If occ is not found blocc is null and alocc is equal to in. Returns blocc
         if(jl <= -ju)    */
           dh[mi][i]=jk;    char *s, *t;
         else    t=in;s=in;
           dh[mi][i]=jk+1;    while ((*in != occ) && (*in != '\0')){
         if(dh[mi][i]==0)      *alocc++ = *in++;
           dh[mi][i]=1; /* At least one step */    }
       }    if( *in == occ){
     }      *(alocc)='\0';
   }      s=++in;
   jmean=sum/k;    }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);   
  }    if (s == t) {/* occ not found */
 /*********** Tricode ****************************/      *(alocc-(in-s))='\0';
 void tricode(int *Tvar, int **nbcode, int imx)      in=s;
 {    }
   int Ndum[20],ij=1, k, j, i;    while ( *in != '\0'){
   int cptcode=0;      *blocc++ = *in++;
   cptcoveff=0;    }
    
   for (k=0; k<19; k++) Ndum[k]=0;    *blocc='\0';
   for (k=1; k<=7; k++) ncodemax[k]=0;    return t;
   }
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  char *cutv(char *blocc, char *alocc, char *in, char occ)
     for (i=1; i<=imx; i++) {  {
       ij=(int)(covar[Tvar[j]][i]);    /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' 
       Ndum[ij]++;       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/       gives blocc="abcdef2ghi" and alocc="j".
       if (ij > cptcode) cptcode=ij;       If occ is not found blocc is null and alocc is equal to in. Returns alocc
     }    */
     char *s, *t;
     for (i=0; i<=cptcode; i++) {    t=in;s=in;
       if(Ndum[i]!=0) ncodemax[j]++;    while (*in != '\0'){
     }      while( *in == occ){
     ij=1;        *blocc++ = *in++;
         s=in;
       }
     for (i=1; i<=ncodemax[j]; i++) {      *blocc++ = *in++;
       for (k=0; k<=19; k++) {    }
         if (Ndum[k] != 0) {    if (s == t) /* occ not found */
           nbcode[Tvar[j]][ij]=k;      *(blocc-(in-s))='\0';
              else
           ij++;      *(blocc-(in-s)-1)='\0';
         }    in=s;
         if (ij > ncodemax[j]) break;    while ( *in != '\0'){
       }        *alocc++ = *in++;
     }    }
   }    
     *alocc='\0';
  for (k=0; k<19; k++) Ndum[k]=0;    return s;
   }
  for (i=1; i<=ncovmodel-2; i++) {  
       ij=Tvar[i];  int nbocc(char *s, char occ)
       Ndum[ij]++;  {
     }    int i,j=0;
     int lg=20;
  ij=1;    i=0;
  for (i=1; i<=10; i++) {    lg=strlen(s);
    if((Ndum[i]!=0) && (i<=ncovcol)){    for(i=0; i<= lg; i++) {
      Tvaraff[ij]=i;      if  (s[i] == occ ) j++;
      ij++;    }
    }    return j;
  }  }
    
     cptcoveff=ij-1;  /* void cutv(char *u,char *v, char*t, char occ) */
 }  /* { */
   /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
 /*********** Health Expectancies ****************/  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   /*      gives u="abcdef2ghi" and v="j" *\/ */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )  /*   int i,lg,j,p=0; */
   /*   i=0; */
 {  /*   lg=strlen(t); */
   /* Health expectancies */  /*   for(j=0; j<=lg-1; j++) { */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   double age, agelim, hf;  /*   } */
   double ***p3mat,***varhe;  
   double **dnewm,**doldm;  /*   for(j=0; j<p; j++) { */
   double *xp;  /*     (u[j] = t[j]); */
   double **gp, **gm;  /*   } */
   double ***gradg, ***trgradg;  /*      u[p]='\0'; */
   int theta;  
   /*    for(j=0; j<= lg; j++) { */
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   xp=vector(1,npar);  /*   } */
   dnewm=matrix(1,nlstate*2,1,npar);  /* } */
   doldm=matrix(1,nlstate*2,1,nlstate*2);  
    #ifdef _WIN32
   fprintf(ficreseij,"# Health expectancies\n");  char * strsep(char **pp, const char *delim)
   fprintf(ficreseij,"# Age");  {
   for(i=1; i<=nlstate;i++)    char *p, *q;
     for(j=1; j<=nlstate;j++)           
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    if ((p = *pp) == NULL)
   fprintf(ficreseij,"\n");      return 0;
     if ((q = strpbrk (p, delim)) != NULL)
   if(estepm < stepm){    {
     printf ("Problem %d lower than %d\n",estepm, stepm);      *pp = q + 1;
   }      *q = '\0';
   else  hstepm=estepm;      }
   /* We compute the life expectancy from trapezoids spaced every estepm months    else
    * This is mainly to measure the difference between two models: for example      *pp = 0;
    * if stepm=24 months pijx are given only every 2 years and by summing them    return p;
    * we are calculating an estimate of the Life Expectancy assuming a linear  }
    * progression inbetween and thus overestimating or underestimating according  #endif
    * to the curvature of the survival function. If, for the same date, we  
    * estimate the model with stepm=1 month, we can keep estepm to 24 months  /********************** nrerror ********************/
    * to compare the new estimate of Life expectancy with the same linear  
    * hypothesis. A more precise result, taking into account a more precise  void nrerror(char error_text[])
    * curvature will be obtained if estepm is as small as stepm. */  {
     fprintf(stderr,"ERREUR ...\n");
   /* For example we decided to compute the life expectancy with the smallest unit */    fprintf(stderr,"%s\n",error_text);
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    exit(EXIT_FAILURE);
      nhstepm is the number of hstepm from age to agelim  }
      nstepm is the number of stepm from age to agelin.  /*********************** vector *******************/
      Look at hpijx to understand the reason of that which relies in memory size  double *vector(int nl, int nh)
      and note for a fixed period like estepm months */  {
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    double *v;
      survival function given by stepm (the optimization length). Unfortunately it    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
      means that if the survival funtion is printed only each two years of age and if    if (!v) nrerror("allocation failure in vector");
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    return v-nl+NR_END;
      results. So we changed our mind and took the option of the best precision.  }
   */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  /************************ free vector ******************/
   void free_vector(double*v, int nl, int nh)
   agelim=AGESUP;  {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    free((FREE_ARG)(v+nl-NR_END));
     /* nhstepm age range expressed in number of stepm */  }
     nstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */  /************************ivector *******************************/
     /* if (stepm >= YEARM) hstepm=1;*/  int *ivector(long nl,long nh)
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int *v;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     gp=matrix(0,nhstepm,1,nlstate*2);    if (!v) nrerror("allocation failure in ivector");
     gm=matrix(0,nhstepm,1,nlstate*2);    return v-nl+NR_END;
   }
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  /******************free ivector **************************/
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    void free_ivector(int *v, long nl, long nh)
    {
     free((FREE_ARG)(v+nl-NR_END));
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  }
   
     /* Computing Variances of health expectancies */  /************************lvector *******************************/
   long *lvector(long nl,long nh)
      for(theta=1; theta <=npar; theta++){  {
       for(i=1; i<=npar; i++){    long *v;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       }    if (!v) nrerror("allocation failure in ivector");
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      return v-nl+NR_END;
    }
       cptj=0;  
       for(j=1; j<= nlstate; j++){  /******************free lvector **************************/
         for(i=1; i<=nlstate; i++){  void free_lvector(long *v, long nl, long nh)
           cptj=cptj+1;  {
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    free((FREE_ARG)(v+nl-NR_END));
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  }
           }  
         }  /******************* imatrix *******************************/
       }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
             /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
        { 
       for(i=1; i<=npar; i++)    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    int **m; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      
          /* allocate pointers to rows */ 
       cptj=0;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       for(j=1; j<= nlstate; j++){    if (!m) nrerror("allocation failure 1 in matrix()"); 
         for(i=1;i<=nlstate;i++){    m += NR_END; 
           cptj=cptj+1;    m -= nrl; 
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    
           }    /* allocate rows and set pointers to them */ 
         }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       for(j=1; j<= nlstate*2; j++)    m[nrl] += NR_END; 
         for(h=0; h<=nhstepm-1; h++){    m[nrl] -= ncl; 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    
         }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
      }    
        /* return pointer to array of pointers to rows */ 
 /* End theta */    return m; 
   } 
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);  
   /****************** free_imatrix *************************/
      for(h=0; h<=nhstepm-1; h++)  void free_imatrix(m,nrl,nrh,ncl,nch)
       for(j=1; j<=nlstate*2;j++)        int **m;
         for(theta=1; theta <=npar; theta++)        long nch,ncl,nrh,nrl; 
           trgradg[h][j][theta]=gradg[h][theta][j];       /* free an int matrix allocated by imatrix() */ 
        { 
     free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
      for(i=1;i<=nlstate*2;i++)    free((FREE_ARG) (m+nrl-NR_END)); 
       for(j=1;j<=nlstate*2;j++)  } 
         varhe[i][j][(int)age] =0.;  
   /******************* matrix *******************************/
      printf("%d|",(int)age);fflush(stdout);  double **matrix(long nrl, long nrh, long ncl, long nch)
      for(h=0;h<=nhstepm-1;h++){  {
       for(k=0;k<=nhstepm-1;k++){    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);    double **m;
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);  
         for(i=1;i<=nlstate*2;i++)    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
           for(j=1;j<=nlstate*2;j++)    if (!m) nrerror("allocation failure 1 in matrix()");
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    m += NR_END;
       }    m -= nrl;
     }  
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
          if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     /* Computing expectancies */    m[nrl] += NR_END;
     for(i=1; i<=nlstate;i++)    m[nrl] -= ncl;
       for(j=1; j<=nlstate;j++)  
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    return m;
              /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
         }     */
   }
     fprintf(ficreseij,"%3.0f",age );  
     cptj=0;  /*************************free matrix ************************/
     for(i=1; i<=nlstate;i++)  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       for(j=1; j<=nlstate;j++){  {
         cptj++;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );    free((FREE_ARG)(m+nrl-NR_END));
       }  }
     fprintf(ficreseij,"\n");  
      /******************* ma3x *******************************/
     free_matrix(gm,0,nhstepm,1,nlstate*2);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     free_matrix(gp,0,nhstepm,1,nlstate*2);  {
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);    double ***m;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   free_vector(xp,1,npar);    if (!m) nrerror("allocation failure 1 in matrix()");
   free_matrix(dnewm,1,nlstate*2,1,npar);    m += NR_END;
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);    m -= nrl;
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);  
 }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 /************ Variance ******************/    m[nrl] += NR_END;
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)    m[nrl] -= ncl;
 {  
   /* Variance of health expectancies */    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   double **dnewm,**doldm;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   int i, j, nhstepm, hstepm, h, nstepm ;    m[nrl][ncl] += NR_END;
   int k, cptcode;    m[nrl][ncl] -= nll;
   double *xp;    for (j=ncl+1; j<=nch; j++) 
   double **gp, **gm;      m[nrl][j]=m[nrl][j-1]+nlay;
   double ***gradg, ***trgradg;    
   double ***p3mat;    for (i=nrl+1; i<=nrh; i++) {
   double age,agelim, hf;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   int theta;      for (j=ncl+1; j<=nch; j++) 
         m[i][j]=m[i][j-1]+nlay;
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");    }
   fprintf(ficresvij,"# Age");    return m; 
   for(i=1; i<=nlstate;i++)    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     for(j=1; j<=nlstate;j++)             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    */
   fprintf(ficresvij,"\n");  }
   
   xp=vector(1,npar);  /*************************free ma3x ************************/
   dnewm=matrix(1,nlstate,1,npar);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   doldm=matrix(1,nlstate,1,nlstate);  {
      free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   if(estepm < stepm){    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     printf ("Problem %d lower than %d\n",estepm, stepm);    free((FREE_ARG)(m+nrl-NR_END));
   }  }
   else  hstepm=estepm;    
   /* For example we decided to compute the life expectancy with the smallest unit */  /*************** function subdirf ***********/
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.  char *subdirf(char fileres[])
      nhstepm is the number of hstepm from age to agelim  {
      nstepm is the number of stepm from age to agelin.    /* Caution optionfilefiname is hidden */
      Look at hpijx to understand the reason of that which relies in memory size    strcpy(tmpout,optionfilefiname);
      and note for a fixed period like k years */    strcat(tmpout,"/"); /* Add to the right */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    strcat(tmpout,fileres);
      survival function given by stepm (the optimization length). Unfortunately it    return tmpout;
      means that if the survival funtion is printed only each two years of age and if  }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  
      results. So we changed our mind and took the option of the best precision.  /*************** function subdirf2 ***********/
   */  char *subdirf2(char fileres[], char *preop)
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  {
   agelim = AGESUP;    
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /* Caution optionfilefiname is hidden */
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    strcpy(tmpout,optionfilefiname);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    strcat(tmpout,"/");
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    strcat(tmpout,preop);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    strcat(tmpout,fileres);
     gp=matrix(0,nhstepm,1,nlstate);    return tmpout;
     gm=matrix(0,nhstepm,1,nlstate);  }
   
     for(theta=1; theta <=npar; theta++){  /*************** function subdirf3 ***********/
       for(i=1; i<=npar; i++){ /* Computes gradient */  char *subdirf3(char fileres[], char *preop, char *preop2)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  {
       }    
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      /* Caution optionfilefiname is hidden */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
       if (popbased==1) {    strcat(tmpout,preop);
         for(i=1; i<=nlstate;i++)    strcat(tmpout,preop2);
           prlim[i][i]=probs[(int)age][i][ij];    strcat(tmpout,fileres);
       }    return tmpout;
    }
       for(j=1; j<= nlstate; j++){   
         for(h=0; h<=nhstepm; h++){  /*************** function subdirfext ***********/
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  char *subdirfext(char fileres[], char *preop, char *postop)
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  {
         }    
       }    strcpy(tmpout,preop);
        strcat(tmpout,fileres);
       for(i=1; i<=npar; i++) /* Computes gradient */    strcat(tmpout,postop);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    return tmpout;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
    /*************** function subdirfext3 ***********/
       if (popbased==1) {  char *subdirfext3(char fileres[], char *preop, char *postop)
         for(i=1; i<=nlstate;i++)  {
           prlim[i][i]=probs[(int)age][i][ij];    
       }    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
       for(j=1; j<= nlstate; j++){    strcat(tmpout,"/");
         for(h=0; h<=nhstepm; h++){    strcat(tmpout,preop);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    strcat(tmpout,fileres);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    strcat(tmpout,postop);
         }    return tmpout;
       }  }
    
       for(j=1; j<= nlstate; j++)  char *asc_diff_time(long time_sec, char ascdiff[])
         for(h=0; h<=nhstepm; h++){  {
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    long sec_left, days, hours, minutes;
         }    days = (time_sec) / (60*60*24);
     } /* End theta */    sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    sec_left = (sec_left) %(60*60);
     minutes = (sec_left) /60;
     for(h=0; h<=nhstepm; h++)    sec_left = (sec_left) % (60);
       for(j=1; j<=nlstate;j++)    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
         for(theta=1; theta <=npar; theta++)    return ascdiff;
           trgradg[h][j][theta]=gradg[h][theta][j];  }
   
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  /***************** f1dim *************************/
     for(i=1;i<=nlstate;i++)  extern int ncom; 
       for(j=1;j<=nlstate;j++)  extern double *pcom,*xicom;
         vareij[i][j][(int)age] =0.;  extern double (*nrfunc)(double []); 
    
     for(h=0;h<=nhstepm;h++){  double f1dim(double x) 
       for(k=0;k<=nhstepm;k++){  { 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    int j; 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    double f;
         for(i=1;i<=nlstate;i++)    double *xt; 
           for(j=1;j<=nlstate;j++)   
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    xt=vector(1,ncom); 
       }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     }    f=(*nrfunc)(xt); 
     free_vector(xt,1,ncom); 
     fprintf(ficresvij,"%.0f ",age );    return f; 
     for(i=1; i<=nlstate;i++)  } 
       for(j=1; j<=nlstate;j++){  
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);  /*****************brent *************************/
       }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     fprintf(ficresvij,"\n");  {
     free_matrix(gp,0,nhstepm,1,nlstate);    /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
     free_matrix(gm,0,nhstepm,1,nlstate);     * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);     * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);     * the minimum is returned as xmin, and the minimum function value is returned as brent , the
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     * returned function value. 
   } /* End age */    */
      int iter; 
   free_vector(xp,1,npar);    double a,b,d,etemp;
   free_matrix(doldm,1,nlstate,1,npar);    double fu=0,fv,fw,fx;
   free_matrix(dnewm,1,nlstate,1,nlstate);    double ftemp=0.;
     double p,q,r,tol1,tol2,u,v,w,x,xm; 
 }    double e=0.0; 
    
 /************ Variance of prevlim ******************/    a=(ax < cx ? ax : cx); 
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    b=(ax > cx ? ax : cx); 
 {    x=w=v=bx; 
   /* Variance of prevalence limit */    fw=fv=fx=(*f)(x); 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    for (iter=1;iter<=ITMAX;iter++) { 
   double **newm;      xm=0.5*(a+b); 
   double **dnewm,**doldm;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   int i, j, nhstepm, hstepm;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   int k, cptcode;      printf(".");fflush(stdout);
   double *xp;      fprintf(ficlog,".");fflush(ficlog);
   double *gp, *gm;  #ifdef DEBUGBRENT
   double **gradg, **trgradg;      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   double age,agelim;      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   int theta;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
      #endif
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   fprintf(ficresvpl,"# Age");        *xmin=x; 
   for(i=1; i<=nlstate;i++)        return fx; 
       fprintf(ficresvpl," %1d-%1d",i,i);      } 
   fprintf(ficresvpl,"\n");      ftemp=fu;
       if (fabs(e) > tol1) { 
   xp=vector(1,npar);        r=(x-w)*(fx-fv); 
   dnewm=matrix(1,nlstate,1,npar);        q=(x-v)*(fx-fw); 
   doldm=matrix(1,nlstate,1,nlstate);        p=(x-v)*q-(x-w)*r; 
          q=2.0*(q-r); 
   hstepm=1*YEARM; /* Every year of age */        if (q > 0.0) p = -p; 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        q=fabs(q); 
   agelim = AGESUP;        etemp=e; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        e=d; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     if (stepm >= YEARM) hstepm=1;                                  d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        else { 
     gradg=matrix(1,npar,1,nlstate);                                  d=p/q; 
     gp=vector(1,nlstate);                                  u=x+d; 
     gm=vector(1,nlstate);                                  if (u-a < tol2 || b-u < tol2) 
                                           d=SIGN(tol1,xm-x); 
     for(theta=1; theta <=npar; theta++){        } 
       for(i=1; i<=npar; i++){ /* Computes gradient */      } else { 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       }      } 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       for(i=1;i<=nlstate;i++)      fu=(*f)(u); 
         gp[i] = prlim[i][i];      if (fu <= fx) { 
            if (u >= x) a=x; else b=x; 
       for(i=1; i<=npar; i++) /* Computes gradient */        SHFT(v,w,x,u) 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        SHFT(fv,fw,fx,fu) 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      } else { 
       for(i=1;i<=nlstate;i++)        if (u < x) a=u; else b=u; 
         gm[i] = prlim[i][i];        if (fu <= fw || w == x) { 
                                   v=w; 
       for(i=1;i<=nlstate;i++)                                  w=u; 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];                                  fv=fw; 
     } /* End theta */                                  fw=fu; 
         } else if (fu <= fv || v == x || v == w) { 
     trgradg =matrix(1,nlstate,1,npar);                                  v=u; 
                                   fv=fu; 
     for(j=1; j<=nlstate;j++)        } 
       for(theta=1; theta <=npar; theta++)      } 
         trgradg[j][theta]=gradg[theta][j];    } 
     nrerror("Too many iterations in brent"); 
     for(i=1;i<=nlstate;i++)    *xmin=x; 
       varpl[i][(int)age] =0.;    return fx; 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  } 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  
     for(i=1;i<=nlstate;i++)  /****************** mnbrak ***********************/
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     fprintf(ficresvpl,"%.0f ",age );              double (*func)(double)) 
     for(i=1; i<=nlstate;i++)  { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  the downhill direction (defined by the function as evaluated at the initial points) and returns
     fprintf(ficresvpl,"\n");  new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
     free_vector(gp,1,nlstate);  values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
     free_vector(gm,1,nlstate);     */
     free_matrix(gradg,1,npar,1,nlstate);    double ulim,u,r,q, dum;
     free_matrix(trgradg,1,nlstate,1,npar);    double fu; 
   } /* End age */  
     double scale=10.;
   free_vector(xp,1,npar);    int iterscale=0;
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);    *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
     *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
 }  
   
 /************ Variance of one-step probabilities  ******************/    /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)    /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
 {    /*   *bx = *ax - (*ax - *bx)/scale; */
   int i, j, i1, k1, j1, z1;    /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
   int k=0,l, cptcode;    /* } */
   double **dnewm,**doldm;  
   double *xp;    if (*fb > *fa) { 
   double *gp, *gm;      SHFT(dum,*ax,*bx,dum) 
   double **gradg, **trgradg;      SHFT(dum,*fb,*fa,dum) 
   double age,agelim, cov[NCOVMAX];    } 
   int theta;    *cx=(*bx)+GOLD*(*bx-*ax); 
   char fileresprob[FILENAMELENGTH];    *fc=(*func)(*cx); 
   char fileresprobcov[FILENAMELENGTH];  #ifdef DEBUG
   char fileresprobcor[FILENAMELENGTH];    printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
     fprintf(ficlog,"mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
   strcpy(fileresprob,"prob");  #endif
   strcat(fileresprob,fileres);    while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc. If fc=inf it exits and if flat fb=fc it exits too.*/
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      r=(*bx-*ax)*(*fb-*fc); 
     printf("Problem with resultfile: %s\n", fileresprob);      q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
   }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   strcpy(fileresprobcov,"probcov");        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
   strcat(fileresprobcov,fileres);      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {      if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
     printf("Problem with resultfile: %s\n", fileresprobcov);        fu=(*func)(u); 
   }  #ifdef DEBUG
   strcpy(fileresprobcor,"probcor");        /* f(x)=A(x-u)**2+f(u) */
   strcat(fileresprobcor,fileres);        double A, fparabu; 
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
     printf("Problem with resultfile: %s\n", fileresprobcor);        fparabu= *fa - A*(*ax-u)*(*ax-u);
   }        printf("\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);        fprintf(ficlog,"\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);        /* And thus,it can be that fu > *fc even if fparabu < *fc */
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);        /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
            (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");        /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
   fprintf(ficresprob,"# Age");  #endif 
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");  #ifdef MNBRAKORIGINAL
   fprintf(ficresprobcov,"# Age");  #else
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");  /*       if (fu > *fc) { */
   fprintf(ficresprobcov,"# Age");  /* #ifdef DEBUG */
   for(i=1; i<=nlstate;i++)  /*       printf("mnbrak4  fu > fc \n"); */
     for(j=1; j<=(nlstate+ndeath);j++){  /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);  /* #endif */
       fprintf(ficresprobcov," p%1d-%1d ",i,j);  /*      /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/  *\/ */
       fprintf(ficresprobcor," p%1d-%1d ",i,j);  /*      /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\\/ *\/ */
     }    /*      dum=u; /\* Shifting c and u *\/ */
   fprintf(ficresprob,"\n");  /*      u = *cx; */
   fprintf(ficresprobcov,"\n");  /*      *cx = dum; */
   fprintf(ficresprobcor,"\n");  /*      dum = fu; */
   xp=vector(1,npar);  /*      fu = *fc; */
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  /*      *fc =dum; */
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));  /*       } else { /\* end *\/ */
    /* #ifdef DEBUG */
   cov[1]=1;  /*       printf("mnbrak3  fu < fc \n"); */
   j=cptcoveff;  /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  /* #endif */
   j1=0;  /*      dum=u; /\* Shifting c and u *\/ */
   for(k1=1; k1<=1;k1++){  /*      u = *cx; */
     for(i1=1; i1<=ncodemax[k1];i1++){  /*      *cx = dum; */
     j1++;  /*      dum = fu; */
   /*      fu = *fc; */
     if  (cptcovn>0) {  /*      *fc =dum; */
       fprintf(ficresprob, "\n#********** Variable ");  /*       } */
       fprintf(ficresprobcov, "\n#********** Variable ");  #ifdef DEBUGMNBRAK
       fprintf(ficresprobcor, "\n#********** Variable ");                   double A, fparabu; 
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
       fprintf(ficresprob, "**********\n#");       fparabu= *fa - A*(*ax-u)*(*ax-u);
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);       printf("\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
       fprintf(ficresprobcov, "**********\n#");       fprintf(ficlog,"\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  #endif
       fprintf(ficresprobcor, "**********\n#");        dum=u; /* Shifting c and u */
     }        u = *cx;
            *cx = dum;
       for (age=bage; age<=fage; age ++){        dum = fu;
         cov[2]=age;        fu = *fc;
         for (k=1; k<=cptcovn;k++) {        *fc =dum;
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];  #endif
         }      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  #ifdef DEBUG
         for (k=1; k<=cptcovprod;k++)        printf("\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
          #endif
         gradg=matrix(1,npar,1,9);        fu=(*func)(u); 
         trgradg=matrix(1,9,1,npar);        if (fu < *fc) { 
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  #ifdef DEBUG
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));                                  printf("\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
                                fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
         for(theta=1; theta <=npar; theta++){  #endif
           for(i=1; i<=npar; i++)                            SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             xp[i] = x[i] + (i==theta ?delti[theta]:0);                                  SHFT(*fb,*fc,fu,(*func)(u)) 
            #ifdef DEBUG
           pmij(pmmij,cov,ncovmodel,xp,nlstate);                                          printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
            #endif
           k=0;        } 
           for(i=1; i<= (nlstate+ndeath); i++){      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
             for(j=1; j<=(nlstate+ndeath);j++){  #ifdef DEBUG
               k=k+1;        printf("\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
               gp[k]=pmmij[i][j];        fprintf(ficlog,"\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
             }  #endif
           }        u=ulim; 
                  fu=(*func)(u); 
           for(i=1; i<=npar; i++)      } else { /* u could be left to b (if r > q parabola has a maximum) */
             xp[i] = x[i] - (i==theta ?delti[theta]:0);  #ifdef DEBUG
            printf("\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);        fprintf(ficlog,"\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
           k=0;  #endif
           for(i=1; i<=(nlstate+ndeath); i++){        u=(*cx)+GOLD*(*cx-*bx); 
             for(j=1; j<=(nlstate+ndeath);j++){        fu=(*func)(u); 
               k=k+1;  #ifdef DEBUG
               gm[k]=pmmij[i][j];        printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
             }        fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
           }  #endif
            } /* end tests */
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)      SHFT(*ax,*bx,*cx,u) 
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        SHFT(*fa,*fb,*fc,fu) 
         }  #ifdef DEBUG
         printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)        fprintf(ficlog, "\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
           for(theta=1; theta <=npar; theta++)  #endif
             trgradg[j][theta]=gradg[theta][j];    } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
          } 
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);  
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);  /*************** linmin ************************/
          /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
         pmij(pmmij,cov,ncovmodel,x,nlstate);  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
          and replaces xi by the actual vector displacement that p was moved. Also returns as fret
         k=0;  the value of func at the returned location p . This is actually all accomplished by calling the
         for(i=1; i<=(nlstate+ndeath); i++){  routines mnbrak and brent .*/
           for(j=1; j<=(nlstate+ndeath);j++){  int ncom; 
             k=k+1;  double *pcom,*xicom;
             gm[k]=pmmij[i][j];  double (*nrfunc)(double []); 
           }   
         }  #ifdef LINMINORIGINAL
        void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         /*printf("\n%d ",(int)age);  #else
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat) 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  #endif
      }*/  { 
     double brent(double ax, double bx, double cx, 
         fprintf(ficresprob,"\n%d ",(int)age);                 double (*f)(double), double tol, double *xmin); 
         fprintf(ficresprobcov,"\n%d ",(int)age);    double f1dim(double x); 
         fprintf(ficresprobcor,"\n%d ",(int)age);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)    int j; 
           fprintf(ficresprob,"%12.3e (%12.3e) ",gm[i],sqrt(doldm[i][j]));    double xx,xmin,bx,ax; 
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    double fx,fb,fa;
           fprintf(ficresprobcov,"%12.3e ",gm[i]);  
           fprintf(ficresprobcor,"%12.3e ",gm[i]);  #ifdef LINMINORIGINAL
         }  #else
         i=0;    double scale=10., axs, xxs; /* Scale added for infinity */
         for (k=1; k<=(nlstate);k++){  #endif
           for (l=1; l<=(nlstate+ndeath);l++){    
             i=i++;    ncom=n; 
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);    pcom=vector(1,n); 
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);    xicom=vector(1,n); 
             for (j=1; j<=i;j++){    nrfunc=func; 
               fprintf(ficresprobcov," %12.3e",doldm[i][j]);    for (j=1;j<=n;j++) { 
               fprintf(ficresprobcor," %12.3e",doldm[i][j]/sqrt(doldm[i][i])/sqrt(doldm[j][j]));      pcom[j]=p[j]; 
             }      xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
           }    } 
         }  
       }  #ifdef LINMINORIGINAL
     }    xx=1.;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  #else
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    axs=0.0;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    xxs=1.;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    do{
   }      xx= xxs;
   free_vector(xp,1,npar);  #endif
   fclose(ficresprob);      ax=0.;
   fclose(ficresprobcov);      mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
   fclose(ficresprobcor);      /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
 }      /* xt[x,j]=pcom[j]+x*xicom[j]  f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and  f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j))   */
       /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
       /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
 /******************* Printing html file ***********/      /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \      /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus  [0:xi[j]]*/
                   int lastpass, int stepm, int weightopt, char model[],\  #ifdef LINMINORIGINAL
                   int imx,int jmin, int jmax, double jmeanint,char optionfile[], \  #else
                   char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\      if (fx != fx){
                   char version[], int popforecast, int estepm ,\                          xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
                   double jprev1, double mprev1,double anprev1, \                          printf("|");
                   double jprev2, double mprev2,double anprev2){                          fprintf(ficlog,"|");
   int jj1, k1, i1, cpt;  #ifdef DEBUGLINMIN
   FILE *fichtm;                          printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx);
   /*char optionfilehtm[FILENAMELENGTH];*/  #endif
       }
   strcpy(optionfilehtm,optionfile);    }while(fx != fx && xxs > 1.e-5);
   strcat(optionfilehtm,".htm");  #endif
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    
     printf("Problem with %s \n",optionfilehtm), exit(0);  #ifdef DEBUGLINMIN
   }    printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
     fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n  #endif
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n  #ifdef LINMINORIGINAL
 \n  #else
 Total number of observations=%d <br>\n          if(fb == fx){ /* Flat function in the direction */
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n                  xmin=xx;
 <hr  size=\"2\" color=\"#EC5E5E\">      *flat=1;
  <ul><li>Parameter files<br>\n          }else{
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n      *flat=0;
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);  #endif
                   /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n    /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    /* fmin = f(p[j] + xmin * xi[j]) */
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n    /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
  - Life expectancies by age and initial health status (estepm=%2d months):    /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
    <a href=\"e%s\">e%s</a> <br>\n</li>", \  #ifdef DEBUG
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    printf("retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
     fprintf(ficlog,"retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n  #endif
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n  #ifdef LINMINORIGINAL
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n  #else
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n                          }
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n  #endif
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n  #ifdef DEBUGLINMIN
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n    printf("linmin end ");
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);    fprintf(ficlog,"linmin end ");
   #endif
  if(popforecast==1) fprintf(fichtm,"\n    for (j=1;j<=n;j++) { 
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n  #ifdef LINMINORIGINAL
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n      xi[j] *= xmin; 
         <br>",fileres,fileres,fileres,fileres);  #else
  else  #ifdef DEBUGLINMIN
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);      if(xxs <1.0)
 fprintf(fichtm," <li>Graphs</li><p>");        printf(" before xi[%d]=%12.8f", j,xi[j]);
   #endif
  m=cptcoveff;      xi[j] *= xmin*xxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  #ifdef DEBUGLINMIN
       if(xxs <1.0)
  jj1=0;        printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs );
  for(k1=1; k1<=m;k1++){  #endif
    for(i1=1; i1<=ncodemax[k1];i1++){  #endif
      jj1++;      p[j] += xi[j]; /* Parameters values are updated accordingly */
      if (cptcovn > 0) {    } 
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  #ifdef DEBUGLINMIN
        for (cpt=1; cpt<=cptcoveff;cpt++)    printf("\n");
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
      }    for (j=1;j<=n;j++) { 
      /* Pij */      printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>      fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          if(j % ncovmodel == 0){
      /* Quasi-incidences */        printf("\n");
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>        fprintf(ficlog,"\n");
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      }
        /* Stable prevalence in each health state */    }
        for(cpt=1; cpt<nlstate;cpt++){  #else
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>  #endif
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    free_vector(xicom,1,n); 
        }    free_vector(pcom,1,n); 
     for(cpt=1; cpt<=nlstate;cpt++) {  } 
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  
 interval) in state (%d): v%s%d%d.png <br>  
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    /*************** powell ************************/
      }  /*
      for(cpt=1; cpt<=nlstate;cpt++) {  Minimization of a function func of n variables. Input consists of an initial starting point
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
      }  such that failure to decrease by more than this amount on one iteration signals doneness. On
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
 health expectancies in states (1) and (2): e%s%d.png<br>  function value at p , and iter is the number of iterations taken. The routine linmin is used.
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);   */
 fprintf(fichtm,"\n</body>");  #ifdef LINMINORIGINAL
    }  #else
  }          int *flatdir; /* Function is vanishing in that direction */
 fclose(fichtm);          int flat=0, flatd=0; /* Function is vanishing in that direction */
 }  #endif
   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 /******************* Gnuplot file **************/              double (*func)(double [])) 
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  { 
   #ifdef LINMINORIGINAL
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;   void linmin(double p[], double xi[], int n, double *fret, 
   int ng;                double (*func)(double [])); 
   strcpy(optionfilegnuplot,optionfilefiname);  #else 
   strcat(optionfilegnuplot,".gp");   void linmin(double p[], double xi[], int n, double *fret,
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {               double (*func)(double []),int *flat); 
     printf("Problem with file %s",optionfilegnuplot);  #endif
   }   int i,ibig,j,jk,k; 
     double del,t,*pt,*ptt,*xit;
 #ifdef windows    double directest;
     fprintf(ficgp,"cd \"%s\" \n",pathc);    double fp,fptt;
 #endif    double *xits;
 m=pow(2,cptcoveff);    int niterf, itmp;
    #ifdef LINMINORIGINAL
  /* 1eme*/  #else
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {    flatdir=ivector(1,n); 
     for (j=1;j<=n;j++) flatdir[j]=0; 
 #ifdef windows  #endif
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);    pt=vector(1,n); 
 #endif    ptt=vector(1,n); 
 #ifdef unix    xit=vector(1,n); 
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    xits=vector(1,n); 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    *fret=(*func)(p); 
 #endif    for (j=1;j<=n;j++) pt[j]=p[j]; 
     rcurr_time = time(NULL);  
 for (i=1; i<= nlstate ; i ++) {    for (*iter=1;;++(*iter)) { 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      fp=(*fret); /* From former iteration or initial value */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      ibig=0; 
 }      del=0.0; 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      rlast_time=rcurr_time;
     for (i=1; i<= nlstate ; i ++) {      /* (void) gettimeofday(&curr_time,&tzp); */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      rcurr_time = time(NULL);  
   else fprintf(ficgp," \%%*lf (\%%*lf)");      curr_time = *localtime(&rcurr_time);
 }      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
      for (i=1; i<= nlstate ; i ++) {  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      for (i=1;i<=n;i++) {
   else fprintf(ficgp," \%%*lf (\%%*lf)");        fprintf(ficrespow," %.12lf", p[i]);
 }        }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      fprintf(ficrespow,"\n");fflush(ficrespow);
 #ifdef unix      printf("\n#model=  1      +     age ");
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");      fprintf(ficlog,"\n#model=  1      +     age ");
 #endif      if(nagesqr==1){
    }          printf("  + age*age  ");
   }          fprintf(ficlog,"  + age*age  ");
   /*2 eme*/      }
       for(j=1;j <=ncovmodel-2;j++){
   for (k1=1; k1<= m ; k1 ++) {        if(Typevar[j]==0) {
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);          printf("  +      V%d  ",Tvar[j]);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);          fprintf(ficlog,"  +      V%d  ",Tvar[j]);
            }else if(Typevar[j]==1) {
     for (i=1; i<= nlstate+1 ; i ++) {          printf("  +    V%d*age ",Tvar[j]);
       k=2*i;          fprintf(ficlog,"  +    V%d*age ",Tvar[j]);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        }else if(Typevar[j]==2) {
       for (j=1; j<= nlstate+1 ; j ++) {          printf("  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }        }
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      printf("\n");
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  /*     printf("12   47.0114589    0.0154322   33.2424412    0.3279905    2.3731903  */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);  /* 13  -21.5392400    0.1118147    1.2680506    1.2973408   -1.0663662  */
       for (j=1; j<= nlstate+1 ; j ++) {      fprintf(ficlog,"\n");
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      for(i=1,jk=1; i <=nlstate; i++){
         else fprintf(ficgp," \%%*lf (\%%*lf)");        for(k=1; k <=(nlstate+ndeath); k++){
 }            if (k != i) {
       fprintf(ficgp,"\" t\"\" w l 0,");            printf("%d%d ",i,k);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);            fprintf(ficlog,"%d%d ",i,k);
       for (j=1; j<= nlstate+1 ; j ++) {            for(j=1; j <=ncovmodel; j++){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              printf("%12.7f ",p[jk]);
   else fprintf(ficgp," \%%*lf (\%%*lf)");              fprintf(ficlog,"%12.7f ",p[jk]);
 }                jk++; 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");            }
       else fprintf(ficgp,"\" t\"\" w l 0,");            printf("\n");
     }            fprintf(ficlog,"\n");
   }          }
          }
   /*3eme*/      }
       if(*iter <=3 && *iter >1){
   for (k1=1; k1<= m ; k1 ++) {        tml = *localtime(&rcurr_time);
     for (cpt=1; cpt<= nlstate ; cpt ++) {        strcpy(strcurr,asctime(&tml));
       k=2+nlstate*(2*cpt-2);        rforecast_time=rcurr_time; 
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        itmp = strlen(strcurr);
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          strcurr[itmp-1]='\0';
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        for(niterf=10;niterf<=30;niterf+=10){
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          forecast_time = *localtime(&rforecast_time);
           strcpy(strfor,asctime(&forecast_time));
 */          itmp = strlen(strfor);
       for (i=1; i< nlstate ; i ++) {          if(strfor[itmp-1]=='\n')
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);            strfor[itmp-1]='\0';
           printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
       }          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
     }        }
   }      }
        for (i=1;i<=n;i++) { /* For each direction i */
   /* CV preval stat */        for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
     for (k1=1; k1<= m ; k1 ++) {        fptt=(*fret); 
     for (cpt=1; cpt<nlstate ; cpt ++) {  #ifdef DEBUG
       k=3;        printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);  #endif
         printf("%d",i);fflush(stdout); /* print direction (parameter) i */
       for (i=1; i< nlstate ; i ++)        fprintf(ficlog,"%d",i);fflush(ficlog);
         fprintf(ficgp,"+$%d",k+i+1);  #ifdef LINMINORIGINAL
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
        #else
       l=3+(nlstate+ndeath)*cpt;        linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);                          flatdir[i]=flat; /* Function is vanishing in that direction i */
       for (i=1; i< nlstate ; i ++) {  #endif
         l=3+(nlstate+ndeath)*cpt;                          /* Outputs are fret(new point p) p is updated and xit rescaled */
         fprintf(ficgp,"+$%d",l+i+1);        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
       }                                  /* because that direction will be replaced unless the gain del is small */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                                    /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
     }                                  /* Unless the n directions are conjugate some gain in the determinant may be obtained */
   }                                    /* with the new direction. */
                                    del=fabs(fptt-(*fret)); 
   /* proba elementaires */                                  ibig=i; 
    for(i=1,jk=1; i <=nlstate; i++){        } 
     for(k=1; k <=(nlstate+ndeath); k++){  #ifdef DEBUG
       if (k != i) {        printf("%d %.12e",i,(*fret));
         for(j=1; j <=ncovmodel; j++){        fprintf(ficlog,"%d %.12e",i,(*fret));
                for (j=1;j<=n;j++) {
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);                                  xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           jk++;                                  printf(" x(%d)=%.12e",j,xit[j]);
           fprintf(ficgp,"\n");                                  fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         }        }
       }        for(j=1;j<=n;j++) {
     }                                  printf(" p(%d)=%.12e",j,p[j]);
    }                                  fprintf(ficlog," p(%d)=%.12e",j,p[j]);
         }
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/        printf("\n");
      for(jk=1; jk <=m; jk++) {        fprintf(ficlog,"\n");
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);  #endif
        if (ng==2)      } /* end loop on each direction i */
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");      /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 
        else      /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
          fprintf(ficgp,"\nset title \"Probability\"\n");      /* New value of last point Pn is not computed, P(n-1) */
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);        for(j=1;j<=n;j++) {
        i=1;                                  if(flatdir[j] >0){
        for(k2=1; k2<=nlstate; k2++) {                                          printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
          k3=i;                                          fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
          for(k=1; k<=(nlstate+ndeath); k++) {                                  }
            if (k != k2){                                  /* printf("\n"); */
              if(ng==2)                                  /* fprintf(ficlog,"\n"); */
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);                          }
              else      /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
              ij=1;        /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
              for(j=3; j <=ncovmodel; j++) {        /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        /* decreased of more than 3.84  */
                  ij++;        /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
                }        /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
                else        /* By adding 10 parameters more the gain should be 18.31 */
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                          
              }        /* Starting the program with initial values given by a former maximization will simply change */
              fprintf(ficgp,")/(1");        /* the scales of the directions and the directions, because the are reset to canonical directions */
                      /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
              for(k1=1; k1 <=nlstate; k1++){          /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);  #ifdef DEBUG
                ij=1;        int k[2],l;
                for(j=3; j <=ncovmodel; j++){        k[0]=1;
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        k[1]=-1;
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        printf("Max: %.12e",(*func)(p));
                    ij++;        fprintf(ficlog,"Max: %.12e",(*func)(p));
                  }        for (j=1;j<=n;j++) {
                  else          printf(" %.12e",p[j]);
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          fprintf(ficlog," %.12e",p[j]);
                }        }
                fprintf(ficgp,")");        printf("\n");
              }        fprintf(ficlog,"\n");
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);        for(l=0;l<=1;l++) {
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          for (j=1;j<=n;j++) {
              i=i+ncovmodel;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
            }            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
          }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
        }          }
      }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
    }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
    fclose(ficgp);        }
 }  /* end gnuplot */  #endif
   
   #ifdef LINMINORIGINAL
 /*************** Moving average **************/  #else
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){        free_ivector(flatdir,1,n); 
   #endif
   int i, cpt, cptcod;        free_vector(xit,1,n); 
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)        free_vector(xits,1,n); 
       for (i=1; i<=nlstate;i++)        free_vector(ptt,1,n); 
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        free_vector(pt,1,n); 
           mobaverage[(int)agedeb][i][cptcod]=0.;        return; 
          } /* enough precision */ 
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){      if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations."); 
       for (i=1; i<=nlstate;i++){      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        ptt[j]=2.0*p[j]-pt[j]; 
           for (cpt=0;cpt<=4;cpt++){        xit[j]=p[j]-pt[j]; 
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        pt[j]=p[j]; 
           }      } 
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      fptt=(*func)(ptt); /* f_3 */
         }  #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
       }                  if (*iter <=4) {
     }  #else
      #endif
 }  #ifdef POWELLNOF3INFF1TEST    /* skips test F3 <F1 */
   #else
       if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
 /************** Forecasting ******************/  #endif
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
          /* From x1 (P0) distance of x2 is at h and x3 is 2h */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
   int *popage;        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
   double *popeffectif,*popcount;        /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
   double ***p3mat;        /* also  lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
   char fileresf[FILENAMELENGTH];        /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
         /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
  agelim=AGESUP;        /*  Even if f3 <f1, directest can be negative and t >0 */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;        /* mu² and del² are equal when f3=f1 */
                           /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                          /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
                            /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0  */
                            /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0  */
   strcpy(fileresf,"f");  #ifdef NRCORIGINAL
   strcat(fileresf,fileres);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
   if((ficresf=fopen(fileresf,"w"))==NULL) {  #else
     printf("Problem with forecast resultfile: %s\n", fileresf);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
   }        t= t- del*SQR(fp-fptt);
   printf("Computing forecasting: result on file '%s' \n", fileresf);  #endif
         directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  #ifdef DEBUG
         printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
   if (mobilav==1) {        fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
     movingaverage(agedeb, fage, ageminpar, mobaverage);               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   }        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   stepsize=(int) (stepm+YEARM-1)/YEARM;        printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
   if (stepm<=12) stepsize=1;        fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
    #endif
   agelim=AGESUP;  #ifdef POWELLORIGINAL
          if (t < 0.0) { /* Then we use it for new direction */
   hstepm=1;  #else
   hstepm=hstepm/stepm;        if (directest*t < 0.0) { /* Contradiction between both tests */
   yp1=modf(dateintmean,&yp);                                  printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
   anprojmean=yp;          printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
   yp2=modf((yp1*12),&yp);          fprintf(ficlog,"directest= %.12lf (if directest<0 or t<0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
   mprojmean=yp;          fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
   yp1=modf((yp2*30.5),&yp);        } 
   jprojmean=yp;        if (directest < 0.0) { /* Then we use it for new direction */
   if(jprojmean==0) jprojmean=1;  #endif
   if(mprojmean==0) jprojmean=1;  #ifdef DEBUGLINMIN
            printf("Before linmin in direction P%d-P0\n",n);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);          for (j=1;j<=n;j++) {
              printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
   for(cptcov=1;cptcov<=i2;cptcov++){            fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            if(j % ncovmodel == 0){
       k=k+1;              printf("\n");
       fprintf(ficresf,"\n#******");              fprintf(ficlog,"\n");
       for(j=1;j<=cptcoveff;j++) {            }
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          }
       }  #endif
       fprintf(ficresf,"******\n");  #ifdef LINMINORIGINAL
       fprintf(ficresf,"# StartingAge FinalAge");          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  #else
                linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
                flatdir[i]=flat; /* Function is vanishing in that direction i */
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {  #endif
         fprintf(ficresf,"\n");          
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    #ifdef DEBUGLINMIN
           for (j=1;j<=n;j++) { 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){            printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
           nhstepm = nhstepm/hstepm;            if(j % ncovmodel == 0){
                        printf("\n");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              fprintf(ficlog,"\n");
           oldm=oldms;savm=savms;            }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            }
          #endif
           for (h=0; h<=nhstepm; h++){          for (j=1;j<=n;j++) { 
             if (h==(int) (calagedate+YEARM*cpt)) {            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
             }          }
             for(j=1; j<=nlstate+ndeath;j++) {  #ifdef LINMINORIGINAL
               kk1=0.;kk2=0;  #else
               for(i=1; i<=nlstate;i++) {                        for (j=1, flatd=0;j<=n;j++) {
                 if (mobilav==1)            if(flatdir[j]>0)
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];              flatd++;
                 else {          }
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          if(flatd >0){
                 }            printf("%d flat directions: ",flatd);
                            fprintf(ficlog,"%d flat directions :",flatd);
               }            for (j=1;j<=n;j++) { 
               if (h==(int)(calagedate+12*cpt)){              if(flatdir[j]>0){
                 fprintf(ficresf," %.3f", kk1);                printf("%d ",j);
                                        fprintf(ficlog,"%d ",j);
               }              }
             }            }
           }            printf("\n");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            fprintf(ficlog,"\n");
         }          }
       }  #endif
     }          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   }          fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
                  
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  #ifdef DEBUG
           printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   fclose(ficresf);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 }          for(j=1;j<=n;j++){
 /************** Forecasting ******************/            printf(" %lf",xit[j]);
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){            fprintf(ficlog," %lf",xit[j]);
            }
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          printf("\n");
   int *popage;          fprintf(ficlog,"\n");
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  #endif
   double *popeffectif,*popcount;        } /* end of t or directest negative */
   double ***p3mat,***tabpop,***tabpopprev;  #ifdef POWELLNOF3INFF1TEST
   char filerespop[FILENAMELENGTH];  #else
         } /* end if (fptt < fp)  */
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  #endif
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
   agelim=AGESUP;      } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;  #else
    #endif
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                  } /* loop iteration */ 
    } 
      
   strcpy(filerespop,"pop");  /**** Prevalence limit (stable or period prevalence)  ****************/
   strcat(filerespop,fileres);    
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres)
     printf("Problem with forecast resultfile: %s\n", filerespop);    {
   }      /**< Computes the prevalence limit in each live state at age x and for covariate combination ij 
   printf("Computing forecasting: result on file '%s' \n", filerespop);       *   (and selected quantitative values in nres)
        *  by left multiplying the unit
   if (cptcoveff==0) ncodemax[cptcoveff]=1;       *  matrix by transitions matrix until convergence is reached with precision ftolpl 
        * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I
   if (mobilav==1) {       * Wx is row vector: population in state 1, population in state 2, population dead
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       * or prevalence in state 1, prevalence in state 2, 0
     movingaverage(agedeb, fage, ageminpar, mobaverage);       * newm is the matrix after multiplications, its rows are identical at a factor.
   }       * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
        * Output is prlim.
   stepsize=(int) (stepm+YEARM-1)/YEARM;       * Initial matrix pimij 
   if (stepm<=12) stepsize=1;       */
      /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
   agelim=AGESUP;    /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
      /*  0,                   0                  , 1} */
   hstepm=1;    /*
   hstepm=hstepm/stepm;     * and after some iteration: */
      /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
   if (popforecast==1) {    /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
     if((ficpop=fopen(popfile,"r"))==NULL) {    /*  0,                   0                  , 1} */
       printf("Problem with population file : %s\n",popfile);exit(0);    /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
     }    /* {0.51571254859325999, 0.4842874514067399, */
     popage=ivector(0,AGESUP);    /*  0.51326036147820708, 0.48673963852179264} */
     popeffectif=vector(0,AGESUP);    /* If we start from prlim again, prlim tends to a constant matrix */
     popcount=vector(0,AGESUP);      
        int i, ii,j,k;
     i=1;      double *min, *max, *meandiff, maxmax,sumnew=0.;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    /* double **matprod2(); */ /* test */
        double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
     imx=i;    double **newm;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    double agefin, delaymax=200. ; /* 100 Max number of years to converge */
   }    int ncvloop=0;
     
   for(cptcov=1;cptcov<=i2;cptcov++){    min=vector(1,nlstate);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    max=vector(1,nlstate);
       k=k+1;    meandiff=vector(1,nlstate);
       fprintf(ficrespop,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {          /* Starting with matrix unity */
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for (ii=1;ii<=nlstate+ndeath;ii++)
       }      for (j=1;j<=nlstate+ndeath;j++){
       fprintf(ficrespop,"******\n");        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficrespop,"# Age");      }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    
       if (popforecast==1)  fprintf(ficrespop," [Population]");    cov[1]=1.;
          
       for (cpt=0; cpt<=0;cpt++) {    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
            for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      ncvloop++;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      newm=savm;
           nhstepm = nhstepm/hstepm;      /* Covariates have to be included here again */
                cov[2]=agefin;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      if(nagesqr==1)
           oldm=oldms;savm=savms;        cov[3]= agefin*agefin;;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
                                  /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
           for (h=0; h<=nhstepm; h++){        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
             if (h==(int) (calagedate+YEARM*cpt)) {        /* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      }
             }      for (k=1; k<=nsq;k++) { /* For single varying covariates only */
             for(j=1; j<=nlstate+ndeath;j++) {                          /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
               kk1=0.;kk2=0;        cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
               for(i=1; i<=nlstate;i++) {                      /* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
                 if (mobilav==1)      }
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      for (k=1; k<=cptcovage;k++){  /* For product with age */
                 else {        if(Dummy[Tvar[Tage[k]]]){
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
                 }        } else{
               }          cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; 
               if (h==(int)(calagedate+12*cpt)){        }
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;        /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
                   /*fprintf(ficrespop," %.3f", kk1);      }
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      for (k=1; k<=cptcovprod;k++){ /* For product without age */
               }        /* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
             }        if(Dummy[Tvard[k][1]==0]){
             for(i=1; i<=nlstate;i++){          if(Dummy[Tvard[k][2]==0]){
               kk1=0.;            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
                 for(j=1; j<=nlstate;j++){          }else{
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
                 }          }
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];        }else{
             }          if(Dummy[Tvard[k][2]==0]){
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)          }else{
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);            cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
           }          }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
         }      }
       }      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   /******/      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                    /* age and covariate values of ij are in 'cov' */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      
           nhstepm = nhstepm/hstepm;      savm=oldm;
                oldm=newm;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;      for(j=1; j<=nlstate; j++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          max[j]=0.;
           for (h=0; h<=nhstepm; h++){        min[j]=1.;
             if (h==(int) (calagedate+YEARM*cpt)) {      }
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      for(i=1;i<=nlstate;i++){
             }        sumnew=0;
             for(j=1; j<=nlstate+ndeath;j++) {        for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
               kk1=0.;kk2=0;        for(j=1; j<=nlstate; j++){ 
               for(i=1; i<=nlstate;i++) {                        prlim[i][j]= newm[i][j]/(1-sumnew);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              max[j]=FMAX(max[j],prlim[i][j]);
               }          min[j]=FMIN(min[j],prlim[i][j]);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);        }
             }      }
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      maxmax=0.;
         }      for(j=1; j<=nlstate; j++){
       }        meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
    }        maxmax=FMAX(maxmax,meandiff[j]);
   }        /* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */
        } /* j loop */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      *ncvyear= (int)age- (int)agefin;
       /* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
   if (popforecast==1) {      if(maxmax < ftolpl){
     free_ivector(popage,0,AGESUP);        /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
     free_vector(popeffectif,0,AGESUP);        free_vector(min,1,nlstate);
     free_vector(popcount,0,AGESUP);        free_vector(max,1,nlstate);
   }        free_vector(meandiff,1,nlstate);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        return prlim;
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      }
   fclose(ficrespop);    } /* age loop */
 }      /* After some age loop it doesn't converge */
     printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
 /***********************************************/  Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
 /**************** Main Program *****************/    /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
 /***********************************************/    free_vector(min,1,nlstate);
     free_vector(max,1,nlstate);
 int main(int argc, char *argv[])    free_vector(meandiff,1,nlstate);
 {    
     return prlim; /* should not reach here */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;  }
   double agedeb, agefin,hf;  
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;  
    /**** Back Prevalence limit (stable or period prevalence)  ****************/
   double fret;  
   double **xi,tmp,delta;   /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
    /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
   double dum; /* Dummy variable */    double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
   double ***p3mat;  {
   int *indx;    /* Computes the prevalence limit in each live state at age x and for covariate combination ij (<=2**cptcoveff) by left multiplying the unit
   char line[MAXLINE], linepar[MAXLINE];       matrix by transitions matrix until convergence is reached with precision ftolpl */
   char title[MAXLINE];    /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    /* Wx is row vector: population in state 1, population in state 2, population dead */
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    /* or prevalence in state 1, prevalence in state 2, 0 */
      /* newm is the matrix after multiplications, its rows are identical at a factor */
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    /* Initial matrix pimij */
     /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
   char filerest[FILENAMELENGTH];    /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
   char fileregp[FILENAMELENGTH];    /*  0,                   0                  , 1} */
   char popfile[FILENAMELENGTH];    /*
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];     * and after some iteration: */
   int firstobs=1, lastobs=10;    /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
   int sdeb, sfin; /* Status at beginning and end */    /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
   int c,  h , cpt,l;    /*  0,                   0                  , 1} */
   int ju,jl, mi;    /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    /* {0.51571254859325999, 0.4842874514067399, */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    /*  0.51326036147820708, 0.48673963852179264} */
   int mobilav=0,popforecast=0;    /* If we start from prlim again, prlim tends to a constant matrix */
   int hstepm, nhstepm;  
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    int i, ii,j,k;
     int first=0;
   double bage, fage, age, agelim, agebase;    double *min, *max, *meandiff, maxmax,sumnew=0.;
   double ftolpl=FTOL;    /* double **matprod2(); */ /* test */
   double **prlim;    double **out, cov[NCOVMAX+1], **bmij();
   double *severity;    double **newm;
   double ***param; /* Matrix of parameters */    double         **dnewm, **doldm, **dsavm;  /* for use */
   double  *p;    double         **oldm, **savm;  /* for use */
   double **matcov; /* Matrix of covariance */  
   double ***delti3; /* Scale */    double agefin, delaymax=200. ; /* 100 Max number of years to converge */
   double *delti; /* Scale */    int ncvloop=0;
   double ***eij, ***vareij;    
   double **varpl; /* Variances of prevalence limits by age */    min=vector(1,nlstate);
   double *epj, vepp;    max=vector(1,nlstate);
   double kk1, kk2;    meandiff=vector(1,nlstate);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;  
      dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
     oldm=oldms; savm=savms;
   char version[80]="Imach version 0.8g, May 2002, INED-EUROREVES ";    
   char *alph[]={"a","a","b","c","d","e"}, str[4];    /* Starting with matrix unity */
     for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=1;j<=nlstate+ndeath;j++){
   char z[1]="c", occ;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 #include <sys/time.h>      }
 #include <time.h>    
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    cov[1]=1.;
      
   /* long total_usecs;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   struct timeval start_time, end_time;    /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
      /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
   getcwd(pathcd, size);      ncvloop++;
       newm=savm; /* oldm should be kept from previous iteration or unity at start */
   printf("\n%s",version);                  /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
   if(argc <=1){      /* Covariates have to be included here again */
     printf("\nEnter the parameter file name: ");      cov[2]=agefin;
     scanf("%s",pathtot);      if(nagesqr==1)
   }        cov[3]= agefin*agefin;;
   else{      for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
     strcpy(pathtot,argv[1]);                          /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
   }        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        /* printf("bprevalim Dummy agefin=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agefin,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
   /*cygwin_split_path(pathtot,path,optionfile);      }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      /* for (k=1; k<=cptcovn;k++) { */
   /* cutv(path,optionfile,pathtot,'\\');*/      /*   /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
       /*   cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);      /*   /\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); *\/ */
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      /* } */
   chdir(path);      for (k=1; k<=nsq;k++) { /* For single varying covariates only */
   replace(pathc,path);                          /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
         cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
 /*-------- arguments in the command line --------*/        /* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
       }
   strcpy(fileres,"r");      /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */
   strcat(fileres, optionfilefiname);      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
   strcat(fileres,".txt");    /* Other files have txt extension */      /*   /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
       /*   cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
   /*---------arguments file --------*/      for (k=1; k<=cptcovage;k++){  /* For product with age */
         if(Dummy[Tvar[Tage[k]]]){
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
     printf("Problem with optionfile %s\n",optionfile);        } else{
     goto end;          cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; 
   }        }
         /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
   strcpy(filereso,"o");      }
   strcat(filereso,fileres);      for (k=1; k<=cptcovprod;k++){ /* For product without age */
   if((ficparo=fopen(filereso,"w"))==NULL) {        /* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        if(Dummy[Tvard[k][1]==0]){
   }          if(Dummy[Tvard[k][2]==0]){
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
   /* Reads comments: lines beginning with '#' */          }else{
   while((c=getc(ficpar))=='#' && c!= EOF){            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);        }else{
     puts(line);          if(Dummy[Tvard[k][2]==0]){
     fputs(line,ficparo);            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
   }          }else{
   ungetc(c,ficpar);            cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
           }
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);        }
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);      }
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);      
 while((c=getc(ficpar))=='#' && c!= EOF){      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     ungetc(c,ficpar);      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     fgets(line, MAXLINE, ficpar);      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     puts(line);      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
     fputs(line,ficparo);      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
   }                  /* ij should be linked to the correct index of cov */
   ungetc(c,ficpar);                  /* age and covariate values ij are in 'cov', but we need to pass
                     * ij for the observed prevalence at age and status and covariate
                       * number:  prevacurrent[(int)agefin][ii][ij]
   covar=matrix(0,NCOVMAX,1,n);                   */
   cptcovn=0;      /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
   ncovmodel=2+cptcovn;      /* if((int)age == 86 || (int)age == 87){ */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      /*   printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
        /*   for(i=1; i<=nlstate+ndeath; i++) { */
   /* Read guess parameters */      /*  printf("%d newm= ",i); */
   /* Reads comments: lines beginning with '#' */      /*  for(j=1;j<=nlstate+ndeath;j++) { */
   while((c=getc(ficpar))=='#' && c!= EOF){      /*    printf("%f ",newm[i][j]); */
     ungetc(c,ficpar);      /*  } */
     fgets(line, MAXLINE, ficpar);      /*  printf("oldm * "); */
     puts(line);      /*  for(j=1;j<=nlstate+ndeath;j++) { */
     fputs(line,ficparo);      /*    printf("%f ",oldm[i][j]); */
   }      /*  } */
   ungetc(c,ficpar);      /*  printf(" bmmij "); */
        /*  for(j=1;j<=nlstate+ndeath;j++) { */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      /*    printf("%f ",pmmij[i][j]); */
     for(i=1; i <=nlstate; i++)      /*  } */
     for(j=1; j <=nlstate+ndeath-1; j++){      /*  printf("\n"); */
       fscanf(ficpar,"%1d%1d",&i1,&j1);      /*   } */
       fprintf(ficparo,"%1d%1d",i1,j1);      /* } */
       printf("%1d%1d",i,j);      savm=oldm;
       for(k=1; k<=ncovmodel;k++){      oldm=newm;
         fscanf(ficpar," %lf",&param[i][j][k]);  
         printf(" %lf",param[i][j][k]);      for(j=1; j<=nlstate; j++){
         fprintf(ficparo," %lf",param[i][j][k]);        max[j]=0.;
       }        min[j]=1.;
       fscanf(ficpar,"\n");      }
       printf("\n");      for(j=1; j<=nlstate; j++){ 
       fprintf(ficparo,"\n");        for(i=1;i<=nlstate;i++){
     }          /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
            bprlim[i][j]= newm[i][j];
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
           min[i]=FMIN(min[i],bprlim[i][j]);
   p=param[1][1];        }
        }
   /* Reads comments: lines beginning with '#' */                  
   while((c=getc(ficpar))=='#' && c!= EOF){      maxmax=0.;
     ungetc(c,ficpar);      for(i=1; i<=nlstate; i++){
     fgets(line, MAXLINE, ficpar);        meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
     puts(line);        maxmax=FMAX(maxmax,meandiff[i]);
     fputs(line,ficparo);        /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */
   }      } /* i loop */
   ungetc(c,ficpar);      *ncvyear= -( (int)age- (int)agefin);
       /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      if(maxmax < ftolpl){
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
   for(i=1; i <=nlstate; i++){        free_vector(min,1,nlstate);
     for(j=1; j <=nlstate+ndeath-1; j++){        free_vector(max,1,nlstate);
       fscanf(ficpar,"%1d%1d",&i1,&j1);        free_vector(meandiff,1,nlstate);
       printf("%1d%1d",i,j);        return bprlim;
       fprintf(ficparo,"%1d%1d",i1,j1);      }
       for(k=1; k<=ncovmodel;k++){    } /* age loop */
         fscanf(ficpar,"%le",&delti3[i][j][k]);      /* After some age loop it doesn't converge */
         printf(" %le",delti3[i][j][k]);    if(first){
         fprintf(ficparo," %le",delti3[i][j][k]);      first=1;
       }      printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\
       fscanf(ficpar,"\n");  Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
       printf("\n");    }
       fprintf(ficparo,"\n");    fprintf(ficlog,"Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
     }  Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
   }    /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
   delti=delti3[1][1];    free_vector(min,1,nlstate);
      free_vector(max,1,nlstate);
   /* Reads comments: lines beginning with '#' */    free_vector(meandiff,1,nlstate);
   while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);    return bprlim; /* should not reach here */
     fgets(line, MAXLINE, ficpar);  }
     puts(line);  
     fputs(line,ficparo);  /*************** transition probabilities ***************/ 
   }  
   ungetc(c,ficpar);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
    {
   matcov=matrix(1,npar,1,npar);    /* According to parameters values stored in x and the covariate's values stored in cov,
   for(i=1; i <=npar; i++){       computes the probability to be observed in state j (after stepm years) being in state i by appying the
     fscanf(ficpar,"%s",&str);       model to the ncovmodel covariates (including constant and age).
     printf("%s",str);       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
     fprintf(ficparo,"%s",str);       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
     for(j=1; j <=i; j++){       ncth covariate in the global vector x is given by the formula:
       fscanf(ficpar," %le",&matcov[i][j]);       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
       printf(" %.5le",matcov[i][j]);       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
       fprintf(ficparo," %.5le",matcov[i][j]);       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
     }       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
     fscanf(ficpar,"\n");       Outputs ps[i][j] or probability to be observed in j being in i according to
     printf("\n");       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
     fprintf(ficparo,"\n");       Sum on j ps[i][j] should equal to 1.
   }    */
   for(i=1; i <=npar; i++)    double s1, lnpijopii;
     for(j=i+1;j<=npar;j++)    /*double t34;*/
       matcov[i][j]=matcov[j][i];    int i,j, nc, ii, jj;
      
   printf("\n");    for(i=1; i<= nlstate; i++){
       for(j=1; j<i;j++){
         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     /*-------- Rewriting paramater file ----------*/          /*lnpijopii += param[i][j][nc]*cov[nc];*/
      strcpy(rfileres,"r");    /* "Rparameterfile */          lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/          /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
      strcat(rfileres,".");    /* */        }
      strcat(rfileres,optionfilext);    /* Other files have txt extension */        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     if((ficres =fopen(rfileres,"w"))==NULL) {        /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       printf("Problem writing new parameter file: %s\n", fileres);goto end;      }
     }      for(j=i+1; j<=nlstate+ndeath;j++){
     fprintf(ficres,"#%s\n",version);        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
              /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
     /*-------- data file ----------*/          lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
     if((fic=fopen(datafile,"r"))==NULL)    {          /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
       printf("Problem with datafile: %s\n", datafile);goto end;        }
     }        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       }
     n= lastobs;    }
     severity = vector(1,maxwav);    
     outcome=imatrix(1,maxwav+1,1,n);    for(i=1; i<= nlstate; i++){
     num=ivector(1,n);      s1=0;
     moisnais=vector(1,n);      for(j=1; j<i; j++){
     annais=vector(1,n);        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     moisdc=vector(1,n);        /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
     andc=vector(1,n);      }
     agedc=vector(1,n);      for(j=i+1; j<=nlstate+ndeath; j++){
     cod=ivector(1,n);        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     weight=vector(1,n);        /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      }
     mint=matrix(1,maxwav,1,n);      /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
     anint=matrix(1,maxwav,1,n);      ps[i][i]=1./(s1+1.);
     s=imatrix(1,maxwav+1,1,n);      /* Computing other pijs */
     adl=imatrix(1,maxwav+1,1,n);          for(j=1; j<i; j++)
     tab=ivector(1,NCOVMAX);        ps[i][j]= exp(ps[i][j])*ps[i][i];
     ncodemax=ivector(1,8);      for(j=i+1; j<=nlstate+ndeath; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
     i=1;      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     while (fgets(line, MAXLINE, fic) != NULL)    {    } /* end i */
       if ((i >= firstobs) && (i <=lastobs)) {    
            for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         for (j=maxwav;j>=1;j--){      for(jj=1; jj<= nlstate+ndeath; jj++){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        ps[ii][jj]=0;
           strcpy(line,stra);        ps[ii][ii]=1;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      }
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    }
         }    
            
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
     /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    /*   } */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    /*   printf("\n "); */
     /* } */
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    /* printf("\n ");printf("%lf ",cov[2]);*/
         for (j=ncovcol;j>=1;j--){    /*
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      for(i=1; i<= npar; i++) printf("%f ",x[i]);
         }                  goto end;*/
         num[i]=atol(stra);    return ps; /* Pointer is unchanged since its call */
          }
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){  
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/  /*************** backward transition probabilities ***************/ 
   
         i=i+1;   /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ageminpar, double agemaxpar, double ***dnewm, double **doldm, double **dsavm, int ij ) */
       }  /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
     }   double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
     /* printf("ii=%d", ij);  {
        scanf("%d",i);*/    /* Computes the backward probability at age agefin and covariate combination ij. In fact cov is already filled and x too.
   imx=i-1; /* Number of individuals */     * Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, and returns in **ps as well as **bmij.
      */
   /* for (i=1; i<=imx; i++){    int i, ii, j,k;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    double **out, **pmij();
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    double sumnew=0.;
     }*/    double agefin;
    /*  for (i=1; i<=imx; i++){    double k3=0.; /* constant of the w_x diagonal matrixe (in order for B to sum to 1 even for death state) */
      if (s[4][i]==9)  s[4][i]=-1;    double **dnewm, **dsavm, **doldm;
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/    double **bbmij;
      
      doldm=ddoldms; /* global pointers */
   /* Calculation of the number of parameter from char model*/    dnewm=ddnewms;
   Tvar=ivector(1,15);    dsavm=ddsavms;
   Tprod=ivector(1,15);    
   Tvaraff=ivector(1,15);    agefin=cov[2];
   Tvard=imatrix(1,15,1,2);    /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
   Tage=ivector(1,15);          /* bmij *//* age is cov[2], ij is included in cov, but we need for
           the observed prevalence (with this covariate ij) at beginning of transition */
   if (strlen(model) >1){    /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
     j=0, j1=0, k1=1, k2=1;  
     j=nbocc(model,'+');    /* P_x */
     j1=nbocc(model,'*');    pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
     cptcovn=j+1;    /* outputs pmmij which is a stochastic matrix in row */
     cptcovprod=j1;  
        /* Diag(w_x) */
     strcpy(modelsav,model);    /* Problem with prevacurrent which can be zero */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    sumnew=0.;
       printf("Error. Non available option model=%s ",model);    /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
       goto end;    for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
     }      /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]);  */
          sumnew+=prevacurrent[(int)agefin][ii][ij];
     for(i=(j+1); i>=1;i--){    }
       cutv(stra,strb,modelsav,'+');    if(sumnew >0.01){  /* At least some value in the prevalence */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      for (ii=1;ii<=nlstate+ndeath;ii++){
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        for (j=1;j<=nlstate+ndeath;j++)
       /*scanf("%d",i);*/          doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
       if (strchr(strb,'*')) {      }
         cutv(strd,strc,strb,'*');    }else{
         if (strcmp(strc,"age")==0) {      for (ii=1;ii<=nlstate+ndeath;ii++){
           cptcovprod--;        for (j=1;j<=nlstate+ndeath;j++)
           cutv(strb,stre,strd,'V');        doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
           Tvar[i]=atoi(stre);      }
           cptcovage++;      /* if(sumnew <0.9){ */
             Tage[cptcovage]=i;      /*   printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
             /*printf("stre=%s ", stre);*/      /* } */
         }    }
         else if (strcmp(strd,"age")==0) {    k3=0.0;  /* We put the last diagonal to 0 */
           cptcovprod--;    for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
           cutv(strb,stre,strc,'V');        doldm[ii][ii]= k3;
           Tvar[i]=atoi(stre);    }
           cptcovage++;    /* End doldm, At the end doldm is diag[(w_i)] */
           Tage[cptcovage]=i;    
         }    /* left Product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm) */
         else {    bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* Bug Valgrind */
           cutv(strb,stre,strc,'V');  
           Tvar[i]=ncovcol+k1;    /* Diag(Sum_i w^i_x p^ij_x */
           cutv(strb,strc,strd,'V');    /* w1 p11 + w2 p21 only on live states N1./N..*N11/N1. + N2./N..*N21/N2.=(N11+N21)/N..=N.1/N.. */
           Tprod[k1]=i;    for (j=1;j<=nlstate+ndeath;j++){
           Tvard[k1][1]=atoi(strc);      sumnew=0.;
           Tvard[k1][2]=atoi(stre);      for (ii=1;ii<=nlstate;ii++){
           Tvar[cptcovn+k2]=Tvard[k1][1];        /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
           for (k=1; k<=lastobs;k++)      } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      for (ii=1;ii<=nlstate+ndeath;ii++){
           k1++;          /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
           k2=k2+2;          /*      dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
         }          /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
       }          /*      dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
       else {          /* }else */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
        /*  scanf("%d",i);*/      } /*End ii */
       cutv(strd,strc,strb,'V');    } /* End j, At the end dsavm is diag[1/(w_1p1i+w_2 p2i)] for ALL states even if the sum is only for live states */
       Tvar[i]=atoi(strc);  
       }    ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* Bug Valgrind */
       strcpy(modelsav,stra);      /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    /* end bmij */
         scanf("%d",i);*/    return ps; /*pointer is unchanged */
     }  }
 }  /*************** transition probabilities ***************/ 
    
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);  double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   printf("cptcovprod=%d ", cptcovprod);  {
   scanf("%d ",i);*/    /* According to parameters values stored in x and the covariate's values stored in cov,
     fclose(fic);       computes the probability to be observed in state j being in state i by appying the
        model to the ncovmodel covariates (including constant and age).
     /*  if(mle==1){*/       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
     if (weightopt != 1) { /* Maximisation without weights*/       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
       for(i=1;i<=n;i++) weight[i]=1.0;       ncth covariate in the global vector x is given by the formula:
     }       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
     /*-calculation of age at interview from date of interview and age at death -*/       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
     agev=matrix(1,maxwav,1,imx);       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
        sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
     for (i=1; i<=imx; i++) {       Outputs ps[i][j] the probability to be observed in j being in j according to
       for(m=2; (m<= maxwav); m++) {       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    */
          anint[m][i]=9999;    double s1, lnpijopii;
          s[m][i]=-1;    /*double t34;*/
        }    int i,j, nc, ii, jj;
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;  
       }    for(i=1; i<= nlstate; i++){
     }      for(j=1; j<i;j++){
         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     for (i=1; i<=imx; i++)  {          /*lnpijopii += param[i][j][nc]*cov[nc];*/
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);          lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
       for(m=1; (m<= maxwav); m++){          /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         if(s[m][i] >0){        }
           if (s[m][i] >= nlstate+1) {        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
             if(agedc[i]>0)        /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
               if(moisdc[i]!=99 && andc[i]!=9999)      }
                 agev[m][i]=agedc[i];      for(j=i+1; j<=nlstate+ndeath;j++){
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
            else {          /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
               if (andc[i]!=9999){          lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
               printf("Warning negative age at death: %d line:%d\n",num[i],i);          /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
               agev[m][i]=-1;        }
               }        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
             }      }
           }    }
           else if(s[m][i] !=9){ /* Should no more exist */    
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    for(i=1; i<= nlstate; i++){
             if(mint[m][i]==99 || anint[m][i]==9999)      s1=0;
               agev[m][i]=1;      for(j=1; j<i; j++){
             else if(agev[m][i] <agemin){        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
               agemin=agev[m][i];        /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      }
             }      for(j=i+1; j<=nlstate+ndeath; j++){
             else if(agev[m][i] >agemax){        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
               agemax=agev[m][i];        /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      }
             }      /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
             /*agev[m][i]=anint[m][i]-annais[i];*/      ps[i][i]=1./(s1+1.);
             /*   agev[m][i] = age[i]+2*m;*/      /* Computing other pijs */
           }      for(j=1; j<i; j++)
           else { /* =9 */        ps[i][j]= exp(ps[i][j])*ps[i][i];
             agev[m][i]=1;      for(j=i+1; j<=nlstate+ndeath; j++)
             s[m][i]=-1;        ps[i][j]= exp(ps[i][j])*ps[i][i];
           }      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         }    } /* end i */
         else /*= 0 Unknown */    
           agev[m][i]=1;    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       }      for(jj=1; jj<= nlstate+ndeath; jj++){
            ps[ii][jj]=0;
     }        ps[ii][ii]=1;
     for (i=1; i<=imx; i++)  {      }
       for(m=1; (m<= maxwav); m++){    }
         if (s[m][i] > (nlstate+ndeath)) {    /* Added for backcast */ /* Transposed matrix too */
           printf("Error: Wrong value in nlstate or ndeath\n");      for(jj=1; jj<= nlstate+ndeath; jj++){
           goto end;      s1=0.;
         }      for(ii=1; ii<= nlstate+ndeath; ii++){
       }        s1+=ps[ii][jj];
     }      }
       for(ii=1; ii<= nlstate; ii++){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        ps[ii][jj]=ps[ii][jj]/s1;
       }
     free_vector(severity,1,maxwav);    }
     free_imatrix(outcome,1,maxwav+1,1,n);    /* Transposition */
     free_vector(moisnais,1,n);    for(jj=1; jj<= nlstate+ndeath; jj++){
     free_vector(annais,1,n);      for(ii=jj; ii<= nlstate+ndeath; ii++){
     /* free_matrix(mint,1,maxwav,1,n);        s1=ps[ii][jj];
        free_matrix(anint,1,maxwav,1,n);*/        ps[ii][jj]=ps[jj][ii];
     free_vector(moisdc,1,n);        ps[jj][ii]=s1;
     free_vector(andc,1,n);      }
     }
        /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
     wav=ivector(1,imx);    /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    /*   } */
        /*   printf("\n "); */
     /* Concatenates waves */    /* } */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    /* printf("\n ");printf("%lf ",cov[2]);*/
     /*
       for(i=1; i<= npar; i++) printf("%f ",x[i]);
       Tcode=ivector(1,100);      goto end;*/
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    return ps;
       ncodemax[1]=1;  }
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  
        
    codtab=imatrix(1,100,1,10);  /**************** Product of 2 matrices ******************/
    h=0;  
    m=pow(2,cptcoveff);  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
    {
    for(k=1;k<=cptcoveff; k++){    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
      for(i=1; i <=(m/pow(2,k));i++){       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
        for(j=1; j <= ncodemax[k]; j++){    /* in, b, out are matrice of pointers which should have been initialized 
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){       before: only the contents of out is modified. The function returns
            h++;       a pointer to pointers identical to out */
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    int i, j, k;
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/    for(i=nrl; i<= nrh; i++)
          }      for(k=ncolol; k<=ncoloh; k++){
        }        out[i][k]=0.;
      }        for(j=ncl; j<=nch; j++)
    }          out[i][k] +=in[i][j]*b[j][k];
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);      }
       codtab[1][2]=1;codtab[2][2]=2; */    return out;
    /* for(i=1; i <=m ;i++){  }
       for(k=1; k <=cptcovn; k++){  
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);  
       }  /************* Higher Matrix Product ***************/
       printf("\n");  
       }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij, int nres )
       scanf("%d",i);*/  {
        /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over 
    /* Calculates basic frequencies. Computes observed prevalence at single age       'nhstepm*hstepm*stepm' months (i.e. until
        and prints on file fileres'p'. */       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        nhstepm*hstepm matrices. 
           Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
           (typically every 2 years instead of every month which is too big 
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       for the memory).
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       Model is determined by parameters x and covariates have to be 
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       included manually here. 
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */       */
        
     /* For Powell, parameters are in a vector p[] starting at p[1]    int i, j, d, h, k;
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    double **out, cov[NCOVMAX+1];
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    double **newm;
     double agexact;
     if(mle==1){    double agebegin, ageend;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }    /* Hstepm could be zero and should return the unit matrix */
        for (i=1;i<=nlstate+ndeath;i++)
     /*--------- results files --------------*/      for (j=1;j<=nlstate+ndeath;j++){
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);        oldm[i][j]=(i==j ? 1.0 : 0.0);
          po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
    jk=1;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    for(h=1; h <=nhstepm; h++){
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      for(d=1; d <=hstepm; d++){
    for(i=1,jk=1; i <=nlstate; i++){        newm=savm;
      for(k=1; k <=(nlstate+ndeath); k++){        /* Covariates have to be included here again */
        if (k != i)        cov[1]=1.;
          {        agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
            printf("%d%d ",i,k);        cov[2]=agexact;
            fprintf(ficres,"%1d%1d ",i,k);        if(nagesqr==1)
            for(j=1; j <=ncovmodel; j++){          cov[3]= agexact*agexact;
              printf("%f ",p[jk]);        for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
              fprintf(ficres,"%f ",p[jk]);                          /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
              jk++;          cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
            }          /* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
            printf("\n");        }
            fprintf(ficres,"\n");        for (k=1; k<=nsq;k++) { /* For single varying covariates only */
          }          /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
      }          cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
    }          /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
  if(mle==1){        }
     /* Computing hessian and covariance matrix */        for (k=1; k<=cptcovage;k++){
     ftolhess=ftol; /* Usually correct */          if(Dummy[Tvar[Tage[k]]]){
     hesscov(matcov, p, npar, delti, ftolhess, func);            cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
  }          } else{
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");            cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; 
     printf("# Scales (for hessian or gradient estimation)\n");          }
      for(i=1,jk=1; i <=nlstate; i++){          /* printf("hPxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
       for(j=1; j <=nlstate+ndeath; j++){        }
         if (j!=i) {        for (k=1; k<=cptcovprod;k++){ /*  */
           fprintf(ficres,"%1d%1d",i,j);          /* printf("hPxij Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
           printf("%1d%1d",i,j);          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
           for(k=1; k<=ncovmodel;k++){        }
             printf(" %.5e",delti[jk]);        /* for (k=1; k<=cptcovn;k++)  */
             fprintf(ficres," %.5e",delti[jk]);        /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
             jk++;        /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
           }        /*        cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
           printf("\n");        /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
           fprintf(ficres,"\n");        /*        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
         }        
       }        
      }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
            /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     k=1;                          /* right multiplication of oldm by the current matrix */
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(i=1;i<=npar;i++){        /* if((int)age == 70){ */
       /*  if (k>nlstate) k=1;        /*        printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
       i1=(i-1)/(ncovmodel*nlstate)+1;        /*        for(i=1; i<=nlstate+ndeath; i++) { */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        /*          printf("%d pmmij ",i); */
       printf("%s%d%d",alph[k],i1,tab[i]);*/        /*          for(j=1;j<=nlstate+ndeath;j++) { */
       fprintf(ficres,"%3d",i);        /*            printf("%f ",pmmij[i][j]); */
       printf("%3d",i);        /*          } */
       for(j=1; j<=i;j++){        /*          printf(" oldm "); */
         fprintf(ficres," %.5e",matcov[i][j]);        /*          for(j=1;j<=nlstate+ndeath;j++) { */
         printf(" %.5e",matcov[i][j]);        /*            printf("%f ",oldm[i][j]); */
       }        /*          } */
       fprintf(ficres,"\n");        /*          printf("\n"); */
       printf("\n");        /*        } */
       k++;        /* } */
     }        savm=oldm;
            oldm=newm;
     while((c=getc(ficpar))=='#' && c!= EOF){      }
       ungetc(c,ficpar);      for(i=1; i<=nlstate+ndeath; i++)
       fgets(line, MAXLINE, ficpar);        for(j=1;j<=nlstate+ndeath;j++) {
       puts(line);          po[i][j][h]=newm[i][j];
       fputs(line,ficparo);          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
     }        }
     ungetc(c,ficpar);      /*printf("h=%d ",h);*/
     estepm=0;    } /* end h */
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);    /*     printf("\n H=%d \n",h); */
     if (estepm==0 || estepm < stepm) estepm=stepm;    return po;
     if (fage <= 2) {  }
       bage = ageminpar;  
       fage = agemaxpar;  /************* Higher Back Matrix Product ***************/
     }  /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
      double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij, int nres )
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");  {
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);       'nhstepm*hstepm*stepm' months (i.e. until
         age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
     while((c=getc(ficpar))=='#' && c!= EOF){       nhstepm*hstepm matrices.
     ungetc(c,ficpar);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step
     fgets(line, MAXLINE, ficpar);       (typically every 2 years instead of every month which is too big
     puts(line);       for the memory).
     fputs(line,ficparo);       Model is determined by parameters x and covariates have to be
   }       included manually here. Then we use a call to bmij(x and cov)
   ungetc(c,ficpar);       The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
      */
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);  
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    int i, j, d, h, k;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    double **out, cov[NCOVMAX+1], **bmij();
          double **newm, ***newmm;
   while((c=getc(ficpar))=='#' && c!= EOF){    double agexact;
     ungetc(c,ficpar);    double agebegin, ageend;
     fgets(line, MAXLINE, ficpar);    double **oldm, **savm;
     puts(line);  
     fputs(line,ficparo);    newmm=po; /* To be saved */
   }    oldm=oldms;savm=savms; /* Global pointers */
   ungetc(c,ficpar);    /* Hstepm could be zero and should return the unit matrix */
      for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        oldm[i][j]=(i==j ? 1.0 : 0.0);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
   fscanf(ficpar,"pop_based=%d\n",&popbased);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   fprintf(ficparo,"pop_based=%d\n",popbased);      for(h=1; h <=nhstepm; h++){
   fprintf(ficres,"pop_based=%d\n",popbased);        for(d=1; d <=hstepm; d++){
          newm=savm;
   while((c=getc(ficpar))=='#' && c!= EOF){        /* Covariates have to be included here again */
     ungetc(c,ficpar);        cov[1]=1.;
     fgets(line, MAXLINE, ficpar);        agexact=age-( (h-1)*hstepm + (d)  )*stepm/YEARM; /* age just before transition, d or d-1? */
     puts(line);        /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
     fputs(line,ficparo);        cov[2]=agexact;
   }        if(nagesqr==1)
   ungetc(c,ficpar);          cov[3]= agexact*agexact;
         for (k=1; k<=cptcovn;k++){
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);        /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);        /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
           /* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
         }
 while((c=getc(ficpar))=='#' && c!= EOF){        for (k=1; k<=nsq;k++) { /* For single varying covariates only */
     ungetc(c,ficpar);          /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
     fgets(line, MAXLINE, ficpar);          cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
     puts(line);          /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
     fputs(line,ficparo);        }
   }        for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
   ungetc(c,ficpar);          if(Dummy[Tvar[Tage[k]]]){
             cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);          } else{
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);            cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; 
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          }
           /* printf("hBxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        }
         for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
 /*------------ gnuplot -------------*/          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);        }                 
          /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
 /*------------ free_vector  -------------*/        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
  chdir(path);  
          /* Careful transposed matrix */
  free_ivector(wav,1,imx);        /* age is in cov[2], prevacurrent at beginning of transition. */
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
  free_ivector(num,1,n);        out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
  free_vector(agedc,1,n);                     1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/        /* if((int)age == 70){ */
  fclose(ficparo);        /*        printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
  fclose(ficres);        /*        for(i=1; i<=nlstate+ndeath; i++) { */
         /*          printf("%d pmmij ",i); */
 /*--------- index.htm --------*/        /*          for(j=1;j<=nlstate+ndeath;j++) { */
         /*            printf("%f ",pmmij[i][j]); */
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);        /*          } */
         /*          printf(" oldm "); */
          /*          for(j=1;j<=nlstate+ndeath;j++) { */
   /*--------------- Prevalence limit --------------*/        /*            printf("%f ",oldm[i][j]); */
          /*          } */
   strcpy(filerespl,"pl");        /*          printf("\n"); */
   strcat(filerespl,fileres);        /*        } */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        /* } */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        savm=oldm;
   }        oldm=newm;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      }
   fprintf(ficrespl,"#Prevalence limit\n");      for(i=1; i<=nlstate+ndeath; i++)
   fprintf(ficrespl,"#Age ");        for(j=1;j<=nlstate+ndeath;j++) {
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);          po[i][j][h]=newm[i][j];
   fprintf(ficrespl,"\n");          /* if(h==nhstepm) */
            /*   printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
   prlim=matrix(1,nlstate,1,nlstate);        }
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      /* printf("h=%d %.1f ",h, agexact); */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    } /* end h */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    return po;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  }
   k=0;  
   agebase=ageminpar;  
   agelim=agemaxpar;  #ifdef NLOPT
   ftolpl=1.e-10;    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
   i1=cptcoveff;    double fret;
   if (cptcovn < 1){i1=1;}    double *xt;
     int j;
   for(cptcov=1;cptcov<=i1;cptcov++){    myfunc_data *d2 = (myfunc_data *) pd;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  /* xt = (p1-1); */
         k=k+1;    xt=vector(1,n); 
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
         fprintf(ficrespl,"\n#******");  
         for(j=1;j<=cptcoveff;j++)    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
         fprintf(ficrespl,"******\n");    printf("Function = %.12lf ",fret);
            for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
         for (age=agebase; age<=agelim; age++){    printf("\n");
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   free_vector(xt,1,n);
           fprintf(ficrespl,"%.0f",age );    return fret;
           for(i=1; i<=nlstate;i++)  }
           fprintf(ficrespl," %.5f", prlim[i][i]);  #endif
           fprintf(ficrespl,"\n");  
         }  /*************** log-likelihood *************/
       }  double func( double *x)
     }  {
   fclose(ficrespl);    int i, ii, j, k, mi, d, kk;
     int ioffset=0;
   /*------------- h Pij x at various ages ------------*/    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
      double **out;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    double lli; /* Individual log likelihood */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    int s1, s2;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
   }    double bbh, survp;
   printf("Computing pij: result on file '%s' \n", filerespij);    long ipmx;
      double agexact;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    /*extern weight */
   /*if (stepm<=24) stepsize=2;*/    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   agelim=AGESUP;    /*for(i=1;i<imx;i++) 
   hstepm=stepsize*YEARM; /* Every year of age */      printf(" %d\n",s[4][i]);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    */
    
   k=0;    ++countcallfunc;
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    cov[1]=1.;
       k=k+1;  
         fprintf(ficrespij,"\n#****** ");    for(k=1; k<=nlstate; k++) ll[k]=0.;
         for(j=1;j<=cptcoveff;j++)    ioffset=0;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    if(mle==1){
         fprintf(ficrespij,"******\n");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                /* Computes the values of the ncovmodel covariates of the model
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */           depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */           to be observed in j being in i according to the model.
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        */
           oldm=oldms;savm=savms;        ioffset=2+nagesqr ;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       /* Fixed */
           fprintf(ficrespij,"# Age");        for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
           for(i=1; i<=nlstate;i++)          cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
             for(j=1; j<=nlstate+ndeath;j++)        }
               fprintf(ficrespij," %1d-%1d",i,j);        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
           fprintf(ficrespij,"\n");           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
            for (h=0; h<=nhstepm; h++){           has been calculated etc */
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        /* For an individual i, wav[i] gives the number of effective waves */
             for(i=1; i<=nlstate;i++)        /* We compute the contribution to Likelihood of each effective transition
               for(j=1; j<=nlstate+ndeath;j++)           mw[mi][i] is real wave of the mi th effectve wave */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);        /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
             fprintf(ficrespij,"\n");           s2=s[mw[mi+1][i]][i];
              }           And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
           fprintf(ficrespij,"\n");           meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
         }        */
     }        for(mi=1; mi<= wav[i]-1; mi++){
   }          for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
             /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);            cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
           }
   fclose(ficrespij);          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /*---------- Forecasting ------------------*/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   if((stepm == 1) && (strcmp(model,".")==0)){            }
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);          for(d=0; d<dh[mi][i]; d++){
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);            newm=savm;
   }            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
   else{            cov[2]=agexact;
     erreur=108;            if(nagesqr==1)
     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);              cov[3]= agexact*agexact;  /* Should be changed here */
   }            for (kk=1; kk<=cptcovage;kk++) {
              if(!FixedV[Tvar[Tage[kk]]])
               cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
   /*---------- Health expectancies and variances ------------*/            else
               cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
   strcpy(filerest,"t");            }
   strcat(filerest,fileres);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   if((ficrest=fopen(filerest,"w"))==NULL) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;            savm=oldm;
   }            oldm=newm;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          } /* end mult */
           
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   strcpy(filerese,"e");          /* But now since version 0.9 we anticipate for bias at large stepm.
   strcat(filerese,fileres);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   if((ficreseij=fopen(filerese,"w"))==NULL) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);           * the nearest (and in case of equal distance, to the lowest) interval but now
   }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
  strcpy(fileresv,"v");                                   * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   strcat(fileresv,fileres);                                   * -stepm/2 to stepm/2 .
   if((ficresvij=fopen(fileresv,"w"))==NULL) {                                   * For stepm=1 the results are the same as for previous versions of Imach.
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);                                   * For stepm > 1 the results are less biased than in previous versions. 
   }                                   */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          s1=s[mw[mi][i]][i];
   calagedate=-1;          s2=s[mw[mi+1][i]][i];
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias bh is positive if real duration
   k=0;           * is higher than the multiple of stepm and negative otherwise.
   for(cptcov=1;cptcov<=i1;cptcov++){           */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       k=k+1;          if( s2 > nlstate){ 
       fprintf(ficrest,"\n#****** ");            /* i.e. if s2 is a death state and if the date of death is known 
       for(j=1;j<=cptcoveff;j++)               then the contribution to the likelihood is the probability to 
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);               die between last step unit time and current  step unit time, 
       fprintf(ficrest,"******\n");               which is also equal to probability to die before dh 
                minus probability to die before dh-stepm . 
       fprintf(ficreseij,"\n#****** ");               In version up to 0.92 likelihood was computed
       for(j=1;j<=cptcoveff;j++)               as if date of death was unknown. Death was treated as any other
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);               health state: the date of the interview describes the actual state
       fprintf(ficreseij,"******\n");               and not the date of a change in health state. The former idea was
                to consider that at each interview the state was recorded
       fprintf(ficresvij,"\n#****** ");               (healthy, disable or death) and IMaCh was corrected; but when we
       for(j=1;j<=cptcoveff;j++)               introduced the exact date of death then we should have modified
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);               the contribution of an exact death to the likelihood. This new
       fprintf(ficresvij,"******\n");               contribution is smaller and very dependent of the step unit
                stepm. It is no more the probability to die between last interview
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);               and month of death but the probability to survive from last
       oldm=oldms;savm=savms;               interview up to one month before death multiplied by the
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);                 probability to die within a month. Thanks to Chris
                 Jackson for correcting this bug.  Former versions increased
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);               mortality artificially. The bad side is that we add another loop
       oldm=oldms;savm=savms;               which slows down the processing. The difference can be up to 10%
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);               lower mortality.
                */
             /* If, at the beginning of the maximization mostly, the
                 cumulative probability or probability to be dead is
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");               constant (ie = 1) over time d, the difference is equal to
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);               0.  out[s1][3] = savm[s1][3]: probability, being at state
       fprintf(ficrest,"\n");               s1 at precedent wave, to be dead a month before current
                wave is equal to probability, being at state s1 at
       epj=vector(1,nlstate+1);               precedent wave, to be dead at mont of the current
       for(age=bage; age <=fage ;age++){               wave. Then the observed probability (that this person died)
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);               is null according to current estimated parameter. In fact,
         if (popbased==1) {               it should be very low but not zero otherwise the log go to
           for(i=1; i<=nlstate;i++)               infinity.
             prlim[i][i]=probs[(int)age][i][k];            */
         }  /* #ifdef INFINITYORIGINAL */
          /*          lli=log(out[s1][s2] - savm[s1][s2]); */
         fprintf(ficrest," %4.0f",age);  /* #else */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  /*          lli=log(mytinydouble); */
             epj[j] += prlim[i][i]*eij[i][j][(int)age];  /*        else */
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
           }  /* #endif */
           epj[nlstate+1] +=epj[j];            lli=log(out[s1][s2] - savm[s1][s2]);
         }            
           } else if  ( s2==-1 ) { /* alive */
         for(i=1, vepp=0.;i <=nlstate;i++)            for (j=1,survp=0. ; j<=nlstate; j++) 
           for(j=1;j <=nlstate;j++)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             vepp += vareij[i][j][(int)age];            /*survp += out[s1][j]; */
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));            lli= log(survp);
         for(j=1;j <=nlstate;j++){          }
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));          else if  (s2==-4) { 
         }            for (j=3,survp=0. ; j<=nlstate; j++)  
         fprintf(ficrest,"\n");              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       }            lli= log(survp); 
     }          } 
   }          else if  (s2==-5) { 
 free_matrix(mint,1,maxwav,1,n);            for (j=1,survp=0. ; j<=2; j++)  
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     free_vector(weight,1,n);            lli= log(survp); 
   fclose(ficreseij);          } 
   fclose(ficresvij);          else{
   fclose(ficrest);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   fclose(ficpar);            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   free_vector(epj,1,nlstate+1);          } 
            /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   /*------- Variance limit prevalence------*/            /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   strcpy(fileresvpl,"vpl");          ipmx +=1;
   strcat(fileresvpl,fileres);          sw += weight[i];
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);          /* if (lli < log(mytinydouble)){ */
     exit(0);          /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
   }          /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          /* } */
         } /* end of wave */
   k=0;      } /* end of individual */
   for(cptcov=1;cptcov<=i1;cptcov++){    }  else if(mle==2){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       k=k+1;        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       fprintf(ficresvpl,"\n#****** ");        for(mi=1; mi<= wav[i]-1; mi++){
       for(j=1;j<=cptcoveff;j++)          for (ii=1;ii<=nlstate+ndeath;ii++)
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for (j=1;j<=nlstate+ndeath;j++){
       fprintf(ficresvpl,"******\n");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                    savm[ii][j]=(ii==j ? 1.0 : 0.0);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);            }
       oldm=oldms;savm=savms;          for(d=0; d<=dh[mi][i]; d++){
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            newm=savm;
     }            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
  }            cov[2]=agexact;
             if(nagesqr==1)
   fclose(ficresvpl);              cov[3]= agexact*agexact;
             for (kk=1; kk<=cptcovage;kk++) {
   /*---------- End : free ----------------*/              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            }
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);            savm=oldm;
              oldm=newm;
            } /* end mult */
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);          s1=s[mw[mi][i]][i];
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);          s2=s[mw[mi+1][i]][i];
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);          bbh=(double)bh[mi][i]/(double)stepm; 
            lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   free_matrix(matcov,1,npar,1,npar);          ipmx +=1;
   free_vector(delti,1,npar);          sw += weight[i];
   free_matrix(agev,1,maxwav,1,imx);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        } /* end of wave */
       } /* end of individual */
   if(erreur >0)    }  else if(mle==3){  /* exponential inter-extrapolation */
     printf("End of Imach with error or warning %d\n",erreur);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   else   printf("End of Imach\n");        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/            for (j=1;j<=nlstate+ndeath;j++){
   /*printf("Total time was %d uSec.\n", total_usecs);*/              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /*------ End -----------*/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
           for(d=0; d<dh[mi][i]; d++){
  end:            newm=savm;
 #ifdef windows            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /* chdir(pathcd);*/            cov[2]=agexact;
 #endif            if(nagesqr==1)
  /*system("wgnuplot graph.plt");*/              cov[3]= agexact*agexact;
  /*system("../gp37mgw/wgnuplot graph.plt");*/            for (kk=1; kk<=cptcovage;kk++) {
  /*system("cd ../gp37mgw");*/              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/            }
  strcpy(plotcmd,GNUPLOTPROGRAM);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
  strcat(plotcmd," ");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
  strcat(plotcmd,optionfilegnuplot);            savm=oldm;
  system(plotcmd);            oldm=newm;
           } /* end mult */
 #ifdef windows        
   while (z[0] != 'q') {          s1=s[mw[mi][i]][i];
     /* chdir(path); */          s2=s[mw[mi+1][i]][i];
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");          bbh=(double)bh[mi][i]/(double)stepm; 
     scanf("%s",z);          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     if (z[0] == 'c') system("./imach");          ipmx +=1;
     else if (z[0] == 'e') system(optionfilehtm);          sw += weight[i];
     else if (z[0] == 'g') system(plotcmd);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     else if (z[0] == 'q') exit(0);        } /* end of wave */
   }      } /* end of individual */
 #endif    }else if (mle==4){  /* ml=4 no inter-extrapolation */
 }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
           for(d=0; d<dh[mi][i]; d++){
             newm=savm;
             agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
             cov[2]=agexact;
             if(nagesqr==1)
               cov[3]= agexact*agexact;
             for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
             }
           
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
             oldm=newm;
           } /* end mult */
         
           s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
           if( s2 > nlstate){ 
             lli=log(out[s1][s2] - savm[s1][s2]);
           } else if  ( s2==-1 ) { /* alive */
             for (j=1,survp=0. ; j<=nlstate; j++) 
               survp += out[s1][j];
             lli= log(survp);
           }else{
             lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }
           ipmx +=1;
           sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         } /* end of wave */
       } /* end of individual */
     }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
           for(d=0; d<dh[mi][i]; d++){
             newm=savm;
             agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
             cov[2]=agexact;
             if(nagesqr==1)
               cov[3]= agexact*agexact;
             for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
             }
           
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
             oldm=newm;
           } /* end mult */
         
           s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ipmx +=1;
           sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         } /* end of wave */
       } /* end of individual */
     } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     return -l;
   }
   
   /*************** log-likelihood *************/
   double funcone( double *x)
   {
     /* Same as func but slower because of a lot of printf and if */
     int i, ii, j, k, mi, d, kk;
     int ioffset=0;
     double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     double **out;
     double lli; /* Individual log likelihood */
     double llt;
     int s1, s2;
     int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
   
     double bbh, survp;
     double agexact;
     double agebegin, ageend;
     /*extern weight */
     /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
     */
     cov[1]=1.;
   
     for(k=1; k<=nlstate; k++) ll[k]=0.;
     ioffset=0;
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       /* ioffset=2+nagesqr+cptcovage; */
       ioffset=2+nagesqr;
       /* Fixed */
       /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
       /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
       for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
         cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
   /*    cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i];  */
   /*    cov[2+6]=covar[Tvar[6]][i];  */
   /*    cov[2+6]=covar[2][i]; V2  */
   /*    cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i];  */
   /*    cov[2+7]=covar[Tvar[7]][i];  */
   /*    cov[2+7]=covar[7][i]; V7=V1*V2  */
   /*    cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i];  */
   /*    cov[2+9]=covar[Tvar[9]][i];  */
   /*    cov[2+9]=covar[1][i]; V1  */
       }
       /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
       /*   cov[++ioffset]=coqvar[TvarFQ[k]][i];/\* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V2 and V1*V2 is fixed (k=6 and 7?)*\/ */
       /* } */
       /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
       /*   cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
       /* } */
       
   
       for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
       /* Wave varying (but not age varying) */
         for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
           /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
           cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
         }
         /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
         /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
         /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
         /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
         /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
         /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */
         /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
         /*        iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
         /*        /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); *\/ */
         /*        cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
         /* } */
         for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
         
         agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
         ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
         for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
         /* for(d=0; d<=0; d++){  /\* Delay between two effective waves Only one matrix to speed up*\/ */
           /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
             and mw[mi+1][i]. dh depends on stepm.*/
           newm=savm;
           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;  /* Here d is needed */
           cov[2]=agexact;
           if(nagesqr==1)
             cov[3]= agexact*agexact;
           for (kk=1; kk<=cptcovage;kk++) {
             if(!FixedV[Tvar[Tage[kk]]])
               cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
             else
               cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
           }
           /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
           /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
           /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
           savm=oldm;
           oldm=newm;
         } /* end mult */
         
         s1=s[mw[mi][i]][i];
         s2=s[mw[mi+1][i]][i];
         /* if(s2==-1){ */
         /*        printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
         /*        /\* exit(1); *\/ */
         /* } */
         bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
          * is higher than the multiple of stepm and negative otherwise.
          */
         if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
         } else if  ( s2==-1 ) { /* alive */
           for (j=1,survp=0. ; j<=nlstate; j++) 
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);
         }else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         } else if(mle==3){  /* exponential inter-extrapolation */
           lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         } else if (mle==4){  /* mle=4 no inter-extrapolation */
           lli=log(out[s1][s2]); /* Original formula */
         } else{  /* mle=0 back to 1 */
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           /*lli=log(out[s1][s2]); */ /* Original formula */
         } /* End of if */
         ipmx +=1;
         sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         if(globpr){
           fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
    %11.6f %11.6f %11.6f ", \
                   num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
                   2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
           for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             llt +=ll[k]*gipmx/gsw;
             fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
           fprintf(ficresilk," %10.6f\n", -llt);
         }
           } /* end of wave */
   } /* end of individual */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   if(globpr==0){ /* First time we count the contributions and weights */
           gipmx=ipmx;
           gsw=sw;
   }
   return -l;
   }
   
   
   /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   {
     /* This routine should help understanding what is done with 
        the selection of individuals/waves and
        to check the exact contribution to the likelihood.
        Plotting could be done.
      */
     int k;
   
     if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ILK_"); 
       strcat(fileresilk,fileresu);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
       fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
       fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
       /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
   
     *fretone=(*funcone)(p);
     if(*globpri !=0){
       fclose(ficresilk);
       if (mle ==0)
         fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
       else if(mle >=1)
         fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
       fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model); 
         
       for (k=1; k<= nlstate ; k++) {
         fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
   <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
       }
       fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
   <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
       fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
   <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
       fflush(fichtm);
     }
     return;
   }
   
   
   /*********** Maximum Likelihood Estimation ***************/
   
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
     int i,j, iter=0;
     double **xi;
     double fret;
     double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
   
   #ifdef NLOPT
     int creturn;
     nlopt_opt opt;
     /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
     double *lb;
     double minf; /* the minimum objective value, upon return */
     double * p1; /* Shifted parameters from 0 instead of 1 */
     myfunc_data dinst, *d = &dinst;
   #endif
   
   
     xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"POW_"); 
     strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     fprintf(ficrespow,"\n");
   #ifdef POWELL
     powell(p,xi,npar,ftol,&iter,&fret,func);
   #endif
   
   #ifdef NLOPT
   #ifdef NEWUOA
     opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   #else
     opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
   #endif
     lb=vector(0,npar-1);
     for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
     nlopt_set_lower_bounds(opt, lb);
     nlopt_set_initial_step1(opt, 0.1);
     
     p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
     d->function = func;
     printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
     nlopt_set_min_objective(opt, myfunc, d);
     nlopt_set_xtol_rel(opt, ftol);
     if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
       printf("nlopt failed! %d\n",creturn); 
     }
     else {
       printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
       printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
       iter=1; /* not equal */
     }
     nlopt_destroy(opt);
   #endif
     free_matrix(xi,1,npar,1,npar);
     fclose(ficrespow);
     printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   
   }
   
   /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   {
     double  **a,**y,*x,pd;
     /* double **hess; */
     int i, j;
     int *indx;
   
     double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
     void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
     double gompertz(double p[]);
     /* hess=matrix(1,npar,1,npar); */
   
     printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
       printf("%d-",i);fflush(stdout);
       fprintf(ficlog,"%d-",i);fflush(ficlog);
      
        hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       
       /*  printf(" %f ",p[i]);
           printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }
     
     for (i=1;i<=npar;i++) {
       for (j=1;j<=npar;j++)  {
         if (j>i) { 
           printf(".%d-%d",i,j);fflush(stdout);
           fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
           
           hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
         }
       }
     }
     printf("\n");
     fprintf(ficlog,"\n");
   
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     
     a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
     x=vector(1,npar);
     indx=ivector(1,npar);
     for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     ludcmp(a,npar,indx,&pd);
   
     for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
       lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
       }
     }
   
     printf("\n#Hessian matrix#\n");
     fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
         printf("%.6e ",hess[i][j]);
         fprintf(ficlog,"%.6e ",hess[i][j]);
       }
       printf("\n");
       fprintf(ficlog,"\n");
     }
   
     /* printf("\n#Covariance matrix#\n"); */
     /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
     /* for (i=1;i<=npar;i++) {  */
     /*   for (j=1;j<=npar;j++) {  */
     /*     printf("%.6e ",matcov[i][j]); */
     /*     fprintf(ficlog,"%.6e ",matcov[i][j]); */
     /*   } */
     /*   printf("\n"); */
     /*   fprintf(ficlog,"\n"); */
     /* } */
   
     /* Recompute Inverse */
     /* for (i=1;i<=npar;i++) */
     /*   for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
     /* ludcmp(a,npar,indx,&pd); */
   
     /*  printf("\n#Hessian matrix recomputed#\n"); */
   
     /* for (j=1;j<=npar;j++) { */
     /*   for (i=1;i<=npar;i++) x[i]=0; */
     /*   x[j]=1; */
     /*   lubksb(a,npar,indx,x); */
     /*   for (i=1;i<=npar;i++){  */
     /*     y[i][j]=x[i]; */
     /*     printf("%.3e ",y[i][j]); */
     /*     fprintf(ficlog,"%.3e ",y[i][j]); */
     /*   } */
     /*   printf("\n"); */
     /*   fprintf(ficlog,"\n"); */
     /* } */
   
     /* Verifying the inverse matrix */
   #ifdef DEBUGHESS
     y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
   
      printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
      fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
   
     for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++){ 
         printf("%.2f ",y[i][j]);
         fprintf(ficlog,"%.2f ",y[i][j]);
       }
       printf("\n");
       fprintf(ficlog,"\n");
     }
   #endif
   
     free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
     free_ivector(indx,1,npar);
     /* free_matrix(hess,1,npar,1,npar); */
   
   
   }
   
   /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   { /* Around values of x, computes the function func and returns the scales delti and hessian */
     int i;
     int l=1, lmax=20;
     double k1,k2, res, fx;
     double p2[MAXPARM+1]; /* identical to x */
     double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     int k=0,kmax=10;
     double l1;
   
     fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
     for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
       l1=pow(10,l);
       delts=delt;
       for(k=1 ; k <kmax; k=k+1){
         delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
         k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
         p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
         
   #ifdef DEBUGHESSII
         printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   #endif
         /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k=kmax;
         }
         else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10;
         }
         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
         }
       } /* End loop k */
     }
     delti[theta]=delts;
     return res; 
     
   }
   
   double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   {
     int i;
     int l=1, lmax=20;
     double k1,k2,k3,k4,res,fx;
     double p2[MAXPARM+1];
     int k, kmax=1;
     double v1, v2, cv12, lc1, lc2;
   
     int firstime=0;
     
     fx=func(x);
     for (k=1; k<=kmax; k=k+10) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
       p2[thetai]=x[thetai]+delti[thetai]*k;
       p2[thetaj]=x[thetaj]+delti[thetaj]*k;
       k1=func(p2)-fx;
     
       p2[thetai]=x[thetai]+delti[thetai]*k;
       p2[thetaj]=x[thetaj]-delti[thetaj]*k;
       k2=func(p2)-fx;
     
       p2[thetai]=x[thetai]-delti[thetai]*k;
       p2[thetaj]=x[thetaj]+delti[thetaj]*k;
       k3=func(p2)-fx;
     
       p2[thetai]=x[thetai]-delti[thetai]*k;
       p2[thetaj]=x[thetaj]-delti[thetaj]*k;
       k4=func(p2)-fx;
       res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
       if(k1*k2*k3*k4 <0.){
         firstime=1;
         kmax=kmax+10;
       }
       if(kmax >=10 || firstime ==1){
         printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
         fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
         printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       }
   #ifdef DEBUGHESSIJ
       v1=hess[thetai][thetai];
       v2=hess[thetaj][thetaj];
       cv12=res;
       /* Computing eigen value of Hessian matrix */
       lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       if ((lc2 <0) || (lc1 <0) ){
         printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
         fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
         printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       }
   #endif
     }
     return res;
   }
   
       /* Not done yet: Was supposed to fix if not exactly at the maximum */
   /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
   /* { */
   /*   int i; */
   /*   int l=1, lmax=20; */
   /*   double k1,k2,k3,k4,res,fx; */
   /*   double p2[MAXPARM+1]; */
   /*   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
   /*   int k=0,kmax=10; */
   /*   double l1; */
     
   /*   fx=func(x); */
   /*   for(l=0 ; l <=lmax; l++){  /\* Enlarging the zone around the Maximum *\/ */
   /*     l1=pow(10,l); */
   /*     delts=delt; */
   /*     for(k=1 ; k <kmax; k=k+1){ */
   /*       delt = delti*(l1*k); */
   /*       for (i=1;i<=npar;i++) p2[i]=x[i]; */
   /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
   /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
   /*       k1=func(p2)-fx; */
         
   /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
   /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
   /*       k2=func(p2)-fx; */
         
   /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
   /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
   /*       k3=func(p2)-fx; */
         
   /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
   /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
   /*       k4=func(p2)-fx; */
   /*       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
   /* #ifdef DEBUGHESSIJ */
   /*       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
   /*       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
   /* #endif */
   /*       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
   /*      k=kmax; */
   /*       } */
   /*       else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
   /*      k=kmax; l=lmax*10; */
   /*       } */
   /*       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  */
   /*      delts=delt; */
   /*       } */
   /*     } /\* End loop k *\/ */
   /*   } */
   /*   delti[theta]=delts; */
   /*   return res;  */
   /* } */
   
   
   /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
   { 
     int i,imax,j,k; 
     double big,dum,sum,temp; 
     double *vv; 
    
     vv=vector(1,n); 
     *d=1.0; 
     for (i=1;i<=n;i++) { 
       big=0.0; 
       for (j=1;j<=n;j++) 
         if ((temp=fabs(a[i][j])) > big) big=temp; 
       if (big == 0.0){
         printf(" Singular Hessian matrix at row %d:\n",i);
         for (j=1;j<=n;j++) {
           printf(" a[%d][%d]=%f,",i,j,a[i][j]);
           fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
         }
         fflush(ficlog);
         fclose(ficlog);
         nrerror("Singular matrix in routine ludcmp"); 
       }
       vv[i]=1.0/big; 
     } 
     for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
         sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
       } 
       big=0.0; 
       for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
         for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
           imax=i; 
         } 
       } 
       if (j != imax) { 
         for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
           a[imax][k]=a[j][k]; 
           a[j][k]=dum; 
         } 
         *d = -(*d); 
         vv[imax]=vv[j]; 
       } 
       indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
         dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       } 
     } 
     free_vector(vv,1,n);  /* Doesn't work */
   ;
   } 
   
   void lubksb(double **a, int n, int *indx, double b[]) 
   { 
     int i,ii=0,ip,j; 
     double sum; 
    
     for (i=1;i<=n;i++) { 
       ip=indx[i]; 
       sum=b[ip]; 
       b[ip]=b[i]; 
       if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else if (sum) ii=i; 
       b[i]=sum; 
     } 
     for (i=n;i>=1;i--) { 
       sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       b[i]=sum/a[i][i]; 
     } 
   } 
   
   void pstamp(FILE *fichier)
   {
     fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
   }
   
   
   
   /************ Frequencies ********************/
   void  freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
                     int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
                     int firstpass,  int lastpass, int stepm, int weightopt, char model[])
   {  /* Some frequencies as well as proposing some starting values */
     
     int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
     int iind=0, iage=0;
     int mi; /* Effective wave */
     int first;
     double ***freq; /* Frequencies */
     double *x, *y, a=0.,b=0.,r=1., sa=0., sb=0.; /* for regression, y=b+m*x and r is the correlation coefficient */
     int no=0, linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb);
     double *meanq;
     double **meanqt;
     double *pp, **prop, *posprop, *pospropt;
     double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
     char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
     double agebegin, ageend;
       
     pp=vector(1,nlstate);
     prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE); 
     posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */ 
     pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ 
     /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
     meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
     meanqt=matrix(1,lastpass,1,nqtveff);
     strcpy(fileresp,"P_");
     strcat(fileresp,fileresu);
     /*strcat(fileresphtm,fileresu);*/
     if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       exit(0);
     }
     
     strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
     if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
       printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
       fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
       fflush(ficlog);
       exit(70); 
     }
     else{
       fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n                                    \
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
               fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
     fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm);
     
     strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
     if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
       printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
       fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
       fflush(ficlog);
       exit(70); 
     } else{
       fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n                                    \
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
               fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
     fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
     
     y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
     x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
     freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
     j1=0;
     
     /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
     j=cptcoveff;  /* Only dummy covariates of the model */
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
     
     /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
        reference=low_education V1=0,V2=0
        med_educ                V1=1 V2=0, 
        high_educ               V1=0 V2=1
        Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff 
     */
     dateintsum=0;
     k2cpt=0;
   
     if(cptcoveff == 0 )
       nl=1;  /* Constant and age model only */
     else
       nl=2;
   
     /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
     /* Loop on nj=1 or 2 if dummy covariates j!=0
      *   Loop on j1(1 to 2**cptcoveff) covariate combination
      *     freq[s1][s2][iage] =0.
      *     Loop on iind
      *       ++freq[s1][s2][iage] weighted
      *     end iind
      *     if covariate and j!0
      *       headers Variable on one line
      *     endif cov j!=0
      *     header of frequency table by age
      *     Loop on age
      *       pp[s1]+=freq[s1][s2][iage] weighted
      *       pos+=freq[s1][s2][iage] weighted
      *       Loop on s1 initial state
      *         fprintf(ficresp
      *       end s1
      *     end age
      *     if j!=0 computes starting values
      *     end compute starting values
      *   end j1
      * end nl 
      */
     for (nj = 1; nj <= nl; nj++){   /* nj= 1 constant model, nl number of loops. */
       if(nj==1)
         j=0;  /* First pass for the constant */
       else{
         j=cptcoveff; /* Other passes for the covariate values */
       }
       first=1;
       for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all covariates combination of the model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
         posproptt=0.;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           scanf("%d", i);*/
         for (i=-5; i<=nlstate+ndeath; i++)  
           for (s2=-5; s2<=nlstate+ndeath; s2++)  
             for(m=iagemin; m <= iagemax+3; m++)
               freq[i][s2][m]=0;
         
         for (i=1; i<=nlstate; i++)  {
           for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0;
           posprop[i]=0;
           pospropt[i]=0;
         }
         /* for (z1=1; z1<= nqfveff; z1++) {   */
         /*   meanq[z1]+=0.; */
         /*   for(m=1;m<=lastpass;m++){ */
         /*        meanqt[m][z1]=0.; */
         /*   } */
         /* } */
         
         /* dateintsum=0; */
         /* k2cpt=0; */
         
         /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
         for (iind=1; iind<=imx; iind++) { /* For each individual iind */
           bool=1;
           if(j !=0){
             if(anyvaryingduminmodel==0){ /* If All fixed covariates */
               if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
                 /* for (z1=1; z1<= nqfveff; z1++) {   */
                 /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
                 /* } */
                 for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
                   /* if(Tvaraff[z1] ==-20){ */
                   /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
                   /* }else  if(Tvaraff[z1] ==-10){ */
                   /*       /\* sumnew+=coqvar[z1][iind]; *\/ */
                   /* }else  */
                   if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
                     /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
                     bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
                     /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", 
                        bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
                        j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
                     /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
                   } /* Onlyf fixed */
                 } /* end z1 */
               } /* cptcovn > 0 */
             } /* end any */
           }/* end j==0 */
           if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
             /* for(m=firstpass; m<=lastpass; m++){ */
             for(mi=1; mi<wav[iind];mi++){ /* For that wave */
               m=mw[mi][iind];
               if(j!=0){
                 if(anyvaryingduminmodel==1){ /* Some are varying covariates */
                   for (z1=1; z1<=cptcoveff; z1++) {
                     if( Fixed[Tmodelind[z1]]==1){
                       iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
                       if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's 
                                                                                         value is -1, we don't select. It differs from the 
                                                                                         constant and age model which counts them. */
                         bool=0; /* not selected */
                     }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
                       if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
                         bool=0;
                       }
                     }
                   }
                 }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
               } /* end j==0 */
               /* bool =0 we keep that guy which corresponds to the combination of dummy values */
               if(bool==1){
                 /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
                    and mw[mi+1][iind]. dh depends on stepm. */
                 agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
                 ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
                 if(m >=firstpass && m <=lastpass){
                   k2=anint[m][iind]+(mint[m][iind]/12.);
                   /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                   if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
                   if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
                   if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
                     prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
                   if (m<lastpass) {
                     /* if(s[m][iind]==4 && s[m+1][iind]==4) */
                     /*   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
                     if(s[m][iind]==-1)
                       printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
                     freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
                     /* if((int)agev[m][iind] == 55) */
                     /*   printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
                     /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
                     freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
                   }
                 } /* end if between passes */  
                 if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
                   dateintsum=dateintsum+k2; /* on all covariates ?*/
                   k2cpt++;
                   /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
                 }
               }else{
                 bool=1;
               }/* end bool 2 */
             } /* end m */
           } /* end bool */
         } /* end iind = 1 to imx */
         /* prop[s][age] is feeded for any initial and valid live state as well as
            freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
         
         
         /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         if(cptcoveff==0 && nj==1) /* no covariate and first pass */
           pstamp(ficresp);
         if  (cptcoveff>0 && j!=0){
           pstamp(ficresp);
           printf( "\n#********** Variable "); 
           fprintf(ficresp, "\n#********** Variable "); 
           fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable "); 
           fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable "); 
           fprintf(ficlog, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++){
             if(!FixedV[Tvaraff[z1]]){
               printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
               fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
               fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
               fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
               fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             }else{
               printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
               fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
               fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
               fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
               fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             }
           }
           printf( "**********\n#");
           fprintf(ficresp, "**********\n#");
           fprintf(ficresphtm, "**********</h3>\n");
           fprintf(ficresphtmfr, "**********</h3>\n");
           fprintf(ficlog, "**********\n");
         }
         fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
         if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
           fprintf(ficresp, " Age");
         if(nj==2) for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         for(i=1; i<=nlstate;i++) {
           if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d)  N(%d)  N  ",i,i);
           fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
         }
         if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
         fprintf(ficresphtm, "\n");
         
         /* Header of frequency table by age */
         fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
         fprintf(ficresphtmfr,"<th>Age</th> ");
         for(s2=-1; s2 <=nlstate+ndeath; s2++){
           for(m=-1; m <=nlstate+ndeath; m++){
             if(s2!=0 && m!=0)
               fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
           }
         }
         fprintf(ficresphtmfr, "\n");
       
         /* For each age */
         for(iage=iagemin; iage <= iagemax+3; iage++){
           fprintf(ficresphtm,"<tr>");
           if(iage==iagemax+1){
             fprintf(ficlog,"1");
             fprintf(ficresphtmfr,"<tr><th>0</th> ");
           }else if(iage==iagemax+2){
             fprintf(ficlog,"0");
             fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
           }else if(iage==iagemax+3){
             fprintf(ficlog,"Total");
             fprintf(ficresphtmfr,"<tr><th>Total</th> ");
           }else{
             if(first==1){
               first=0;
               printf("See log file for details...\n");
             }
             fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
             fprintf(ficlog,"Age %d", iage);
           }
           for(s1=1; s1 <=nlstate ; s1++){
             for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
               pp[s1] += freq[s1][m][iage]; 
           }
           for(s1=1; s1 <=nlstate ; s1++){
             for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[s1][m][iage];
             if(pp[s1]>=1.e-10){
               if(first==1){
                 printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
               }
               fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
             }else{
               if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
             }
           }
         
           for(s1=1; s1 <=nlstate ; s1++){ 
             /* posprop[s1]=0; */
             for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
               pp[s1] += freq[s1][m][iage];
           }       /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
         
           for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
             pos += pp[s1]; /* pos is the total number of transitions until this age */
             posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
                                               from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
             pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
                                             from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
           }
           
           /* Writing ficresp */
           if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
             if( iage <= iagemax){
               fprintf(ficresp," %d",iage);
             }
           }else if( nj==2){
             if( iage <= iagemax){
               fprintf(ficresp," %d",iage);
               for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             }
           }
           for(s1=1; s1 <=nlstate ; s1++){
             if(pos>=1.e-5){
               if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
             }else{
               if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
             }
             if( iage <= iagemax){
               if(pos>=1.e-5){
                 if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
                   fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
                 }else if( nj==2){
                   fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
                 }
                 fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
                 /*probs[iage][s1][j1]= pp[s1]/pos;*/
                 /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
               } else{
                 if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
                 fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
               }
             }
             pospropt[s1] +=posprop[s1];
           } /* end loop s1 */
           /* pospropt=0.; */
           for(s1=-1; s1 <=nlstate+ndeath; s1++){
             for(m=-1; m <=nlstate+ndeath; m++){
               if(freq[s1][m][iage] !=0 ) { /* minimizing output */
                 if(first==1){
                   printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
                 }
                 /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
                 fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
               }
               if(s1!=0 && m!=0)
                 fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
             }
           } /* end loop s1 */
           posproptt=0.; 
           for(s1=1; s1 <=nlstate; s1++){
             posproptt += pospropt[s1];
           }
           fprintf(ficresphtmfr,"</tr>\n ");
           fprintf(ficresphtm,"</tr>\n");
           if((cptcoveff==0 && nj==1)|| nj==2 ) {
             if(iage <= iagemax)
               fprintf(ficresp,"\n");
           }
           if(first==1)
             printf("Others in log...\n");
           fprintf(ficlog,"\n");
         } /* end loop age iage */
         
         fprintf(ficresphtm,"<tr><th>Tot</th>");
         for(s1=1; s1 <=nlstate ; s1++){
           if(posproptt < 1.e-5){
             fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt); 
           }else{
             fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);  
           }
         }
         fprintf(ficresphtm,"</tr>\n");
         fprintf(ficresphtm,"</table>\n");
         fprintf(ficresphtmfr,"</table>\n");
         if(posproptt < 1.e-5){
           fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
           fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
           fprintf(ficlog,"#  This combination (%d) is not valid and no result will be produced\n",j1);
           printf("#  This combination (%d) is not valid and no result will be produced\n",j1);
           invalidvarcomb[j1]=1;
         }else{
           fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
           invalidvarcomb[j1]=0;
         }
         fprintf(ficresphtmfr,"</table>\n");
         fprintf(ficlog,"\n");
         if(j!=0){
           printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
           for(i=1,s1=1; i <=nlstate; i++){
             for(k=1; k <=(nlstate+ndeath); k++){
               if (k != i) {
                 for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
                   if(jj==1){  /* Constant case (in fact cste + age) */
                     if(j1==1){ /* All dummy covariates to zero */
                       freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
                       freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
                       printf("%d%d ",i,k);
                       fprintf(ficlog,"%d%d ",i,k);
                       printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]));
                       fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
                       pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
                     }
                   }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
                     for(iage=iagemin; iage <= iagemax+3; iage++){
                       x[iage]= (double)iage;
                       y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
                       /* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */
                     }
                     /* Some are not finite, but linreg will ignore these ages */
                     no=0;
                     linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
                     pstart[s1]=b;
                     pstart[s1-1]=a;
                   }else if( j1!=1 && (j1==2 || (log(j1-1.)/log(2.)-(int)(log(j1-1.)/log(2.))) <0.010) && ( TvarsDind[(int)(log(j1-1.)/log(2.))+1]+2+nagesqr == jj)  && Dummy[jj-2-nagesqr]==0){ /* We want only if the position, jj, in model corresponds to unique covariate equal to 1 in j1 combination */ 
                     printf("j1=%d, jj=%d, (int)(log(j1-1.)/log(2.))+1=%d, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(int)(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
                     printf("j1=%d, jj=%d, (log(j1-1.)/log(2.))+1=%f, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
                     pstart[s1]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));
                     printf("%d%d ",i,k);
                     fprintf(ficlog,"%d%d ",i,k);
                     printf("s1=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",s1,i,k,s1,p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3],freq[i][k][iagemax+4],freq[i][i][iagemax+4], log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])),(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]), sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]+1/freq[i][k][iagemax+4]+1/freq[i][i][iagemax+4]));
                   }else{ /* Other cases, like quantitative fixed or varying covariates */
                     ;
                   }
                   /* printf("%12.7f )", param[i][jj][k]); */
                   /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
                   s1++; 
                 } /* end jj */
               } /* end k!= i */
             } /* end k */
           } /* end i, s1 */
         } /* end j !=0 */
       } /* end selected combination of covariate j1 */
       if(j==0){ /* We can estimate starting values from the occurences in each case */
         printf("#Freqsummary: Starting values for the constants:\n");
         fprintf(ficlog,"\n");
         for(i=1,s1=1; i <=nlstate; i++){
           for(k=1; k <=(nlstate+ndeath); k++){
             if (k != i) {
               printf("%d%d ",i,k);
               fprintf(ficlog,"%d%d ",i,k);
               for(jj=1; jj <=ncovmodel; jj++){
                 pstart[s1]=p[s1]; /* Setting pstart to p values by default */
                 if(jj==1){ /* Age has to be done */
                   pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
                   printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
                   fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
                 }
                 /* printf("%12.7f )", param[i][jj][k]); */
                 /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
                 s1++; 
               }
               printf("\n");
               fprintf(ficlog,"\n");
             }
           }
         }
         printf("#Freqsummary\n");
         fprintf(ficlog,"\n");
         for(s1=-1; s1 <=nlstate+ndeath; s1++){
           for(s2=-1; s2 <=nlstate+ndeath; s2++){
             /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
             printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
             fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
             /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
             /*   printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
             /*   fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
             /* } */
           }
         } /* end loop s1 */
         
         printf("\n");
         fprintf(ficlog,"\n");
       } /* end j=0 */
     } /* end j */
   
     if(mle == -2){  /* We want to use these values as starting values */
       for(i=1, jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j!=i){
             /*ca[0]= k+'a'-1;ca[1]='\0';*/
             printf("%1d%1d",i,j);
             fprintf(ficparo,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               /*    printf(" %lf",param[i][j][k]); */
               /*    fprintf(ficparo," %lf",param[i][j][k]); */
               p[jk]=pstart[jk];
               printf(" %f ",pstart[jk]);
               fprintf(ficparo," %f ",pstart[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficparo,"\n");
           }
         }
       }
     } /* end mle=-2 */
     dateintmean=dateintsum/k2cpt; 
     
     fclose(ficresp);
     fclose(ficresphtm);
     fclose(ficresphtmfr);
     free_vector(meanq,1,nqfveff);
     free_matrix(meanqt,1,lastpass,1,nqtveff);
     free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
     free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
     free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
     free_vector(pospropt,1,nlstate);
     free_vector(posprop,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
     free_vector(pp,1,nlstate);
     /* End of freqsummary */
   }
   
   /* Simple linear regression */
   int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
   
     /* y=a+bx regression */
     double   sumx = 0.0;                        /* sum of x                      */
     double   sumx2 = 0.0;                       /* sum of x**2                   */
     double   sumxy = 0.0;                       /* sum of x * y                  */
     double   sumy = 0.0;                        /* sum of y                      */
     double   sumy2 = 0.0;                       /* sum of y**2                   */
     double   sume2 = 0.0;                       /* sum of square or residuals */
     double yhat;
     
     double denom=0;
     int i;
     int ne=*no;
     
     for ( i=ifi, ne=0;i<=ila;i++) {
       if(!isfinite(x[i]) || !isfinite(y[i])){
         /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
         continue;
       }
       ne=ne+1;
       sumx  += x[i];       
       sumx2 += x[i]*x[i];  
       sumxy += x[i] * y[i];
       sumy  += y[i];      
       sumy2 += y[i]*y[i]; 
       denom = (ne * sumx2 - sumx*sumx);
       /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
     } 
     
     denom = (ne * sumx2 - sumx*sumx);
     if (denom == 0) {
       // vertical, slope m is infinity
       *b = INFINITY;
       *a = 0;
       if (r) *r = 0;
       return 1;
     }
     
     *b = (ne * sumxy  -  sumx * sumy) / denom;
     *a = (sumy * sumx2  -  sumx * sumxy) / denom;
     if (r!=NULL) {
       *r = (sumxy - sumx * sumy / ne) /          /* compute correlation coeff     */
         sqrt((sumx2 - sumx*sumx/ne) *
              (sumy2 - sumy*sumy/ne));
     }
     *no=ne;
     for ( i=ifi, ne=0;i<=ila;i++) {
       if(!isfinite(x[i]) || !isfinite(y[i])){
         /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
         continue;
       }
       ne=ne+1;
       yhat = y[i] - *a -*b* x[i];
       sume2  += yhat * yhat ;       
       
       denom = (ne * sumx2 - sumx*sumx);
       /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
     } 
     *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
     *sa= *sb * sqrt(sumx2/ne);
     
     return 0; 
   }
   
   /************ Prevalence ********************/
   void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
     */
    
     int i, m, jk, j1, bool, z1,j, iv;
     int mi; /* Effective wave */
     int iage;
     double agebegin, ageend;
   
     double **prop;
     double posprop; 
     double  y2; /* in fractional years */
     int iagemin, iagemax;
     int first; /** to stop verbosity which is redirected to log file */
   
     iagemin= (int) agemin;
     iagemax= (int) agemax;
     /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j1=0;
     
     /*j=cptcoveff;*/
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
     first=1;
     for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
       for (i=1; i<=nlstate; i++)  
         for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
           prop[i][iage]=0.0;
       printf("Prevalence combination of varying and fixed dummies %d\n",j1);
       /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
       fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
       
       for (i=1; i<=imx; i++) { /* Each individual */
         bool=1;
         /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
         for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
           m=mw[mi][i];
           /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
           /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
           for (z1=1; z1<=cptcoveff; z1++){
             if( Fixed[Tmodelind[z1]]==1){
               iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
               if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
                 bool=0;
             }else if( Fixed[Tmodelind[z1]]== 0)  /* fixed */
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
                 bool=0;
               }
           }
           if(bool==1){ /* Otherwise we skip that wave/person */
             agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
             /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
             if(m >=firstpass && m <=lastpass){
               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
                   printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m); 
                   exit(1);
                 }
                 if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
                   prop[s[m][i]][iagemax+3] += weight[i]; 
                 } /* end valid statuses */ 
               } /* end selection of dates */
             } /* end selection of waves */
           } /* end bool */
         } /* end wave */
       } /* end individual */
       for(i=iagemin; i <= iagemax+3; i++){  
         for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
           posprop += prop[jk][i]; 
         } 
         
         for(jk=1; jk <=nlstate ; jk++){       
           if( i <=  iagemax){ 
             if(posprop>=1.e-5){ 
               probs[i][jk][j1]= prop[jk][i]/posprop;
             } else{
               if(first==1){
                 first=0;
                 printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
                 fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
               }else{
                 fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
               }
             }
           } 
         }/* end jk */ 
       }/* end i */ 
        /*} *//* end i1 */
     } /* end j1 */
     
     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
   }  /* End of prevalence */
   
   /************* Waves Concatenation ***************/
   
   void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
   {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        Death is a valid wave (if date is known).
        mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
        dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
     */
   
     int i=0, mi=0, m=0, mli=0;
     /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        double sum=0., jmean=0.;*/
     int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
     int j, k=0,jk, ju, jl;
     double sum=0.;
     first=0;
     firstwo=0;
     firsthree=0;
     firstfour=0;
     jmin=100000;
     jmax=-1;
     jmean=0.;
   
   /* Treating live states */
     for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
       mi=0;  /* First valid wave */
       mli=0; /* Last valid wave */
       m=firstpass;
       while(s[m][i] <= nlstate){  /* a live state */
         if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
           mli=m-1;/* mw[++mi][i]=m-1; */
         }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
           mw[++mi][i]=m;
           mli=m;
         } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */
         if(m < lastpass){ /* m < lastpass, standard case */
           m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
         }
         else{ /* m >= lastpass, eventual special issue with warning */
   #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
           break;
   #else
           if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
             if(firsthree == 0){
               printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p%d%d .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
               firsthree=1;
             }
             fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p%d%d .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
             mw[++mi][i]=m;
             mli=m;
           }
           if(s[m][i]==-2){ /* Vital status is really unknown */
             nbwarn++;
             if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */
               printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
               fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
             }
             break;
           }
           break;
   #endif
         }/* End m >= lastpass */
       }/* end while */
   
       /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */
       /* After last pass */
   /* Treating death states */
       if (s[m][i] > nlstate){  /* In a death state */
         /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
         /* } */
         mi++;     /* Death is another wave */
         /* if(mi==0)  never been interviewed correctly before death */
         /* Only death is a correct wave */
         mw[mi][i]=m;
       } /* else not in a death state */
   #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
       else if ((int) andc[i] != 9999) {  /* Date of death is known */
         if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
           if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
             nbwarn++;
             if(firstfiv==0){
               printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
               firstfiv=1;
             }else{
               fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
             }
           }else{ /* Death occured afer last wave potential bias */
             nberr++;
             if(firstwo==0){
               printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
               firstwo=1;
             }
             fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
           }
         }else{ /* if date of interview is unknown */
           /* death is known but not confirmed by death status at any wave */
           if(firstfour==0){
             printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
             firstfour=1;
           }
           fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
         }
       } /* end if date of death is known */
   #endif
       wav[i]=mi; /* mi should be the last effective wave (or mli) */
       /* wav[i]=mw[mi][i]; */
       if(mi==0){
         nbwarn++;
         if(first==0){
           printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           first=1;
         }
         if(first==1){
           fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         }
       } /* end mi==0 */
     } /* End individuals */
     /* wav and mw are no more changed */
           
     
     for(i=1; i<=imx; i++){
       for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
           dh[mi][i]=1;
         else{
           if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
             if (agedc[i] < 2*AGESUP) {
               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
                 nberr++;
                 printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 j=1; /* Temporary Dangerous patch */
                 printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                 fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               }
               k=k+1;
               if (j >= jmax){
                 jmax=j;
                 ijmax=i;
               }
               if (j <= jmin){
                 jmin=j;
                 ijmin=i;
               }
               sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
           }
           else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
                                           
             k=k+1;
             if (j >= jmax) {
               jmax=j;
               ijmax=i;
             }
             else if (j <= jmin){
               jmin=j;
               ijmin=i;
             }
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
             if(j<0){
               nberr++;
               printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             }
             sum=sum+j;
           }
           jk= j/stepm;
           jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             if(jl==0){
               dh[mi][i]=jk;
               bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
                     * to avoid the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
               bh[mi][i]=ju;
             }
           }else{
             if(jl <= -ju){
               dh[mi][i]=jk;
               bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
                                    */
             }
             else{
               dh[mi][i]=jk+1;
               bh[mi][i]=ju;
             }
             if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
               /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
             }
           } /* end if mle */
         }
       } /* end wave */
     }
     jmean=sum/k;
     printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
     fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
   }
   
   /*********** Tricode ****************************/
    void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
    {
      /**< Uses cptcovn+2*cptcovprod as the number of covariates */
      /*     Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
       * Boring subroutine which should only output nbcode[Tvar[j]][k]
       * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
       * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
       */
   
      int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
      int modmaxcovj=0; /* Modality max of covariates j */
      int cptcode=0; /* Modality max of covariates j */
      int modmincovj=0; /* Modality min of covariates j */
   
   
      /* cptcoveff=0;  */
      /* *cptcov=0; */
    
      for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   
      /* Loop on covariates without age and products and no quantitative variable */
      /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
      for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
        for (j=-1; (j < maxncov); j++) Ndum[j]=0;
        if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */ 
          switch(Fixed[k]) {
          case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
            for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/
              ij=(int)(covar[Tvar[k]][i]);
              /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
               * If product of Vn*Vm, still boolean *:
               * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
               * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
              /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                 modality of the nth covariate of individual i. */
              if (ij > modmaxcovj)
                modmaxcovj=ij; 
              else if (ij < modmincovj) 
                modmincovj=ij; 
              if ((ij < -1) && (ij > NCOVMAX)){
                printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
                exit(1);
              }else
                Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
              /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
              /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
              /* getting the maximum value of the modality of the covariate
                 (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
                 female ies 1, then modmaxcovj=1.
              */
            } /* end for loop on individuals i */
            printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
            fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
            cptcode=modmaxcovj;
            /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
            /*for (i=0; i<=cptcode; i++) {*/
            for (j=modmincovj;  j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
              printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
              fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
              if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
                if( j != -1){
                  ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
                                     covariate for which somebody answered excluding 
                                     undefined. Usually 2: 0 and 1. */
                }
                ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
                                        covariate for which somebody answered including 
                                        undefined. Usually 3: -1, 0 and 1. */
              }    /* In fact  ncodemax[k]=2 (dichotom. variables only) but it could be more for
                    * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
            } /* Ndum[-1] number of undefined modalities */
                           
            /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
            /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
            /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
            /* modmincovj=3; modmaxcovj = 7; */
            /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
            /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
            /*              defining two dummy variables: variables V1_1 and V1_2.*/
            /* nbcode[Tvar[j]][ij]=k; */
            /* nbcode[Tvar[j]][1]=0; */
            /* nbcode[Tvar[j]][2]=1; */
            /* nbcode[Tvar[j]][3]=2; */
            /* To be continued (not working yet). */
            ij=0; /* ij is similar to i but can jump over null modalities */
            for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
              if (Ndum[i] == 0) { /* If nobody responded to this modality k */
                break;
              }
              ij++;
              nbcode[Tvar[k]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/
              cptcode = ij; /* New max modality for covar j */
            } /* end of loop on modality i=-1 to 1 or more */
            break;
          case 1: /* Testing on varying covariate, could be simple and
                   * should look at waves or product of fixed *
                   * varying. No time to test -1, assuming 0 and 1 only */
            ij=0;
            for(i=0; i<=1;i++){
              nbcode[Tvar[k]][++ij]=i;
            }
            break;
          default:
            break;
          } /* end switch */
        } /* end dummy test */
       
        /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
        /*         /\*recode from 0 *\/ */
        /*                                      k is a modality. If we have model=V1+V1*sex  */
        /*                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
        /*                                   But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
        /*         } */
        /*         /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
        /*         if (ij > ncodemax[j]) { */
        /*           printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
        /*           fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
        /*           break; */
        /*         } */
        /*   }  /\* end of loop on modality k *\/ */
      } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
     
      for (k=-1; k< maxncov; k++) Ndum[k]=0; 
      /* Look at fixed dummy (single or product) covariates to check empty modalities */
      for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ 
        /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
        ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */ 
        Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */
        /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1,  {2, 1, 1, 1, 2, 1, 1, 0, 0} */
      } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
     
      ij=0;
      /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
      for (k=1; k<=  cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
        /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
        /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
        if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
          /* If product not in single variable we don't print results */
          /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
          ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
          Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/
          Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
          TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */
          if(Fixed[k]!=0)
            anyvaryingduminmodel=1;
          /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
          /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
          /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
          /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
          /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
          /*   Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
        } 
      } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
      /* ij--; */
      /* cptcoveff=ij; /\*Number of total covariates*\/ */
      *cptcov=ij; /*Number of total real effective covariates: effective
                   * because they can be excluded from the model and real
                   * if in the model but excluded because missing values, but how to get k from ij?*/
      for(j=ij+1; j<= cptcovt; j++){
        Tvaraff[j]=0;
        Tmodelind[j]=0;
      }
      for(j=ntveff+1; j<= cptcovt; j++){
        TmodelInvind[j]=0;
      }
      /* To be sorted */
      ;
    }
   
   
   /*********** Health Expectancies ****************/
   
    void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[], int nres )
   
   {
     /* Health expectancies, no variances */
     int i, j, nhstepm, hstepm, h, nstepm;
     int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     double ***p3mat;
     double eip;
   
     /* pstamp(ficreseij); */
     fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++){
         fprintf(ficreseij," e%1d%1d ",i,j);
       }
       fprintf(ficreseij," e%1d. ",i);
     }
     fprintf(ficreseij,"\n");
   
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason which relies in memory size consideration
        and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     agelim=AGESUP;
     /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       
   /* nhstepm age range expressed in number of stepm */
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);  
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       
       printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       
       /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0;
         for(j=1; j<=nlstate;j++){
           eip +=eij[i][j][(int)age];
           fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
         fprintf(ficreseij,"%9.4f", eip );
       }
       fprintf(ficreseij,"\n");
       
     }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
     
   }
   
    void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[], int nres )
   
   {
     /* Covariances of health expectancies eij and of total life expectancies according
        to initial status i, ei. .
     */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
     double *xp, *xm;
     double **gp, **gm;
     double ***gradg, ***trgradg;
     int theta;
   
     double eip, vip;
   
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
     xm=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
     pstamp(ficresstdeij);
     fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficresstdeij,"# Age");
     for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++)
         fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficresstdeij," e%1d. ",i);
     }
     fprintf(ficresstdeij,"\n");
   
     pstamp(ficrescveij);
     fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
         for(i2=1; i2<=nlstate;i2++)
           for(j2=1; j2<=nlstate;j2++){
             cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
               fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           }
       }
     fprintf(ficrescveij,"\n");
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
                   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                   
       /* Computing  Variances of health expectancies */
       /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
         }
         hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);  
                           
         for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
               gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             }
           }
         }
                           
         for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
       }/* End theta */
       
       
       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
       
                   
       for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
                   
       printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(ij=1;ij<=nlstate*nlstate;ij++)
             for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
       }
                   
       /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);  
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
                                           
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
                                           
           }
   
       /* Standard deviation of expectancies ij */         
       fprintf(ficresstdeij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0.;
         vip=0.;
         for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
       fprintf(ficresstdeij,"\n");
                   
       /* Variance of expectancies ij */           
       fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       fprintf(ficrescveij,"\n");
                   
     }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
           
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
    
   /************ Variance ******************/
    void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)
    {
      /** Variance of health expectancies 
       *  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
       * double **newm;
       * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav) 
       */
     
      /* int movingaverage(); */
      double **dnewm,**doldm;
      double **dnewmp,**doldmp;
      int i, j, nhstepm, hstepm, h, nstepm ;
      int k;
      double *xp;
      double **gp, **gm;  /**< for var eij */
      double ***gradg, ***trgradg; /**< for var eij */
      double **gradgp, **trgradgp; /**< for var p point j */
      double *gpp, *gmp; /**< for var p point j */
      double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
      double ***p3mat;
      double age,agelim, hf;
      /* double ***mobaverage; */
      int theta;
      char digit[4];
      char digitp[25];
   
      char fileresprobmorprev[FILENAMELENGTH];
   
      if(popbased==1){
        if(mobilav!=0)
          strcpy(digitp,"-POPULBASED-MOBILAV_");
        else strcpy(digitp,"-POPULBASED-NOMOBIL_");
      }
      else 
        strcpy(digitp,"-STABLBASED_");
   
      /* if (mobilav!=0) { */
      /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
      /*   if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
      /*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
      /*     printf(" Error in movingaverage mobilav=%d\n",mobilav); */
      /*   } */
      /* } */
   
      strcpy(fileresprobmorprev,"PRMORPREV-"); 
      sprintf(digit,"%-d",ij);
      /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
      strcat(fileresprobmorprev,digit); /* Tvar to be done */
      strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
      strcat(fileresprobmorprev,fileresu);
      if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobmorprev);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
      }
      printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      pstamp(ficresprobmorprev);
      fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
      fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
      for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
        fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
      }
      for(j=1;j<=cptcoveff;j++) 
        fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
      fprintf(ficresprobmorprev,"\n");
   
      fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
        fprintf(ficresprobmorprev," p.%-d SE",j);
        for(i=1; i<=nlstate;i++)
          fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
      }  
      fprintf(ficresprobmorprev,"\n");
     
      fprintf(ficgp,"\n# Routine varevsij");
      fprintf(ficgp,"\nunset title \n");
      /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   
      varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      pstamp(ficresvij);
      fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
      if(popbased==1)
        fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
      else
        fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
      fprintf(ficresvij,"# Age");
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
          fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
      fprintf(ficresvij,"\n");
   
      xp=vector(1,npar);
      dnewm=matrix(1,nlstate,1,npar);
      doldm=matrix(1,nlstate,1,nlstate);
      dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
      doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
      gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
      gpp=vector(nlstate+1,nlstate+ndeath);
      gmp=vector(nlstate+1,nlstate+ndeath);
      trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
      if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
      }
      else  hstepm=estepm;   
      /* For example we decided to compute the life expectancy with the smallest unit */
      /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         nhstepm is the number of hstepm from age to agelim 
         nstepm is the number of stepm from age to agelim. 
         Look at function hpijx to understand why because of memory size limitations, 
         we decided (b) to get a life expectancy respecting the most precise curvature of the
         survival function given by stepm (the optimization length). Unfortunately it
         means that if the survival funtion is printed every two years of age and if
         you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         results. So we changed our mind and took the option of the best precision.
      */
      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      agelim = AGESUP;
      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
        nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
        gp=matrix(0,nhstepm,1,nlstate);
        gm=matrix(0,nhstepm,1,nlstate);
                   
                   
        for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
          }
          /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and 
           * returns into prlim .
           */              
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
   
          /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
          if (popbased==1) {
            if(mobilav ==0){
              for(i=1; i<=nlstate;i++)
                prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
            }
          }
          /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}_x\f$ at horizon h.
           */                      
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=0 to nhstepm */
          /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}_x\f$, which are the probability
           * at horizon h in state j including mortality.
           */
          for(j=1; j<= nlstate; j++){
            for(h=0; h<=nhstepm; h++){
              for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                gp[h][j] += prlim[i][i]*p3mat[i][j][h];
            }
          }
          /* Next for computing shifted+ probability of death (h=1 means
             computed over hstepm matrices product = hstepm*stepm months) 
             as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
          */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
            for(i=1,gpp[j]=0.; i<= nlstate; i++)
              gpp[j] += prlim[i][i]*p3mat[i][j][1];
          }
          
          /* Again with minus shift */
                           
          for(i=1; i<=npar; i++) /* Computes gradient x - delta */
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
                           
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
                           
          if (popbased==1) {
            if(mobilav ==0){
              for(i=1; i<=nlstate;i++)
                prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
            }
          }
                           
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  
                           
          for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
            for(h=0; h<=nhstepm; h++){
              for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                gm[h][j] += prlim[i][i]*p3mat[i][j][h];
            }
          }
          /* This for computing probability of death (h=1 means
             computed over hstepm matrices product = hstepm*stepm months) 
             as a weighted average of prlim.
          */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
            for(i=1,gmp[j]=0.; i<= nlstate; i++)
              gmp[j] += prlim[i][i]*p3mat[i][j][1];
          }    
          /* end shifting computations */
   
          /**< Computing gradient matrix at horizon h 
           */
          for(j=1; j<= nlstate; j++) /* vareij */
            for(h=0; h<=nhstepm; h++){
              gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
            }
          /**< Gradient of overall mortality p.3 (or p.j) 
           */
          for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
            gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
          }
                           
        } /* End theta */
        
        /* We got the gradient matrix for each theta and state j */                
        trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
                   
        for(h=0; h<=nhstepm; h++) /* veij */
          for(j=1; j<=nlstate;j++)
            for(theta=1; theta <=npar; theta++)
              trgradg[h][j][theta]=gradg[h][theta][j];
                   
        for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
          for(theta=1; theta <=npar; theta++)
            trgradgp[j][theta]=gradgp[theta][j];
        /**< as well as its transposed matrix 
         */                
                   
        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        for(i=1;i<=nlstate;i++)
          for(j=1;j<=nlstate;j++)
            vareij[i][j][(int)age] =0.;
   
        /* Computing trgradg by matcov by gradg at age and summing over h
         * and k (nhstepm) formula 15 of article
         * Lievre-Brouard-Heathcote
         */
        
        for(h=0;h<=nhstepm;h++){
          for(k=0;k<=nhstepm;k++){
            matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
            for(i=1;i<=nlstate;i++)
              for(j=1;j<=nlstate;j++)
                vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
          }
        }
                   
        /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
         * p.j overall mortality formula 49 but computed directly because
         * we compute the grad (wix pijx) instead of grad (pijx),even if
         * wix is independent of theta.
         */
        matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
        matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
        for(j=nlstate+1;j<=nlstate+ndeath;j++)
          for(i=nlstate+1;i<=nlstate+ndeath;i++)
            varppt[j][i]=doldmp[j][i];
        /* end ppptj */
        /*  x centered again */
                   
        prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
                   
        if (popbased==1) {
          if(mobilav ==0){
            for(i=1; i<=nlstate;i++)
              prlim[i][i]=probs[(int)age][i][ij];
          }else{ /* mobilav */ 
            for(i=1; i<=nlstate;i++)
              prlim[i][i]=mobaverage[(int)age][i][ij];
          }
        }
                   
        /* This for computing probability of death (h=1 means
           computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           as a weighted average of prlim.
        */
        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);  
        for(j=nlstate+1;j<=nlstate+ndeath;j++){
          for(i=1,gmp[j]=0.;i<= nlstate; i++) 
            gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
        }    
        /* end probability of death */
                   
        fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
        for(j=nlstate+1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
          for(i=1; i<=nlstate;i++){
            fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
          }
        } 
        fprintf(ficresprobmorprev,"\n");
                   
        fprintf(ficresvij,"%.0f ",age );
        for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++){
            fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
          }
        fprintf(ficresvij,"\n");
        free_matrix(gp,0,nhstepm,1,nlstate);
        free_matrix(gm,0,nhstepm,1,nlstate);
        free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
        free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      } /* End age */
      free_vector(gpp,nlstate+1,nlstate+ndeath);
      free_vector(gmp,nlstate+1,nlstate+ndeath);
      free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
      free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
      fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
      /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
      fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
      fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
      /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
      /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
      /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
      fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
      fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
      fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
      fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
      fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
      /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.svg\"> <br>\n", stepm,YEARM,digitp,digit);
       */
      /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
      fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
   
      free_vector(xp,1,npar);
      free_matrix(doldm,1,nlstate,1,nlstate);
      free_matrix(dnewm,1,nlstate,1,npar);
      free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
      free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
      fclose(ficresprobmorprev);
      fflush(ficgp);
      fflush(fichtm); 
    }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
    void varprevlim(char fileresvpl[], FILE *ficresvpl, double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[], int nres)
   {
     /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   
     double **dnewmpar,**doldm;
     int i, j, nhstepm, hstepm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mgm, **mgp;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age ");
     if(nresult >=1)
       fprintf(ficresvpl," Result# ");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewmpar=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       mgp=matrix(1,npar,1,nlstate);
       mgm=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
           prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
         else
           prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
         for(i=1;i<=nlstate;i++){
           gp[i] = prlim[i][i];
           mgp[theta][i] = prlim[i][i];
         }
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
           prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
         else
           prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
         for(i=1;i<=nlstate;i++){
           gm[i] = prlim[i][i];
           mgm[theta][i] = prlim[i][i];
         }
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
       /*   printf("\nmgm mgp %d ",(int)age); */
       /*   for(j=1; j<=nlstate;j++){ */
       /*  printf(" %d ",j); */
       /*  for(theta=1; theta <=npar; theta++) */
       /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
       /*  printf("\n "); */
       /*   } */
       /* } */
       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
       /*   printf("\n gradg %d ",(int)age); */
       /*   for(j=1; j<=nlstate;j++){ */
       /*  printf("%d ",j); */
       /*  for(theta=1; theta <=npar; theta++) */
       /*    printf("%d %lf ",theta,gradg[theta][j]); */
       /*  printf("\n "); */
       /*   } */
       /* } */
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       if((int)age==79 ||(int)age== 80  ||(int)age== 81){
       matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
       }else{
       matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
       }
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       if(nresult >=1)
         fprintf(ficresvpl,"%d ",nres );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(mgm,1,npar,1,nlstate);
       free_matrix(mgp,1,npar,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewmpar,1,nlstate,1,nlstate);
   
   }
   
   
   /************ Variance of backprevalence limit ******************/
    void varbrevlim(char fileresvbl[], FILE  *ficresvbl, double **varbpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **bprlim, double ftolpl, int mobilavproj, int *ncvyearp, int ij, char strstart[], int nres)
   {
     /* Variance of backward prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   
     double **dnewmpar,**doldm;
     int i, j, nhstepm, hstepm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mgm, **mgp;
     double age,agelim;
     int theta;
     
     pstamp(ficresvbl);
     fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
     fprintf(ficresvbl,"# Age ");
     if(nresult >=1)
       fprintf(ficresvbl," Result# ");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvbl," %1d-%1d",i,i);
     fprintf(ficresvbl,"\n");
   
     xp=vector(1,npar);
     dnewmpar=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGEINF;
     for (age=fage; age>=bage; age --){ /* If stepm=6 months */
       nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       mgp=matrix(1,npar,1,nlstate);
       mgm=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         if(mobilavproj > 0 )
           bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
         else
           bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
         for(i=1;i<=nlstate;i++){
           gp[i] = bprlim[i][i];
           mgp[theta][i] = bprlim[i][i];
         }
        for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
          if(mobilavproj > 0 )
           bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
          else
           bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
         for(i=1;i<=nlstate;i++){
           gm[i] = bprlim[i][i];
           mgm[theta][i] = bprlim[i][i];
         }
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
       /*   printf("\nmgm mgp %d ",(int)age); */
       /*   for(j=1; j<=nlstate;j++){ */
       /*  printf(" %d ",j); */
       /*  for(theta=1; theta <=npar; theta++) */
       /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
       /*  printf("\n "); */
       /*   } */
       /* } */
       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
       /*   printf("\n gradg %d ",(int)age); */
       /*   for(j=1; j<=nlstate;j++){ */
       /*  printf("%d ",j); */
       /*  for(theta=1; theta <=npar; theta++) */
       /*    printf("%d %lf ",theta,gradg[theta][j]); */
       /*  printf("\n "); */
       /*   } */
       /* } */
   
       for(i=1;i<=nlstate;i++)
         varbpl[i][(int)age] =0.;
       if((int)age==79 ||(int)age== 80  ||(int)age== 81){
       matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
       }else{
       matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
       }
       for(i=1;i<=nlstate;i++)
         varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvbl,"%.0f ",age );
       if(nresult >=1)
         fprintf(ficresvbl,"%d ",nres );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
       fprintf(ficresvbl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(mgm,1,npar,1,nlstate);
       free_matrix(mgp,1,npar,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewmpar,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
    {
      int i, j=0,  k1, l1, tj;
      int k2, l2, j1,  z1;
      int k=0, l;
      int first=1, first1, first2;
      double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
      double **dnewm,**doldm;
      double *xp;
      double *gp, *gm;
      double **gradg, **trgradg;
      double **mu;
      double age, cov[NCOVMAX+1];
      double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
      int theta;
      char fileresprob[FILENAMELENGTH];
      char fileresprobcov[FILENAMELENGTH];
      char fileresprobcor[FILENAMELENGTH];
      double ***varpij;
   
      strcpy(fileresprob,"PROB_"); 
      strcat(fileresprob,fileres);
      if((ficresprob=fopen(fileresprob,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprob);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
      }
      strcpy(fileresprobcov,"PROBCOV_"); 
      strcat(fileresprobcov,fileresu);
      if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobcov);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
      }
      strcpy(fileresprobcor,"PROBCOR_"); 
      strcat(fileresprobcor,fileresu);
      if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobcor);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
      }
      printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
      fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
      printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      pstamp(ficresprob);
      fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
      fprintf(ficresprob,"# Age");
      pstamp(ficresprobcov);
      fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
      fprintf(ficresprobcov,"# Age");
      pstamp(ficresprobcor);
      fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
      fprintf(ficresprobcor,"# Age");
   
   
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprob," p%1d-%1d (SE)",i,j);
          fprintf(ficresprobcov," p%1d-%1d ",i,j);
          fprintf(ficresprobcor," p%1d-%1d ",i,j);
        }  
      /* fprintf(ficresprob,"\n");
         fprintf(ficresprobcov,"\n");
         fprintf(ficresprobcor,"\n");
      */
      xp=vector(1,npar);
      dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
      varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
      first=1;
      fprintf(ficgp,"\n# Routine varprob");
      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
      fprintf(fichtm,"\n");
   
      fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. %s</li>\n",optionfilehtmcov,optionfilehtmcov);
      fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
      fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
      fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
      cov[1]=1;
      /* tj=cptcoveff; */
      tj = (int) pow(2,cptcoveff);
      if (cptcovn<1) {tj=1;ncodemax[1]=1;}
      j1=0;
      for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates or only once*/
        if  (cptcovn>0) {
          fprintf(ficresprob, "\n#********** Variable "); 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
          fprintf(ficresprob, "**********\n#\n");
          fprintf(ficresprobcov, "\n#********** Variable "); 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
          fprintf(ficresprobcov, "**********\n#\n");
                           
          fprintf(ficgp, "\n#********** Variable "); 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
          fprintf(ficgp, "**********\n#\n");
                           
                           
          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
                           
          fprintf(ficresprobcor, "\n#********** Variable ");    
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
          fprintf(ficresprobcor, "**********\n#");    
          if(invalidvarcomb[j1]){
            fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1); 
            fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1); 
            continue;
          }
        }
        gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
        trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
        gp=vector(1,(nlstate)*(nlstate+ndeath));
        gm=vector(1,(nlstate)*(nlstate+ndeath));
        for (age=bage; age<=fage; age ++){ 
          cov[2]=age;
          if(nagesqr==1)
            cov[3]= age*age;
          for (k=1; k<=cptcovn;k++) {
            cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
            /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
                                                                       * 1  1 1 1 1
                                                                       * 2  2 1 1 1
                                                                       * 3  1 2 1 1
                                                                       */
            /* nbcode[1][1]=0 nbcode[1][2]=1;*/
          }
          /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
          for (k=1; k<=cptcovprod;k++)
            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
                           
                           
          for(theta=1; theta <=npar; theta++){
            for(i=1; i<=npar; i++)
              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
                                   
            pmij(pmmij,cov,ncovmodel,xp,nlstate);
                                   
            k=0;
            for(i=1; i<= (nlstate); i++){
              for(j=1; j<=(nlstate+ndeath);j++){
                k=k+1;
                gp[k]=pmmij[i][j];
              }
            }
                                   
            for(i=1; i<=npar; i++)
              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
                                   
            pmij(pmmij,cov,ncovmodel,xp,nlstate);
            k=0;
            for(i=1; i<=(nlstate); i++){
              for(j=1; j<=(nlstate+ndeath);j++){
                k=k+1;
                gm[k]=pmmij[i][j];
              }
            }
                                   
            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
          }
   
          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
            for(theta=1; theta <=npar; theta++)
              trgradg[j][theta]=gradg[theta][j];
                           
          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
                           
          pmij(pmmij,cov,ncovmodel,x,nlstate);
                           
          k=0;
          for(i=1; i<=(nlstate); i++){
            for(j=1; j<=(nlstate+ndeath);j++){
              k=k+1;
              mu[k][(int) age]=pmmij[i][j];
            }
          }
          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
              varpij[i][j][(int)age] = doldm[i][j];
                           
          /*printf("\n%d ",(int)age);
            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
            }*/
                           
          fprintf(ficresprob,"\n%d ",(int)age);
          fprintf(ficresprobcov,"\n%d ",(int)age);
          fprintf(ficresprobcor,"\n%d ",(int)age);
                           
          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
          }
          i=0;
          for (k=1; k<=(nlstate);k++){
            for (l=1; l<=(nlstate+ndeath);l++){ 
              i++;
              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
              for (j=1; j<=i;j++){
                /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
              }
            }
          }/* end of loop for state */
        } /* end of loop for age */
        free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
        free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
        free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
        free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       
        /* Confidence intervalle of pij  */
        /*
          fprintf(ficgp,"\nunset parametric;unset label");
          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
        */
                   
        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
        first1=1;first2=2;
        for (k2=1; k2<=(nlstate);k2++){
          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
            if(l2==k2) continue;
            j=(k2-1)*(nlstate+ndeath)+l2;
            for (k1=1; k1<=(nlstate);k1++){
              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                if(l1==k1) continue;
                i=(k1-1)*(nlstate+ndeath)+l1;
                if(i<=j) continue;
                for (age=bage; age<=fage; age ++){ 
                  if ((int)age %5==0){
                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                    mu1=mu[i][(int) age]/stepm*YEARM ;
                    mu2=mu[j][(int) age]/stepm*YEARM;
                    c12=cv12/sqrt(v1*v2);
                    /* Computing eigen value of matrix of covariance */
                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                    if ((lc2 <0) || (lc1 <0) ){
                      if(first2==1){
                        first1=0;
                        printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                      }
                      fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                      /* lc1=fabs(lc1); */ /* If we want to have them positive */
                      /* lc2=fabs(lc2); */
                    }
                                                                   
                    /* Eigen vectors */
                    if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
                      printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
                      fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
                      v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
                    }else
                      v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                    /*v21=sqrt(1.-v11*v11); *//* error */
                    v21=(lc1-v1)/cv12*v11;
                    v12=-v21;
                    v22=v11;
                    tnalp=v21/v11;
                    if(first1==1){
                      first1=0;
                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                    }
                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                    /*printf(fignu*/
                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                    if(first==1){
                      first=0;
                      fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
                      fprintf(ficgp,"\nset parametric;unset label");
                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                      fprintf(ficgp,"\nset ter svg size 640, 480");
                      fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">                                                                                                                                           \
   %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
                              subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,      \
                              subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                      fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                      fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",      \
                              mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
                              mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
                    }else{
                      first=0;
                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \
                              mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)),   \
                              mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
                    }/* if first */
                  } /* age mod 5 */
                } /* end loop age */
                fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                first=1;
              } /*l12 */
            } /* k12 */
          } /*l1 */
        }/* k1 */
      }  /* loop on combination of covariates j1 */
      free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
      free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
      free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
      free_vector(xp,1,npar);
      fclose(ficresprob);
      fclose(ficresprobcov);
      fclose(ficresprobcor);
      fflush(ficgp);
      fflush(fichtmcov);
    }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \
                     double jprev1, double mprev1,double anprev1, double dateprev1, double dateproj1, double dateback1, \
                     double jprev2, double mprev2,double anprev2, double dateprev2, double dateproj2, double dateback2){
     int jj1, k1, i1, cpt, k4, nres;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li> model=1+age+%s\n \
   </ul>", model);
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
      fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
      fprintf(fichtm,"<li> - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
      fprintf(fichtm,",  <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
      fprintf(fichtm,"\
    - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
      fprintf(fichtm,"\
    - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
      if(prevfcast==1){
        fprintf(fichtm,"\
    - Prevalence projections by age and states:                            \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
      }
   
   
      m=pow(2,cptcoveff);
      if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
      fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
      jj1=0;
   
      fprintf(fichtm," \n<ul>");
      for(nres=1; nres <= nresult; nres++) /* For each resultline */
      for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
        if(m != 1 && TKresult[nres]!= k1)
          continue;
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
          for (cpt=1; cpt<=cptcoveff;cpt++){ 
            fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
          }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
            fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
          }
          fprintf(fichtm,"\">");
          
          /* if(nqfveff+nqtveff 0) */ /* Test to be done */
          fprintf(fichtm,"************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++){ 
            fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
          }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
            fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
          }
          if(invalidvarcomb[k1]){
            fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1); 
            continue;
          }
          fprintf(fichtm,"</a></li>");
        } /* cptcovn >0 */
      }
        fprintf(fichtm," \n</ul>");
   
      jj1=0;
   
      for(nres=1; nres <= nresult; nres++) /* For each resultline */
      for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
        if(m != 1 && TKresult[nres]!= k1)
          continue;
   
        /* for(i1=1; i1<=ncodemax[k1];i1++){ */
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"\n<p><a name=\"rescov");
          for (cpt=1; cpt<=cptcoveff;cpt++){ 
            fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
          }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
            fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
          }
          fprintf(fichtm,"\"</a>");
    
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++){ 
            fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
            printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
            /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
            /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
          }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
         }
          
          /* if(nqfveff+nqtveff 0) */ /* Test to be done */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
          if(invalidvarcomb[k1]){
            fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1); 
            printf("\nCombination (%d) ignored because no cases \n",k1); 
            continue;
          }
        }
        /* aij, bij */
        fprintf(fichtm,"<br>- Logit model (yours is: logit(pij)=log(pij/pii)= aij+ bij age+%s) as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \
   <img src=\"%s_%d-1-%d.svg\">",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
        /* Pij */
        fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2-%d.svg\">%s_%d-2-%d.svg</a><br> \
   <img src=\"%s_%d-2-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
    incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \
   divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3-%d.svg\">%s_%d-3-%d.svg</a><br> \
   <img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres); 
        /* Survival functions (period) in state j */
        for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
   <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
        }
        /* State specific survival functions (period) */
        for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
    Or probability to survive in various states (1 to %d) being in state %d at different ages.     \
    <a href=\"%s_%d-%d-%d.svg\">%s_%d%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
        }
        /* Period (stable) prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
   <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
        }
        if(backcast==1){
          /* Period (stable) back prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
   <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
          }
        }
        if(prevfcast==1){
          /* Projection of prevalence up to period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
   <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateproj1, dateproj2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
          }
        }
        if(backcast==1){
         /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
    from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \
    account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \
   with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
    <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
          }
        }
            
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a> <br> \
   <img src=\"%s_%d-%d-%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
        }
        /* } /\* end i1 *\/ */
      }/* End k1 */
      fprintf(fichtm,"</ul>");
   
      fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
    - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
   But because parameters are usually highly correlated (a higher incidence of disability \
   and a higher incidence of recovery can give very close observed transition) it might \
   be very useful to look not only at linear confidence intervals estimated from the \
   variances but at the covariance matrix. And instead of looking at the estimated coefficients \
   (parameters) of the logistic regression, it might be more meaningful to visualize the \
   covariance matrix of the one-step probabilities. \
   See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
   
      fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
      fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
   
      fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
      fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
      fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
      fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
              estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
      fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
              estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
      fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
              subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
      fflush(fichtm);
      fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
      m=pow(2,cptcoveff);
      if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
      jj1=0;
   
      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
      for(k1=1; k1<=m;k1++){
        if(m != 1 && TKresult[nres]!= k1)
          continue;
        /* for(i1=1; i1<=ncodemax[k1];i1++){ */
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++)  /**< cptcoveff number of variables */
            fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
            /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }
   
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   
          if(invalidvarcomb[k1]){
            fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1); 
            continue;
          }
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>\n <br>\
   <img src=\"%s_%d-%d-%d.svg\">",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences:  <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\
   <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
        /* } /\* end i1 *\/ */
      }/* End k1 */
     }/* End nres */
      fprintf(fichtm,"</ul>");
      fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int backcast, char pathc[], double p[], int offyear, int offbyear){
   
     char dirfileres[132],optfileres[132];
     char gplotcondition[132], gplotlabel[132];
     int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;
     int lv=0, vlv=0, kl=0;
     int ng=0;
     int vpopbased;
     int ioffset; /* variable offset for columns */
     int iyearc=1; /* variable column for year of projection  */
     int iagec=1; /* variable column for age of projection  */
     int nres=0; /* Index of resultline */
     int istart=1; /* For starting graphs in projections */
   
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
     /*#endif */
     m=pow(2,cptcoveff);
   
     /* diagram of the model */
     fprintf(ficgp,"\n#Diagram of the model \n");
     fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
     fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
     fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i*10+j from cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.95*(cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0) - cos(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta2:0)), -0.95*(sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) - sin(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
   
     fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] arrow (%d+1)*10+i from cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.80*(cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0)  ), -0.80*(sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
     fprintf(ficgp,"\n#show arrow\nunset label\n");
     fprintf(ficgp,"\n#States labels, starting from 2 (2-i) instead of (1-i), was (i-1)\nset for [i=1:%d] label i sprintf(\"State %%d\",i) center at cos(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)), yoff+sin(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)) font \"helvetica, 16\" tc rgbcolor \"blue\"\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
     fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0.  font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
     fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
     fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
     fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
   
     /* Contribution to likelihood */
     /* Plot the probability implied in the likelihood */
     fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
     /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
     fprintf(ficgp,"\nset ter pngcairo size 640, 480");
   /* nice for mle=4 plot by number of matrix products.
      replot  "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
   /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)"  */
     /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
     fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
     fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
     fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
     fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
     for (i=1; i<= nlstate ; i ++) {
       fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
       fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot  \"%s\"",subdirf(fileresilk));
       fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
       for (j=2; j<= nlstate+ndeath ; j ++) {
         fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
       }
       fprintf(ficgp,";\nset out; unset ylabel;\n"); 
     }
     /* unset log; plot  "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u  2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */                
     /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
     /* fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
     fprintf(ficgp,"\nset out;unset log\n");
     /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
       for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
         for(nres=1; nres <= nresult; nres++){ /* For each resultline */
           /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
           if(m != 1 && TKresult[nres]!= k1)
             continue;
           /* We are interested in selected combination by the resultline */
           /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
           fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
           strcpy(gplotlabel,"(");
           for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
             lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
             /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
             /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
             vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
             /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
             /* printf(" V%d=%d ",Tvaraff[k],vlv); */
             fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
           }
           for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
             /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
             fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           }
           strcpy(gplotlabel+strlen(gplotlabel),")");
           /* printf("\n#\n"); */
           fprintf(ficgp,"\n#\n");
           if(invalidvarcomb[k1]){
             /*k1=k1-1;*/ /* To be checked */
             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
             continue;
           }
         
           fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
           fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
           /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
           fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
           fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
           /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
         /* k1-1 error should be nres-1*/
           for (i=1; i<= nlstate ; i ++) {
             if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
             else        fprintf(ficgp," %%*lf (%%*lf)");
           }
           fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
           for (i=1; i<= nlstate ; i ++) {
             if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
             else fprintf(ficgp," %%*lf (%%*lf)");
           } 
           fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres); 
           for (i=1; i<= nlstate ; i ++) {
             if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
             else fprintf(ficgp," %%*lf (%%*lf)");
           }  
           /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
           
           fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
           if(cptcoveff ==0){
             fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3",      2+3*(cpt-1),  cpt );
           }else{
             kl=0;
             for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
               vlv= nbcode[Tvaraff[k]][lv];
               kl++;
               /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
               /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
               /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
               /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
               if(k==cptcoveff){
                 fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
                         2+cptcoveff*2+3*(cpt-1),  cpt );  /* 4 or 6 ?*/
               }else{
                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
                 kl++;
               }
             } /* end covariate */
           } /* end if no covariate */
   
           if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
             /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
             fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
             if(cptcoveff ==0){
               fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3",    2+(cpt-1),  cpt );
             }else{
               kl=0;
               for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                 vlv= nbcode[Tvaraff[k]][lv];
                 kl++;
                 /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
                 /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
                 /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
                 /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
                 if(k==cptcoveff){
                   fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
                           2+cptcoveff*2+(cpt-1),  cpt );  /* 4 or 6 ?*/
                 }else{
                   fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
                   kl++;
                 }
               } /* end covariate */
             } /* end if no covariate */
             if(backcast == 1){
               fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
               /* k1-1 error should be nres-1*/
               for (i=1; i<= nlstate ; i ++) {
                 if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                 else        fprintf(ficgp," %%*lf (%%*lf)");
               }
               fprintf(ficgp,"\" t\"Backward (stable) prevalence\" w l lt 6 dt 3,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
               for (i=1; i<= nlstate ; i ++) {
                 if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                 else fprintf(ficgp," %%*lf (%%*lf)");
               } 
               fprintf(ficgp,"\" t\"95%% CI\" w l lt 4,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres); 
               for (i=1; i<= nlstate ; i ++) {
                 if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                 else fprintf(ficgp," %%*lf (%%*lf)");
               } 
               fprintf(ficgp,"\" t\"\" w l lt 4");
             } /* end if backprojcast */
           } /* end if backcast */
           /* fprintf(ficgp,"\nset out ;unset label;\n"); */
           fprintf(ficgp,"\nset out ;unset title;\n");
         } /* nres */
       } /* k1 */
     } /* cpt */
   
     
     /*2 eme*/
     for (k1=1; k1<= m ; k1 ++){  
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(m != 1 && TKresult[nres]!= k1)
           continue;
         fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
         strcpy(gplotlabel,"(");
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv];
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
         }
         /* for(k=1; k <= ncovds; k++){ */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }
         strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){
           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
           continue;
         }
                           
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
           fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
           if(vpopbased==0){
             fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
           }else
             fprintf(ficgp,"\nreplot ");
           for (i=1; i<= nlstate+1 ; i ++) {
             k=2*i;
             fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased);
             for (j=1; j<= nlstate+1 ; j ++) {
               if (j==i) fprintf(ficgp," %%lf (%%lf)");
               else fprintf(ficgp," %%*lf (%%*lf)");
             }   
             if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
             else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
             fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
             for (j=1; j<= nlstate+1 ; j ++) {
               if (j==i) fprintf(ficgp," %%lf (%%lf)");
               else fprintf(ficgp," %%*lf (%%*lf)");
             }   
             fprintf(ficgp,"\" t\"\" w l lt 0,");
             fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
             for (j=1; j<= nlstate+1 ; j ++) {
               if (j==i) fprintf(ficgp," %%lf (%%lf)");
               else fprintf(ficgp," %%*lf (%%*lf)");
             }   
             if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
             else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
           } /* state */
         } /* vpopbased */
         fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
       } /* end nres */
     } /* k1 end 2 eme*/
           
           
     /*3eme*/
     for (k1=1; k1<= m ; k1 ++){
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(m != 1 && TKresult[nres]!= k1)
           continue;
   
         for (cpt=1; cpt<= nlstate ; cpt ++) {
           fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);
           strcpy(gplotlabel,"(");
           for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
             lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
             /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
             /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
             vlv= nbcode[Tvaraff[k]][lv];
             fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
           }
           for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
             fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           }       
           strcpy(gplotlabel+strlen(gplotlabel),")");
           fprintf(ficgp,"\n#\n");
           if(invalidvarcomb[k1]){
             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
             continue;
           }
                           
           /*       k=2+nlstate*(2*cpt-2); */
           k=2+(nlstate+1)*(cpt-1);
           fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
           fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
           fprintf(ficgp,"set ter svg size 640, 480\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),nres-1,nres-1,k,cpt);
           /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
             for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
             fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
             fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
             for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
             fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                                   
           */
           for (i=1; i< nlstate ; i ++) {
             fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+i,cpt,i+1);
             /*    fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
                                   
           } 
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+nlstate,cpt);
         }
         fprintf(ficgp,"\nunset label;\n");
       } /* end nres */
     } /* end kl 3eme */
     
     /* 4eme */
     /* Survival functions (period) from state i in state j by initial state i */
     for (k1=1; k1<=m; k1++){    /* For each covariate and each value */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(m != 1 && TKresult[nres]!= k1)
           continue;
         for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
           strcpy(gplotlabel,"(");
           fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
           for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
             lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
             /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
             /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
             vlv= nbcode[Tvaraff[k]][lv];
             fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
           }
           for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
             fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           }       
           strcpy(gplotlabel+strlen(gplotlabel),")");
           fprintf(ficgp,"\n#\n");
           if(invalidvarcomb[k1]){
             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
             continue;
           }
         
           fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
           fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
           fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
   set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
           k=3;
           for (i=1; i<= nlstate ; i ++){
             if(i==1){
               fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
             }else{
               fprintf(ficgp,", '' ");
             }
             l=(nlstate+ndeath)*(i-1)+1;
             fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
             for (j=2; j<= nlstate+ndeath ; j ++)
               fprintf(ficgp,"+$%d",k+l+j-1);
             fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
           } /* nlstate */
           fprintf(ficgp,"\nset out; unset label;\n");
         } /* end cpt state*/ 
       } /* end nres */
     } /* end covariate k1 */  
   
   /* 5eme */
     /* Survival functions (period) from state i in state j by final state j */
     for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(m != 1 && TKresult[nres]!= k1)
           continue;
         for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
           strcpy(gplotlabel,"(");
           fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
           for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
             lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
             /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
             /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
             vlv= nbcode[Tvaraff[k]][lv];
             fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
           }
           for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
             fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           }       
           strcpy(gplotlabel+strlen(gplotlabel),")");
           fprintf(ficgp,"\n#\n");
           if(invalidvarcomb[k1]){
             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
             continue;
           }
         
           fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
           fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
           fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
   set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
           k=3;
           for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
             if(j==1)
               fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
             else
               fprintf(ficgp,", '' ");
             l=(nlstate+ndeath)*(cpt-1) +j;
             fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
             /* for (i=2; i<= nlstate+ndeath ; i ++) */
             /*   fprintf(ficgp,"+$%d",k+l+i-1); */
             fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
           } /* nlstate */
           fprintf(ficgp,", '' ");
           fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
           for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
             l=(nlstate+ndeath)*(cpt-1) +j;
             if(j < nlstate)
               fprintf(ficgp,"$%d +",k+l);
             else
               fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
           }
           fprintf(ficgp,"\nset out; unset label;\n");
         } /* end cpt state*/ 
       } /* end covariate */  
     } /* end nres */
     
   /* 6eme */
     /* CV preval stable (period) for each covariate */
     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)
         continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
         strcpy(gplotlabel,"(");      
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv];
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
         }
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         } 
         strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){
           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
           continue;
         }
         
         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
         fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
         k=3; /* Offset */
         for (i=1; i<= nlstate ; i ++){ /* State of origin */
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=2; j<= nlstate ; j ++)
             fprintf(ficgp,"+$%d",k+l+j-1);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\nset out; unset label;\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     
   /* 7eme */
     if(backcast == 1){
       /* CV back preval stable (period) for each covariate */
       for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(m != 1 && TKresult[nres]!= k1)
           continue;
         for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
           strcpy(gplotlabel,"(");      
           fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
           for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
             lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
             /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
             /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
             vlv= nbcode[Tvaraff[k]][lv];
             fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
           }
           for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
             fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           }       
           strcpy(gplotlabel+strlen(gplotlabel),")");
           fprintf(ficgp,"\n#\n");
           if(invalidvarcomb[k1]){
             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
             continue;
           }
           
           fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
           fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
           fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
           k=3; /* Offset */
           for (i=1; i<= nlstate ; i ++){ /* State of arrival */
             if(i==1)
               fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
             else
               fprintf(ficgp,", '' ");
             /* l=(nlstate+ndeath)*(i-1)+1; */
             l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
             /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
             /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
             fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
             /* for (j=2; j<= nlstate ; j ++) */
             /*    fprintf(ficgp,"+$%d",k+l+j-1); */
             /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
             fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
           } /* nlstate */
           fprintf(ficgp,"\nset out; unset label;\n");
         } /* end cpt state*/ 
       } /* end covariate */  
     } /* End if backcast */
     
     /* 8eme */
     if(prevfcast==1){
       /* Projection from cross-sectional to stable (period) for each covariate */
       
       for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(m != 1 && TKresult[nres]!= k1)
           continue;
         for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
           strcpy(gplotlabel,"(");      
           fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
           for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
             lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
             /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
             /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
             vlv= nbcode[Tvaraff[k]][lv];
             fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
           }
           for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
             fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           }       
           strcpy(gplotlabel+strlen(gplotlabel),")");
           fprintf(ficgp,"\n#\n");
           if(invalidvarcomb[k1]){
             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
             continue;
           }
           
           fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
           fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
           fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
           fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
   set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
   
           /* for (i=1; i<= nlstate+1 ; i ++){  /\* nlstate +1 p11 p21 p.1 *\/ */
           istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
           /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
           for (i=istart; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
             /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
             /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
             /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
             /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
             if(i==istart){
               fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
             }else{
               fprintf(ficgp,",\\\n '' ");
             }
             if(cptcoveff ==0){ /* No covariate */
               ioffset=2; /* Age is in 2 */
               /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
               /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
               /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
               /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
               fprintf(ficgp," u %d:(", ioffset); 
               if(i==nlstate+1){
                 fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ",        \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
                 fprintf(ficgp,",\\\n '' ");
                 fprintf(ficgp," u %d:(",ioffset); 
                 fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
                        offyear,                           \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate );
               }else
                 fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",      \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
             }else{ /* more than 2 covariates */
               ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
               /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
               /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
               iyearc=ioffset-1;
               iagec=ioffset;
               fprintf(ficgp," u %d:(",ioffset); 
               kl=0;
               strcpy(gplotcondition,"(");
               for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                 vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
                 kl++;
                 sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
                 kl++;
                 if(k <cptcoveff && cptcoveff>1)
                   sprintf(gplotcondition+strlen(gplotcondition)," && ");
               }
               strcpy(gplotcondition+strlen(gplotcondition),")");
               /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
               /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
               /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
               /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
               if(i==nlstate+1){
                 fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
                 fprintf(ficgp,",\\\n '' ");
                 fprintf(ficgp," u %d:(",iagec); 
                 fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
                         iyearc, iagec, offyear,                           \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
   /*  '' u 6:(($1==1 && $2==0  && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
               }else{
                 fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
               }
             } /* end if covariate */
           } /* nlstate */
           fprintf(ficgp,"\nset out; unset label;\n");
         } /* end cpt state*/
       } /* end covariate */
     } /* End if prevfcast */
     
     if(backcast==1){
       /* Back projection from cross-sectional to stable (mixed) for each covariate */
       
       for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(m != 1 && TKresult[nres]!= k1)
           continue;
         for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
           strcpy(gplotlabel,"(");      
           fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
           for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
             lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
             /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
             /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
             vlv= nbcode[Tvaraff[k]][lv];
             fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
           }
           for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
             fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           }       
           strcpy(gplotlabel+strlen(gplotlabel),")");
           fprintf(ficgp,"\n#\n");
           if(invalidvarcomb[k1]){
             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
             continue;
           }
           
           fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
           fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
           fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
           fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
   set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
   
           /* for (i=1; i<= nlstate+1 ; i ++){  /\* nlstate +1 p11 p21 p.1 *\/ */
           istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
           /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
           for (i=istart; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
             /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
             /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
             /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
             /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
             if(i==istart){
               fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
             }else{
               fprintf(ficgp,",\\\n '' ");
             }
             if(cptcoveff ==0){ /* No covariate */
               ioffset=2; /* Age is in 2 */
               /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
               /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
               /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
               /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
               fprintf(ficgp," u %d:(", ioffset); 
               if(i==nlstate+1){
                 fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
                 fprintf(ficgp,",\\\n '' ");
                 fprintf(ficgp," u %d:(",ioffset); 
                 fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
                        offbyear,                          \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
               }else
                 fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ",      \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
             }else{ /* more than 2 covariates */
               ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
               /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
               /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
               iyearc=ioffset-1;
               iagec=ioffset;
               fprintf(ficgp," u %d:(",ioffset); 
               kl=0;
               strcpy(gplotcondition,"(");
               for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                 vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
                 kl++;
                 sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
                 kl++;
                 if(k <cptcoveff && cptcoveff>1)
                   sprintf(gplotcondition+strlen(gplotcondition)," && ");
               }
               strcpy(gplotcondition+strlen(gplotcondition),")");
               /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
               /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
               /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
               /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
               if(i==nlstate+1){
                 fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
                 fprintf(ficgp,",\\\n '' ");
                 fprintf(ficgp," u %d:(",iagec); 
                 /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
                 fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
                         iyearc,iagec,offbyear,                            \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
   /*  '' u 6:(($1==1 && $2==0  && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
               }else{
                 /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
                 fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
               }
             } /* end if covariate */
           } /* nlstate */
           fprintf(ficgp,"\nset out; unset label;\n");
         } /* end cpt state*/
       } /* end covariate */
     } /* End if backcast */
     
     
     /* 9eme writing MLE parameters */
     fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
     for(i=1,jk=1; i <=nlstate; i++){
       fprintf(ficgp,"# initial state %d\n",i);
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           fprintf(ficgp,"#   current state %d\n",k);
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
             jk++; 
           }
           fprintf(ficgp,"\n");
         }
       }
     }
     fprintf(ficgp,"##############\n#\n");
     
     /*goto avoid;*/
     /* 10eme Graphics of probabilities or incidences using written MLE parameters */
     fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
     fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
     fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
     fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
     fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
     fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
     fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
     fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
     fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
     fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
     fprintf(ficgp,"#\n");
     for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
       fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
       fprintf(ficgp,"#model=%s \n",model);
       fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
       fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
       for(k1=1; k1 <=m; k1++)  /* For each combination of covariate */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(m != 1 && TKresult[nres]!= k1)
           continue;
         fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1);
         strcpy(gplotlabel,"(");
         /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
         for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv];
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
         }
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         } 
         strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");
         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
         fprintf(ficgp,"\nset key outside ");
         /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
         fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
         fprintf(ficgp,"\nset ter svg size 640, 480 ");
         if (ng==1){
           fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
           fprintf(ficgp,"\nunset log y");
         }else if (ng==2){
           fprintf(ficgp,"\nset ylabel \"Probability\"\n");
           fprintf(ficgp,"\nset log y");
         }else if (ng==3){
           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
           fprintf(ficgp,"\nset log y");
         }else
           fprintf(ficgp,"\nunset title ");
         fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
         i=1;
         for(k2=1; k2<=nlstate; k2++) {
           k3=i;
           for(k=1; k<=(nlstate+ndeath); k++) {
             if (k != k2){
               switch( ng) {
               case 1:
                 if(nagesqr==0)
                   fprintf(ficgp," p%d+p%d*x",i,i+1);
                 else /* nagesqr =1 */
                   fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                 break;
               case 2: /* ng=2 */
                 if(nagesqr==0)
                   fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                 else /* nagesqr =1 */
                   fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                 break;
               case 3:
                 if(nagesqr==0)
                   fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                 else /* nagesqr =1 */
                   fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
                 break;
               }
               ij=1;/* To be checked else nbcode[0][0] wrong */
               ijp=1; /* product no age */
               /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
               for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
                 /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
                 if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
                   if(j==Tage[ij]) { /* Product by age  To be looked at!!*/
                     if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
                       if(DummyV[j]==0){
                         fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
                       }else{ /* quantitative */
                         fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
                         /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                       }
                       ij++;
                     }
                   } 
                 }else if(cptcovprod >0){
                   if(j==Tprod[ijp]) { /* */ 
                     /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
                     if(ijp <=cptcovprod) { /* Product */
                       if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
                         if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
                           /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
                           fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
                         }else{ /* Vn is dummy and Vm is quanti */
                           /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
                           fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                         }
                       }else{ /* Vn*Vm Vn is quanti */
                         if(DummyV[Tvard[ijp][2]]==0){
                           fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
                         }else{ /* Both quanti */
                           fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                         }
                       }
                       ijp++;
                     }
                   } /* end Tprod */
                 } else{  /* simple covariate */
                   /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
                   if(Dummy[j]==0){
                     fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /*  */
                   }else{ /* quantitative */
                     fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
                     /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                   }
                 } /* end simple */
               } /* end j */
             }else{
               i=i-ncovmodel;
               if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
                 fprintf(ficgp," (1.");
             }
             
             if(ng != 1){
               fprintf(ficgp,")/(1");
               
               for(cpt=1; cpt <=nlstate; cpt++){ 
                 if(nagesqr==0)
                   fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
                 else /* nagesqr =1 */
                   fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1,k3+(cpt-1)*ncovmodel+1+nagesqr);
                  
                 ij=1;
                 for(j=3; j <=ncovmodel-nagesqr; j++){
                    if(cptcovage >0){ 
                      if((j-2)==Tage[ij]) { /* Bug valgrind */
                        if(ij <=cptcovage) { /* Bug valgrind */
                          fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
                          /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                          ij++;
                        }
                      }
                    }else
                      fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */
                 }
                 fprintf(ficgp,")");
               }
               fprintf(ficgp,")");
               if(ng ==2)
                 fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
               else /* ng= 3 */
                 fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
             }else{ /* end ng <> 1 */
               if( k !=k2) /* logit p11 is hard to draw */
                 fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
             }
             if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
               fprintf(ficgp,",");
             if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
               fprintf(ficgp,",");
             i=i+ncovmodel;
           } /* end k */
         } /* end k2 */
         /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
         fprintf(ficgp,"\n set out; unset title;set key default;\n");
       } /* end k1 */
     } /* end ng */
     /* avoid: */
     fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
    int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
      
      int i, cpt, cptcod;
      int modcovmax =1;
      int mobilavrange, mob;
      int iage=0;
   
      double sum=0., sumr=0.;
      double age;
      double *sumnewp, *sumnewm, *sumnewmr;
      double *agemingood, *agemaxgood; 
      double *agemingoodr, *agemaxgoodr; 
     
     
      /* modcovmax=2*cptcoveff;  Max number of modalities. We suppose  */
      /*              a covariate has 2 modalities, should be equal to ncovcombmax   */
   
      sumnewp = vector(1,ncovcombmax);
      sumnewm = vector(1,ncovcombmax);
      sumnewmr = vector(1,ncovcombmax);
      agemingood = vector(1,ncovcombmax);  
      agemingoodr = vector(1,ncovcombmax); 
      agemaxgood = vector(1,ncovcombmax);
      agemaxgoodr = vector(1,ncovcombmax);
   
      for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
        sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
        sumnewp[cptcod]=0.;
        agemingood[cptcod]=0, agemingoodr[cptcod]=0;
        agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
      }
      if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
     
      if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
        if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */
        else mobilavrange=mobilav;
        for (age=bage; age<=fage; age++)
          for (i=1; i<=nlstate;i++)
            for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
              mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
        /* We keep the original values on the extreme ages bage, fage and for 
           fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
           we use a 5 terms etc. until the borders are no more concerned. 
        */ 
        for (mob=3;mob <=mobilavrange;mob=mob+2){
          for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
            for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
              sumnewm[cptcod]=0.;
              for (i=1; i<=nlstate;i++){
                mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                for (cpt=1;cpt<=(mob-1)/2;cpt++){
                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                }
                mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
                sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
              } /* end i */
              if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
            } /* end cptcod */
          }/* end age */
        }/* end mob */
      }else{
        printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
        return -1;
      }
   
      for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
        /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
        if(invalidvarcomb[cptcod]){
          printf("\nCombination (%d) ignored because no cases \n",cptcod); 
          continue;
        }
   
        for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
          sumnewm[cptcod]=0.;
          sumnewmr[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
            sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
          }
          if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
            agemingoodr[cptcod]=age;
          }
          if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
              agemingood[cptcod]=age;
          }
        } /* age */
        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
          sumnewm[cptcod]=0.;
          sumnewmr[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
            sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
          }
          if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
            agemaxgoodr[cptcod]=age;
          }
          if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
            agemaxgood[cptcod]=age;
          }
        } /* age */
        /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
        /* but they will change */
        for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
          sumnewm[cptcod]=0.;
          sumnewmr[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
            sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
          }
          if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
            if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
              agemaxgoodr[cptcod]=age;  /* age min */
              for (i=1; i<=nlstate;i++)
                mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
            }else{ /* bad we change the value with the values of good ages */
              for (i=1; i<=nlstate;i++){
                mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
              } /* i */
            } /* end bad */
          }else{
            if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
              agemaxgood[cptcod]=age;
            }else{ /* bad we change the value with the values of good ages */
              for (i=1; i<=nlstate;i++){
                mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
              } /* i */
            } /* end bad */
          }/* end else */
          sum=0.;sumr=0.;
          for (i=1; i<=nlstate;i++){
            sum+=mobaverage[(int)age][i][cptcod];
            sumr+=probs[(int)age][i][cptcod];
          }
          if(fabs(sum - 1.) > 1.e-3) { /* bad */
            printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
          } /* end bad */
          /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
          if(fabs(sumr - 1.) > 1.e-3) { /* bad */
            printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
          } /* end bad */
        }/* age */
   
        for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
          sumnewm[cptcod]=0.;
          sumnewmr[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
            sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
          } 
          if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
            if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
              agemingoodr[cptcod]=age;
              for (i=1; i<=nlstate;i++)
                mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
            }else{ /* bad we change the value with the values of good ages */
              for (i=1; i<=nlstate;i++){
                mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
              } /* i */
            } /* end bad */
          }else{
            if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
              agemingood[cptcod]=age;
            }else{ /* bad */
              for (i=1; i<=nlstate;i++){
                mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
              } /* i */
            } /* end bad */
          }/* end else */
          sum=0.;sumr=0.;
          for (i=1; i<=nlstate;i++){
            sum+=mobaverage[(int)age][i][cptcod];
            sumr+=mobaverage[(int)age][i][cptcod];
          }
          if(fabs(sum - 1.) > 1.e-3) { /* bad */
            printf("Moving average B1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you decrease fage=%d?\n",cptcod, sum, (int) age, (int)fage);
          } /* end bad */
          /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
          if(fabs(sumr - 1.) > 1.e-3) { /* bad */
            printf("Moving average B2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase fage=%d\n",cptcod,sumr, (int)age, (int)fage);
          } /* end bad */
        }/* age */
   
                   
        for (age=bage; age<=fage; age++){
          /* printf("%d %d ", cptcod, (int)age); */
          sumnewp[cptcod]=0.;
          sumnewm[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewp[cptcod]+=probs[(int)age][i][cptcod];
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
            /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
          }
          /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
        }
        /* printf("\n"); */
        /* } */
   
        /* brutal averaging */
        /* for (i=1; i<=nlstate;i++){ */
        /*   for (age=1; age<=bage; age++){ */
        /*          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
        /*          /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
        /*   }      */
        /*   for (age=fage; age<=AGESUP; age++){ */
        /*          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
        /*          /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
        /*   } */
        /* } /\* end i status *\/ */
        /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
        /*   for (age=1; age<=AGESUP; age++){ */
        /*          /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
        /*          mobaverage[(int)age][i][cptcod]=0.; */
        /*   } */
        /* } */
      }/* end cptcod */
      free_vector(agemaxgoodr,1, ncovcombmax);
      free_vector(agemaxgood,1, ncovcombmax);
      free_vector(agemingood,1, ncovcombmax);
      free_vector(agemingoodr,1, ncovcombmax);
      free_vector(sumnewmr,1, ncovcombmax);
      free_vector(sumnewm,1, ncovcombmax);
      free_vector(sumnewp,1, ncovcombmax);
      return 0;
    }/* End movingaverage */
    
   
   /************** Forecasting ******************/
    void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     /* double ***mobaverage; */
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
     */
     /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
     /*          firstpass, lastpass,  stepm,  weightopt, model); */
    
     strcpy(fileresf,"F_"); 
     strcat(fileresf,fileresu);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
     fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else{
       hstepm=estepm;   
     }
     if(estepm > stepm){ /* Yes every two year */
       stepsize=2;
     }
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=pow(2,cptcoveff);
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
     
   /*            if (h==(int)(YEARM*yearp)){ */
     for(nres=1; nres <= nresult; nres++) /* For each resultline */
     for(k=1; k<=i1;k++){
       if(i1 != 1 && TKresult[nres]!= k)
         continue;
       if(invalidvarcomb[k]){
         printf("\nCombination (%d) projection ignored because no cases \n",k); 
         continue;
       }
       fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
       for(j=1;j<=cptcoveff;j++) {
         fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
         fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
       }
       fprintf(ficresf," yearproj age");
       for(j=1; j<=nlstate+ndeath;j++){ 
         for(i=1; i<=nlstate;i++)        
           fprintf(ficresf," p%d%d",i,j);
         fprintf(ficresf," wp.%d",j);
       }
       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
         fprintf(ficresf,"\n");
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
         /* for (agec=fage; agec>=(ageminpar-1); agec--){  */
         for (agec=fage; agec>=(bage); agec--){ 
           nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
           nhstepm = nhstepm/hstepm; 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           /* We compute pii at age agec over nhstepm);*/
           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
           /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
           for (h=0; h<=nhstepm; h++){
             if (h*hstepm/YEARM*stepm ==yearp) {
               break;
             }
           }
           fprintf(ficresf,"\n");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
           
           for(j=1; j<=nlstate+ndeath;j++) {
             ppij=0.;
             for(i=1; i<=nlstate;i++) {
               if (mobilav>=1)
                ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
               else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
               }
               fprintf(ficresf," %.3f", p3mat[i][j][h]);
             } /* end i */
             fprintf(ficresf," %.3f", ppij);
           }/* end j */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         } /* end agec */
         /* diffyear=(int) anproj1+yearp-ageminpar-1; */
         /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
       } /* end yearp */
     } /* end  k */
           
     fclose(ficresf);
     printf("End of Computing forecasting \n");
     fprintf(ficlog,"End of Computing forecasting\n");
   
   }
   
   /************** Back Forecasting ******************/
    void prevbackforecast(char fileres[], double ***prevacurrent, double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){
     /* back1, year, month, day of starting backection
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anback2 year of end of backprojection (same day and month as back1).
        prevacurrent and prev are prevalences.
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
     double agec; /* generic age */
     double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     /* double ***mobaverage; */
     char fileresfb[FILENAMELENGTH];
    
     agelim=AGEINF;
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
     */
     /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
     /*          firstpass, lastpass,  stepm,  weightopt, model); */
   
     /*Do we need to compute prevalence again?*/
   
     /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
     
     strcpy(fileresfb,"FB_");
     strcat(fileresfb,fileresu);
     if((ficresfb=fopen(fileresfb,"w"))==NULL) {
       printf("Problem with back forecast resultfile: %s\n", fileresfb);
       fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
     }
     printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
     fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
     
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
     
      
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else{
       hstepm=estepm;   
     }
     if(estepm >= stepm){ /* Yes every two year */
       stepsize=2;
     }
     
     hstepm=hstepm/stepm;
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
     
     i1=pow(2,cptcoveff);
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
     printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
     
     fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
     
     for(nres=1; nres <= nresult; nres++) /* For each resultline */
     for(k=1; k<=i1;k++){
       if(i1 != 1 && TKresult[nres]!= k)
         continue;
       if(invalidvarcomb[k]){
         printf("\nCombination (%d) projection ignored because no cases \n",k); 
         continue;
       }
       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
       for(j=1;j<=cptcoveff;j++) {
         fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
         fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
       }
       fprintf(ficresfb," yearbproj age");
       for(j=1; j<=nlstate+ndeath;j++){
         for(i=1; i<=nlstate;i++)
           fprintf(ficresfb," b%d%d",i,j);
         fprintf(ficresfb," b.%d",j);
       }
       for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {
         /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  */
         fprintf(ficresfb,"\n");
         fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);
         /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
         /* for (agec=bage; agec<=agemax-1; agec++){  /\* testing *\/ */
         for (agec=bage; agec<=fage; agec++){  /* testing */
           /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
           nhstepm=(int) (agec-agelim) *YEARM/stepm;/*     nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
           nhstepm = nhstepm/hstepm;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           /* computes hbxij at age agec over 1 to nhstepm */
           /* printf("####prevbackforecast debug  agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
           hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
           /* hpxij(p3mat,nhstepm,agec,hstepm,p,             nlstate,stepm,oldm,savm, k,nres); */
           /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
           /* printf(" agec=%.2f\n",agec);fflush(stdout); */
           for (h=0; h<=nhstepm; h++){
             if (h*hstepm/YEARM*stepm ==-yearp) {
               break;
             }
           }
           fprintf(ficresfb,"\n");
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec-h*hstepm/YEARM*stepm);
           for(i=1; i<=nlstate+ndeath;i++) {
             ppij=0.;ppi=0.;
             for(j=1; j<=nlstate;j++) {
               /* if (mobilav==1) */
               ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
               ppi=ppi+prevacurrent[(int)agec][j][k];
               /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
               /* ppi=ppi+mobaverage[(int)agec][j][k]; */
                 /* else { */
                 /*        ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
                 /* } */
               fprintf(ficresfb," %.3f", p3mat[i][j][h]);
             } /* end j */
             if(ppi <0.99){
               printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
               fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
             }
             fprintf(ficresfb," %.3f", ppij);
           }/* end j */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         } /* end agec */
       } /* end yearp */
     } /* end k */
     
     /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
     
     fclose(ficresfb);
     printf("End of Computing Back forecasting \n");
     fprintf(ficlog,"End of Computing Back forecasting\n");
           
   }
   
   /* Variance of prevalence limit: varprlim */
    void varprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **prlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
       /*------- Variance of period (stable) prevalence------*/   
    
      char fileresvpl[FILENAMELENGTH];  
      FILE *ficresvpl;
      double **oldm, **savm;
      double **varpl; /* Variances of prevalence limits by age */   
      int i1, k, nres, j ;
      
       strcpy(fileresvpl,"VPL_");
       strcat(fileresvpl,fileresu);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
       fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
       
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
       
       i1=pow(2,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       for(nres=1; nres <= nresult; nres++) /* For each resultline */
       for(k=1; k<=i1;k++){
         if(i1 != 1 && TKresult[nres]!= k)
           continue;
         fprintf(ficresvpl,"\n#****** ");
         printf("\n#****** ");
         fprintf(ficlog,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
         } 
         fprintf(ficresvpl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       
       fclose(ficresvpl);
       printf("done variance-covariance of period prevalence\n");fflush(stdout);
       fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
   
    }
   /* Variance of back prevalence: varbprlim */
    void varbprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **bprlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
         /*------- Variance of back (stable) prevalence------*/
   
      char fileresvbl[FILENAMELENGTH];  
      FILE  *ficresvbl;
   
      double **oldm, **savm;
      double **varbpl; /* Variances of back prevalence limits by age */   
      int i1, k, nres, j ;
   
      strcpy(fileresvbl,"VBL_");
      strcat(fileresvbl,fileresu);
      if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
        printf("Problem with variance of back (stable) prevalence  resultfile: %s\n", fileresvbl);
        exit(0);
      }
      printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
      fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
      
      
      i1=pow(2,cptcoveff);
      if (cptcovn < 1){i1=1;}
      
      for(nres=1; nres <= nresult; nres++) /* For each resultline */
        for(k=1; k<=i1;k++){
          if(i1 != 1 && TKresult[nres]!= k)
            continue;
          fprintf(ficresvbl,"\n#****** ");
          printf("\n#****** ");
          fprintf(ficlog,"\n#****** ");
          for(j=1;j<=cptcoveff;j++) {
            fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
            fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
            printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
          }
          for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
            printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
            fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
            fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
          }
          fprintf(ficresvbl,"******\n");
          printf("******\n");
          fprintf(ficlog,"******\n");
          
          varbpl=matrix(1,nlstate,(int) bage, (int) fage);
          oldm=oldms;savm=savms;
          
          varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
          free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
          /*}*/
        }
      
      fclose(ficresvbl);
      printf("done variance-covariance of back prevalence\n");fflush(stdout);
      fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
   
    } /* End of varbprlim */
   
   /************** Forecasting *****not tested NB*************/
   /* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */
     
   /*   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
   /*   int *popage; */
   /*   double calagedatem, agelim, kk1, kk2; */
   /*   double *popeffectif,*popcount; */
   /*   double ***p3mat,***tabpop,***tabpopprev; */
   /*   /\* double ***mobaverage; *\/ */
   /*   char filerespop[FILENAMELENGTH]; */
   
   /*   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   /*   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   /*   agelim=AGESUP; */
   /*   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
     
   /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
     
     
   /*   strcpy(filerespop,"POP_");  */
   /*   strcat(filerespop,fileresu); */
   /*   if((ficrespop=fopen(filerespop,"w"))==NULL) { */
   /*     printf("Problem with forecast resultfile: %s\n", filerespop); */
   /*     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
   /*   } */
   /*   printf("Computing forecasting: result on file '%s' \n", filerespop); */
   /*   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
   
   /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */
   
   /*   /\* if (mobilav!=0) { *\/ */
   /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
   /*   /\*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
   /*   /\*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
   /*   /\*     printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
   /*   /\*   } *\/ */
   /*   /\* } *\/ */
   
   /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */
   /*   if (stepm<=12) stepsize=1; */
     
   /*   agelim=AGESUP; */
     
   /*   hstepm=1; */
   /*   hstepm=hstepm/stepm;  */
           
   /*   if (popforecast==1) { */
   /*     if((ficpop=fopen(popfile,"r"))==NULL) { */
   /*       printf("Problem with population file : %s\n",popfile);exit(0); */
   /*       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
   /*     }  */
   /*     popage=ivector(0,AGESUP); */
   /*     popeffectif=vector(0,AGESUP); */
   /*     popcount=vector(0,AGESUP); */
       
   /*     i=1;    */
   /*     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
       
   /*     imx=i; */
   /*     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
   /*   } */
     
   /*   for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
   /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
   /*       k=k+1; */
   /*       fprintf(ficrespop,"\n#******"); */
   /*       for(j=1;j<=cptcoveff;j++) { */
   /*      fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
   /*       } */
   /*       fprintf(ficrespop,"******\n"); */
   /*       fprintf(ficrespop,"# Age"); */
   /*       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
   /*       if (popforecast==1)  fprintf(ficrespop," [Population]"); */
         
   /*       for (cpt=0; cpt<=0;cpt++) {  */
   /*      fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
           
   /*      for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){  */
   /*        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  */
   /*        nhstepm = nhstepm/hstepm;  */
             
   /*        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
   /*        oldm=oldms;savm=savms; */
   /*        hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
             
   /*        for (h=0; h<=nhstepm; h++){ */
   /*          if (h==(int) (calagedatem+YEARM*cpt)) { */
   /*            fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
   /*          }  */
   /*          for(j=1; j<=nlstate+ndeath;j++) { */
   /*            kk1=0.;kk2=0; */
   /*            for(i=1; i<=nlstate;i++) {               */
   /*              if (mobilav==1)  */
   /*                kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
   /*              else { */
   /*                kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
   /*              } */
   /*            } */
   /*            if (h==(int)(calagedatem+12*cpt)){ */
   /*              tabpop[(int)(agedeb)][j][cptcod]=kk1; */
   /*              /\*fprintf(ficrespop," %.3f", kk1); */
   /*                if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
   /*            } */
   /*          } */
   /*          for(i=1; i<=nlstate;i++){ */
   /*            kk1=0.; */
   /*            for(j=1; j<=nlstate;j++){ */
   /*              kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  */
   /*            } */
   /*            tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
   /*          } */
               
   /*          if (h==(int)(calagedatem+12*cpt)) */
   /*            for(j=1; j<=nlstate;j++)  */
   /*              fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
   /*        } */
   /*        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
   /*      } */
   /*       } */
         
   /*       /\******\/ */
         
   /*       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  */
   /*      fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
   /*      for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){  */
   /*        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  */
   /*        nhstepm = nhstepm/hstepm;  */
             
   /*        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
   /*        oldm=oldms;savm=savms; */
   /*        hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
   /*        for (h=0; h<=nhstepm; h++){ */
   /*          if (h==(int) (calagedatem+YEARM*cpt)) { */
   /*            fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
   /*          }  */
   /*          for(j=1; j<=nlstate+ndeath;j++) { */
   /*            kk1=0.;kk2=0; */
   /*            for(i=1; i<=nlstate;i++) {               */
   /*              kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];     */
   /*            } */
   /*            if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);         */
   /*          } */
   /*        } */
   /*        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
   /*      } */
   /*       } */
   /*     }  */
   /*   } */
     
   /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
     
   /*   if (popforecast==1) { */
   /*     free_ivector(popage,0,AGESUP); */
   /*     free_vector(popeffectif,0,AGESUP); */
   /*     free_vector(popcount,0,AGESUP); */
   /*   } */
   /*   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   /*   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   /*   fclose(ficrespop); */
   /* } /\* End of popforecast *\/ */
    
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32];
     int i,j, k, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=1;i<=imx ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
   
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.svg\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter svg size 640, 480\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i=0, j=0, n=0, iv=0, v;
     int lstra;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     char *stratrunc;
   
     DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
     FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
   
     for(v=1; v <=ncovcol;v++){
       DummyV[v]=0;
       FixedV[v]=0;
     }
     for(v=ncovcol+1; v <=ncovcol+nqv;v++){
       DummyV[v]=1;
       FixedV[v]=0;
     }
     for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
       DummyV[v]=0;
       FixedV[v]=1;
     }
     for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
       DummyV[v]=1;
       FixedV[v]=1;
     }
     for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
       printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
       fprintf(ficlog,"Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
     }
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
       fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       strcpy(line, linetmp);
       
       /* Loops on waves */
       for (j=maxwav;j>=1;j--){
         for (iv=nqtv;iv>=1;iv--){  /* Loop  on time varying quantitative variables */
           cutv(stra, strb, line, ' '); 
           if(strb[0]=='.') { /* Missing value */
             lval=-1;
             cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
             cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
             if(isalpha(strb[1])) { /* .m or .d Really Missing value */
               printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);
               fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
               return 1;
             }
           }else{
             errno=0;
             /* what_kind_of_number(strb); */
             dval=strtod(strb,&endptr); 
             /* if( strb[0]=='\0' || (*endptr != '\0')){ */
             /* if(strb != endptr && *endptr == '\0') */
             /*    dval=dlval; */
             /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
             if( strb[0]=='\0' || (*endptr != '\0')){
               printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
               fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
               return 1;
             }
             cotqvar[j][iv][i]=dval; 
             cotvar[j][ntv+iv][i]=dval; 
           }
           strcpy(line,stra);
         }/* end loop ntqv */
         
         for (iv=ntv;iv>=1;iv--){  /* Loop  on time varying dummies */
           cutv(stra, strb, line, ' '); 
           if(strb[0]=='.') { /* Missing value */
             lval=-1;
           }else{
             errno=0;
             lval=strtol(strb,&endptr,10); 
             /*    if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
             if( strb[0]=='\0' || (*endptr != '\0')){
               printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
               fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);
               return 1;
             }
           }
           if(lval <-1 || lval >1){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n                 \
    build V1=0 V2=0 for the reference value (1),\n                         \
           V1=1 V2=0 for (2) \n                                            \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n                                \
    Exiting.\n",lval,linei, i,line,j);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n                 \
    build V1=0 V2=0 for the reference value (1),\n                         \
           V1=1 V2=0 for (2) \n                                            \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n                                \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
             return 1;
           }
           cotvar[j][iv][i]=(double)(lval);
           strcpy(line,stra);
         }/* end loop ntv */
         
         /* Statuses  at wave */
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing value */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         
         s[j][i]=lval;
         
         /* Date of Interview */
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
         }
         else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* End loop on waves */
       
       /* Date of death */
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
         return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       /* Date of birth */
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
         return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
         return 1;
         
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       /* Sample weight */
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (iv=nqv;iv>=1;iv--){  /* Loop  on fixed quantitative variables */
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing value */
           lval=-1;
         }else{
           errno=0;
           /* what_kind_of_number(strb); */
           dval=strtod(strb,&endptr);
           /* if(strb != endptr && *endptr == '\0') */
           /*   dval=dlval; */
           /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);fflush(ficlog);
             return 1;
           }
           coqvar[iv][i]=dval; 
           covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */ 
         }
         strcpy(line,stra);
       }/* end loop nqv */
       
       /* Covariate values */
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing covariate value */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n                 \
    build V1=0 V2=0 for the reference value (1),\n                         \
           V1=1 V2=0 for (2) \n                                            \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n                                \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n                 \
    build V1=0 V2=0 for the reference value (1),\n                         \
           V1=1 V2=0 for (2) \n                                            \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n                                \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
       
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     
     *imax=i-1; /* Number of individuals */
     fclose(fic);
     
     return (0);
     /* endread: */
     printf("Exiting readdata: ");
     fclose(fic);
     return (1);
   }
   
   void removefirstspace(char **stri){/*, char stro[]) {*/
     char *p1 = *stri, *p2 = *stri;
     while (*p2 == ' ')
       p2++; 
     /* while ((*p1++ = *p2++) !=0) */
     /*   ; */
     /* do */
     /*   while (*p2 == ' ') */
     /*     p2++; */
     /* while (*p1++ == *p2++); */
     *stri=p2; 
   }
   
   int decoderesult ( char resultline[], int nres)
   /**< This routine decode one result line and returns the combination # of dummy covariates only **/
   {
     int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
     char resultsav[MAXLINE];
     int resultmodel[MAXLINE];
     int modelresult[MAXLINE];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     removefirstspace(&resultline);
     printf("decoderesult:%s\n",resultline);
   
     if (strstr(resultline,"v") !=0){
       printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
       fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
       return 1;
     }
     trimbb(resultsav, resultline);
     if (strlen(resultsav) >1){
       j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
     }
     if(j == 0){ /* Resultline but no = */
       TKresult[nres]=0; /* Combination for the nresult and the model */
       return (0);
     }
       
     if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
       printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
       fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
     }
     for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
       if(nbocc(resultsav,'=') >1){
          cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' 
                                         resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
          cutl(strc,strd,strb,'=');  /* strb:V4=1 strc=1 strd=V4 */
       }else
         cutl(strc,strd,resultsav,'=');
       Tvalsel[k]=atof(strc); /* 1 */
       
       cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
       Tvarsel[k]=atoi(strc);
       /* Typevarsel[k]=1;  /\* 1 for age product *\/ */
       /* cptcovsel++;     */
       if (nbocc(stra,'=') >0)
         strcpy(resultsav,stra); /* and analyzes it */
     }
     /* Checking for missing or useless values in comparison of current model needs */
     for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
       if(Typevar[k1]==0){ /* Single covariate in model */
         match=0;
         for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
           if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5   */
             modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
             match=1;
             break;
           }
         }
         if(match == 0){
           printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
         }
       }
     }
     /* Checking for missing or useless values in comparison of current model needs */
     for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
       match=0;
       for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         if(Typevar[k1]==0){ /* Single */
           if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4   */
             resultmodel[k1]=k2;  /* resultmodel[2]=1 resultmodel[1]=2  resultmodel[3]=3  resultmodel[6]=4 resultmodel[9]=5 */
             ++match;
           }
         }
       }
       if(match == 0){
         printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
       }else if(match > 1){
         printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
       }
     }
         
     /* We need to deduce which combination number is chosen and save quantitative values */
     /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
     /* result line V4=1 V5=25.1 V3=0  V2=8 V1=1 */
     /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
     /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
     /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
     /*    1 0 0 0 */
     /*    2 1 0 0 */
     /*    3 0 1 0 */ 
     /*    4 1 1 0 */ /* V4=1, V3=1, V1=0 */
     /*    5 0 0 1 */
     /*    6 1 0 1 */ /* V4=1, V3=0, V1=1 */
     /*    7 0 1 1 */
     /*    8 1 1 1 */
     /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
     /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
     /* V5*age V5 known which value for nres?  */
     /* Tqinvresult[2]=8 Tqinvresult[1]=25.1  */
     for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
       if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
         k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
         k2=(int)Tvarsel[k3]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
         k+=Tvalsel[k3]*pow(2,k4);  /*  Tvalsel[1]=1  */
         Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1)  Tresult[nres][2]=0(V3=0) */
         Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
         Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
         printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
         k4++;;
       }  else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
         k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
         k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
         Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
         Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
         Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
         printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
         k4q++;;
       }
     }
     
     TKresult[nres]=++k; /* Combination for the nresult and the model */
     return (0);
   }
   
   int decodemodel( char model[], int lastobs)
    /**< This routine decodes the model and returns:
           * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
           * - nagesqr = 1 if age*age in the model, otherwise 0.
           * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
           * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
           * - cptcovage number of covariates with age*products =2
           * - cptcovs number of simple covariates
           * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
           *     which is a new column after the 9 (ncovcol) variables. 
           * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
           * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
           *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
           * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
           */
   {
     int i, j, k, ks, v;
     int  j1, k1, k2, k3, k4;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
     char *strpt;
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       strcpy(modelsav,model); 
       if ((strpt=strstr(model,"age*age")) !=0){
         printf(" strpt=%s, model=%s\n",strpt, model);
         if(strpt != model){
           printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
    'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
    corresponding column of parameters.\n",model);
           fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
    'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
    corresponding column of parameters.\n",model); fflush(ficlog);
           return 1;
         }
         nagesqr=1;
         if (strstr(model,"+age*age") !=0)
           substrchaine(modelsav, model, "+age*age");
         else if (strstr(model,"age*age+") !=0)
           substrchaine(modelsav, model, "age*age+");
         else 
           substrchaine(modelsav, model, "age*age");
       }else
         nagesqr=0;
       if (strlen(modelsav) >1){
         j=nbocc(modelsav,'+'); /**< j=Number of '+' */
         j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
         cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2  */
         cptcovt= j+1; /* Number of total covariates in the model, not including
                        * cst, age and age*age 
                        * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
         /* including age products which are counted in cptcovage.
          * but the covariates which are products must be treated 
          * separately: ncovn=4- 2=2 (V1+V3). */
         cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
         cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
         
         
         /*   Design
          *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
          *  <          ncovcol=8                >
          * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
          *   k=  1    2      3       4     5       6      7        8
          *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
          *  covar[k,i], value of kth covariate if not including age for individual i:
          *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
          *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
          *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
          *  Tage[++cptcovage]=k
          *       if products, new covar are created after ncovcol with k1
          *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
          *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
          *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
          *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
          *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
          *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
          *  <          ncovcol=8                >
          *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
          *          k=  1    2      3       4     5       6      7        8    9   10   11  12
          *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
          * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
          * p Tprod[1]@2={                         6, 5}
          *p Tvard[1][1]@4= {7, 8, 5, 6}
          * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
          *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
          *How to reorganize?
          * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
          * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
          *       {2,   1,     4,      8,    5,      6,     3,       7}
          * Struct []
          */
         
         /* This loop fills the array Tvar from the string 'model'.*/
         /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
         /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
         /*        k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
         /*        k=3 V4 Tvar[k=3]= 4 (from V4) */
         /*        k=2 V1 Tvar[k=2]= 1 (from V1) */
         /*        k=1 Tvar[1]=2 (from V2) */
         /*        k=5 Tvar[5] */
         /* for (k=1; k<=cptcovn;k++) { */
         /*        cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
         /*        } */
         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
         /*
          * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
         for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
           Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
         }
         cptcovage=0;
         for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
           cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                            modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
           if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
           /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
           /*scanf("%d",i);*/
           if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
             cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
             if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
               /* covar is not filled and then is empty */
               cptcovprod--;
               cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
               Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
               Typevar[k]=1;  /* 1 for age product */
               cptcovage++; /* Sums the number of covariates which include age as a product */
               Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
               /*printf("stre=%s ", stre);*/
             } else if (strcmp(strd,"age")==0) { /* or age*Vn */
               cptcovprod--;
               cutl(stre,strb,strc,'V');
               Tvar[k]=atoi(stre);
               Typevar[k]=1;  /* 1 for age product */
               cptcovage++;
               Tage[cptcovage]=k;
             } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
               /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
               cptcovn++;
               cptcovprodnoage++;k1++;
               cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
               Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
                                                   because this model-covariate is a construction we invent a new column
                                                   which is after existing variables ncovcol+nqv+ntv+nqtv + k1
                                                   If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                                   Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
               Typevar[k]=2;  /* 2 for double fixed dummy covariates */
               cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
               Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
               Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
               Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
               Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
               k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
               /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
               /* Tvar[cptcovt+k2+1]=Tvard[k1][2];  /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
               /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
               /*                     1  2   3      4     5 | Tvar[5+1)=1, Tvar[7]=2   */
               for (i=1; i<=lastobs;i++){
                 /* Computes the new covariate which is a product of
                    covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
                 covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
               }
             } /* End age is not in the model */
           } /* End if model includes a product */
           else { /* no more sum */
             /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
             /*  scanf("%d",i);*/
             cutl(strd,strc,strb,'V');
             ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
             cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
             Tvar[k]=atoi(strd);
             Typevar[k]=0;  /* 0 for simple covariates */
           }
           strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
                                   /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
                                     scanf("%d",i);*/
         } /* end of loop + on total covariates */
       } /* end if strlen(modelsave == 0) age*age might exist */
     } /* end if strlen(model == 0) */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
     
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
        printf("cptcovprod=%d ", cptcovprod);
        fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
        scanf("%d ",i);*/
   
   
   /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
      of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
   /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1  = 5 possible variables data: 2 fixed 3, varying
      model=        V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
      k =           1    2   3     4       5       6      7      8        9
      Tvar[k]=      5    4   3 1+1+2+1+1=6 5       2      7      1        5
      Typevar[k]=   0    0   0     2       1       0      2      1        1
      Fixed[k]      1    1   1     1       3       0    0 or 2   2        3
      Dummy[k]      1    0   0     0       3       1      1      2        3
             Tmodelind[combination of covar]=k;
   */  
   /* Dispatching between quantitative and time varying covariates */
     /* If Tvar[k] >ncovcol it is a product */
     /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p  Vp=Vn*Vm for product */
           /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
     printf("Model=%s\n\
   Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
   Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
   Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
     fprintf(ficlog,"Model=%s\n\
   Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
   Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
   Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
     for(k=1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
     for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
       if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
         Fixed[k]= 0;
         Dummy[k]= 0;
         ncoveff++;
         ncovf++;
         nsd++;
         modell[k].maintype= FTYPE;
         TvarsD[nsd]=Tvar[k];
         TvarsDind[nsd]=k;
         TvarF[ncovf]=Tvar[k];
         TvarFind[ncovf]=k;
         TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
       }else if( Tvar[k] <=ncovcol &&  Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
         Fixed[k]= 0;
         Dummy[k]= 0;
         ncoveff++;
         ncovf++;
         modell[k].maintype= FTYPE;
         TvarF[ncovf]=Tvar[k];
         TvarFind[ncovf]=k;
         TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
       }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){/* Remind that product Vn*Vm are added in k Only simple fixed quantitative variable */
         Fixed[k]= 0;
         Dummy[k]= 1;
         nqfveff++;
         modell[k].maintype= FTYPE;
         modell[k].subtype= FQ;
         nsq++;
         TvarsQ[nsq]=Tvar[k];
         TvarsQind[nsq]=k;
         ncovf++;
         TvarF[ncovf]=Tvar[k];
         TvarFind[ncovf]=k;
         TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
         TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
       }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
         Fixed[k]= 1;
         Dummy[k]= 0;
         ntveff++; /* Only simple time varying dummy variable */
         modell[k].maintype= VTYPE;
         modell[k].subtype= VD;
         nsd++;
         TvarsD[nsd]=Tvar[k];
         TvarsDind[nsd]=k;
         ncovv++; /* Only simple time varying variables */
         TvarV[ncovv]=Tvar[k];
         TvarVind[ncovv]=k; /* TvarVind[2]=2  TvarVind[3]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
         TvarVD[ntveff]=Tvar[k]; /* TvarVD[1]=V4  TvarVD[2]=V3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
         TvarVDind[ntveff]=k; /* TvarVDind[1]=2 TvarVDind[2]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
         printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);
         printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
       }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv  && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
         Fixed[k]= 1;
         Dummy[k]= 1;
         nqtveff++;
         modell[k].maintype= VTYPE;
         modell[k].subtype= VQ;
         ncovv++; /* Only simple time varying variables */
         nsq++;
         TvarsQ[nsq]=Tvar[k];
         TvarsQind[nsq]=k;
         TvarV[ncovv]=Tvar[k];
         TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
         TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
         TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
         TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
         /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
         printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);
         printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
       }else if (Typevar[k] == 1) {  /* product with age */
         ncova++;
         TvarA[ncova]=Tvar[k];
         TvarAind[ncova]=k;
         if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
           Fixed[k]= 2;
           Dummy[k]= 2;
           modell[k].maintype= ATYPE;
           modell[k].subtype= APFD;
           /* ncoveff++; */
         }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
           Fixed[k]= 2;
           Dummy[k]= 3;
           modell[k].maintype= ATYPE;
           modell[k].subtype= APFQ;                /*      Product age * fixed quantitative */
           /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */
         }else if( Tvar[k] <=ncovcol+nqv+ntv ){
           Fixed[k]= 3;
           Dummy[k]= 2;
           modell[k].maintype= ATYPE;
           modell[k].subtype= APVD;                /*      Product age * varying dummy */
           /* ntveff++; /\* Only simple time varying dummy variable *\/ */
         }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
           Fixed[k]= 3;
           Dummy[k]= 3;
           modell[k].maintype= ATYPE;
           modell[k].subtype= APVQ;                /*      Product age * varying quantitative */
           /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
         }
       }else if (Typevar[k] == 2) {  /* product without age */
         k1=Tposprod[k];
         if(Tvard[k1][1] <=ncovcol){
           if(Tvard[k1][2] <=ncovcol){
             Fixed[k]= 1;
             Dummy[k]= 0;
             modell[k].maintype= FTYPE;
             modell[k].subtype= FPDD;              /*      Product fixed dummy * fixed dummy */
             ncovf++; /* Fixed variables without age */
             TvarF[ncovf]=Tvar[k];
             TvarFind[ncovf]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv){
             Fixed[k]= 0;  /* or 2 ?*/
             Dummy[k]= 1;
             modell[k].maintype= FTYPE;
             modell[k].subtype= FPDQ;              /*      Product fixed dummy * fixed quantitative */
             ncovf++; /* Varying variables without age */
             TvarF[ncovf]=Tvar[k];
             TvarFind[ncovf]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[k]= 1;
             Dummy[k]= 0;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDD;              /*      Product fixed dummy * varying dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDQ;              /*      Product fixed dummy * varying quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }
         }else if(Tvard[k1][1] <=ncovcol+nqv){
           if(Tvard[k1][2] <=ncovcol){
             Fixed[k]= 0;  /* or 2 ?*/
             Dummy[k]= 1;
             modell[k].maintype= FTYPE;
             modell[k].subtype= FPDQ;              /*      Product fixed quantitative * fixed dummy */
             ncovf++; /* Fixed variables without age */
             TvarF[ncovf]=Tvar[k];
             TvarFind[ncovf]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDQ;              /*      Product fixed quantitative * varying dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPQQ;              /*      Product fixed quantitative * varying quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }
         }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
           if(Tvard[k1][2] <=ncovcol){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDD;              /*      Product time varying dummy * fixed dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDQ;              /*      Product time varying dummy * fixed quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[k]= 1;
             Dummy[k]= 0;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDD;              /*      Product time varying dummy * time varying dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDQ;              /*      Product time varying dummy * time varying quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }
         }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
           if(Tvard[k1][2] <=ncovcol){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDQ;              /*      Product time varying quantitative * fixed dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPQQ;              /*      Product time varying quantitative * fixed quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDQ;              /*      Product time varying quantitative * time varying dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPQQ;              /*      Product time varying quantitative * time varying quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }
         }else{
           printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
           fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
         } /*end k1*/
       }else{
         printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
         fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
       }
       printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
       printf("           modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
       fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
     }
     /* Searching for doublons in the model */
     for(k1=1; k1<= cptcovt;k1++){
       for(k2=1; k2 <k1;k2++){
         if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){
           if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
             if(Tvar[k1]==Tvar[k2]){
               printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
               fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
               return(1);
             }
           }else if (Typevar[k1] ==2){
             k3=Tposprod[k1];
             k4=Tposprod[k2];
             if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) || ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){
               printf("Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
               fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
               return(1);
             }
           }
         }
       }
     }
     printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
     fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
     printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
     fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     /*endread:*/
     printf("Exiting decodemodel: ");
     return (1);
   }
   
   int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {/* Check ages at death */
     int i, m;
     int firstone=0;
     
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
             s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr = *nberr + 1;
           if(firstone == 0){
             firstone=1;
           printf("Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\nOther similar cases in log file\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
           }
           fprintf(ficlog,"Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
           s[m][i]=-1;  /* Droping the death status */
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           (*nberr)++;
           printf("Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\nOther similar cases in log file\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
           fprintf(ficlog,"Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
           s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0  || s[m][i]==-1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ /* What if s[m][i]=-1 */
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0){
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
                 agev[m][i]=agedc[i];
                 /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               }else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
             } /* agedc > 0 */
           } /* end if */
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           } /* en if 9*/
           else { /* =9 */
             /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else if(s[m][i]==0) /*= 0 Unknown */
           agev[m][i]=1;
         else{
           printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]); 
           fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]); 
           agev[m][i]=0;
         }
       } /* End for lastpass */
     }
       
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           (*nberr)++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
    /* endread:*/
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   
   void syscompilerinfo(int logged)
    {
      /* #include "syscompilerinfo.h"*/
      /* command line Intel compiler 32bit windows, XP compatible:*/
      /* /GS /W3 /Gy
         /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
         "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
         "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
         /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
      */ 
      /* 64 bits */
      /*
        /GS /W3 /Gy
        /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
        /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
        /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
        "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
      /* Optimization are useless and O3 is slower than O2 */
      /*
        /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" 
        /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo 
        /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel 
        /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" 
      */
      /* Link is */ /* /OUT:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
         /PDB:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
         "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
         "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
         "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
         /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
         /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
         uiAccess='false'"
         /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
         /NOLOGO /TLBID:1
      */
   #if defined __INTEL_COMPILER
   #if defined(__GNUC__)
           struct utsname sysInfo;  /* For Intel on Linux and OS/X */
   #endif
   #elif defined(__GNUC__) 
   #ifndef  __APPLE__
   #include <gnu/libc-version.h>  /* Only on gnu */
   #endif
      struct utsname sysInfo;
      int cross = CROSS;
      if (cross){
              printf("Cross-");
              if(logged) fprintf(ficlog, "Cross-");
      }
   #endif
   
   #include <stdint.h>
   
      printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
   #if defined(__clang__)
      printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
   #endif
   #if defined(__ICC) || defined(__INTEL_COMPILER)
      printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
   #endif
   #if defined(__GNUC__) || defined(__GNUG__)
      printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
   #endif
   #if defined(__HP_cc) || defined(__HP_aCC)
      printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
   #endif
   #if defined(__IBMC__) || defined(__IBMCPP__)
      printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
   #endif
   #if defined(_MSC_VER)
      printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
   #endif
   #if defined(__PGI)
      printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
   #endif
   #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
      printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
   #endif
      printf(" for "); if (logged) fprintf(ficlog, " for ");
      
   // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
   #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
       // Windows (x64 and x86)
      printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
   #elif __unix__ // all unices, not all compilers
       // Unix
      printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
   #elif __linux__
       // linux
      printf("linux ");if(logged) fprintf(ficlog,"linux ");
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
      printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
   #endif
   
   /*  __MINGW32__   */
   /*  __CYGWIN__   */
   /* __MINGW64__  */
   // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
   /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
   /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
   /* _WIN64  // Defined for applications for Win64. */
   /* _M_X64 // Defined for compilations that target x64 processors. */
   /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
   
   #if UINTPTR_MAX == 0xffffffff
      printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
   #else
      printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
   #endif
   
   #if defined(__GNUC__)
   # if defined(__GNUC_PATCHLEVEL__)
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100 \
                               + __GNUC_PATCHLEVEL__)
   # else
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100)
   # endif
      printf(" using GNU C version %d.\n", __GNUC_VERSION__);
      if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
   
      if (uname(&sysInfo) != -1) {
        printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
            if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
      //#ifndef __INTEL_COMPILER 
   #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
   #endif
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
   
   }
   
   int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     int i, j, k, i1, k4=0, nres=0 ;
     /* double ftolpl = 1.e-10; */
     double age, agebase, agelim;
     double tot;
   
     strcpy(filerespl,"PL_");
     strcat(filerespl,fileresu);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
     }
     printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
     pstamp(ficrespl);
     fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
   
     agebase=ageminpar;
     agelim=agemaxpar;
   
     /* i1=pow(2,ncoveff); */
     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
     if (cptcovn < 1){i1=1;}
   
     for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(i1 != 1 && TKresult[nres]!= k)
           continue;
   
         /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
         /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
         //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         /* k=k+1; */
         /* to clean */
         //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
         fprintf(ficrespl,"#******");
         printf("#******");
         fprintf(ficlog,"#******");
         for(j=1;j<=cptcoveff ;j++) {/* all covariates */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
         if(invalidvarcomb[k]){
           printf("\nCombination (%d) ignored because no case \n",k); 
           fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k); 
           fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k); 
           continue;
         }
   
         fprintf(ficrespl,"#Age ");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
         fprintf(ficrespl,"Total Years_to_converge\n");
       
         for (age=agebase; age<=agelim; age++){
           /* for (age=agebase; age<=agebase; age++){ */
           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           tot=0.;
           for(i=1; i<=nlstate;i++){
             tot +=  prlim[i][i];
             fprintf(ficrespl," %.5f", prlim[i][i]);
           }
           fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
         } /* Age */
         /* was end of cptcod */
       } /* cptcov */
     } /* nres */
     return 0;
   }
   
   int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
           /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
           
           /* Computes the back prevalence limit  for any combination      of covariate values 
      * at any age between ageminpar and agemaxpar
            */
     int i, j, k, i1, nres=0 ;
     /* double ftolpl = 1.e-10; */
     double age, agebase, agelim;
     double tot;
     /* double ***mobaverage; */
     /* double      **dnewm, **doldm, **dsavm;  /\* for use *\/ */
   
     strcpy(fileresplb,"PLB_");
     strcat(fileresplb,fileresu);
     if((ficresplb=fopen(fileresplb,"w"))==NULL) {
       printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
       fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
     }
     printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
     fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
     pstamp(ficresplb);
     fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
     fprintf(ficresplb,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
     fprintf(ficresplb,"\n");
     
     
     /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
     
     agebase=ageminpar;
     agelim=agemaxpar;
     
     
     i1=pow(2,cptcoveff);
     if (cptcovn < 1){i1=1;}
     
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
        if(i1 != 1 && TKresult[nres]!= k)
           continue;
         //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
         fprintf(ficresplb,"#******");
         printf("#******");
         fprintf(ficlog,"#******");
         for(j=1;j<=cptcoveff ;j++) {/* all covariates */
           fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
         }
         fprintf(ficresplb,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
         if(invalidvarcomb[k]){
           printf("\nCombination (%d) ignored because no cases \n",k); 
           fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k); 
           fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k); 
           continue;
         }
       
         fprintf(ficresplb,"#Age ");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
         fprintf(ficresplb,"Total Years_to_converge\n");
       
       
         for (age=agebase; age<=agelim; age++){
           /* for (age=agebase; age<=agebase; age++){ */
           if(mobilavproj > 0){
             /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
             /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
             bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
           }else if (mobilavproj == 0){
             printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
             fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
             exit(1);
           }else{
             /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
             bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
             /* printf("TOTOT\n"); */
             /* exit(1); */
           }
           fprintf(ficresplb,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           tot=0.;
           for(i=1; i<=nlstate;i++){
             tot +=  bprlim[i][i];
             fprintf(ficresplb," %.5f", bprlim[i][i]);
           }
           fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
         } /* Age */
         /* was end of cptcod */
         /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
       } /* end of any combination */
     } /* end of nres */  
     /* hBijx(p, bage, fage); */
     /* fclose(ficrespijb); */
     
     return 0;
   }
    
   int hPijx(double *p, int bage, int fage){
       /*------------- h Pij x at various ages ------------*/
   
     int stepsize;
     int agelim;
     int hstepm;
     int nhstepm;
     int h, i, i1, j, k, k4, nres=0;
   
     double agedeb;
     double ***p3mat;
   
       strcpy(filerespij,"PIJ_");  strcat(filerespij,fileresu);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
                   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       i1= pow(2,cptcoveff);
                   /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
                   /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
                   /*      k=k+1;  */
       for(nres=1; nres <= nresult; nres++) /* For each resultline */
       for(k=1; k<=i1;k++){
         if(i1 != 1 && TKresult[nres]!= k)
           continue;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }
         fprintf(ficrespij,"******\n");
         
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
           
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
             fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
         /*}*/
       }
       return 0;
   }
    
    int hBijx(double *p, int bage, int fage, double ***prevacurrent){
       /*------------- h Bij x at various ages ------------*/
   
     int stepsize;
     /* int agelim; */
           int ageminl;
     int hstepm;
     int nhstepm;
     int h, i, i1, j, k, nres;
           
     double agedeb;
     double ***p3mat;
           
     strcpy(filerespijb,"PIJB_");  strcat(filerespijb,fileresu);
     if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
       printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
       fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
     }
     printf("Computing pij back: result on file '%s' \n", filerespijb);
     fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
     
     /* agelim=AGESUP; */
     ageminl=30;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
     
     /* hstepm=1;   aff par mois*/
     pstamp(ficrespijb);
     fprintf(ficrespijb,"#****** h Bij x Back probability to be in state i at age x-h being in j at x: B1j+B2j+...=1 ");
     i1= pow(2,cptcoveff);
     /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
     /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
     /*    k=k+1;  */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
         if(i1 != 1 && TKresult[nres]!= k)
           continue;
         fprintf(ficrespijb,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)
           fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
         }
         fprintf(ficrespijb,"******\n");
         if(invalidvarcomb[k]){  /* Is it necessary here? */
           fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k); 
           continue;
         }
         
         /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
         for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
           /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
           nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
           
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
           
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
           /* and memory limitations if stepm is small */
   
           /* oldm=oldms;savm=savms; */
           /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
           hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
           /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
           fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespijb," %1d-%1d",i,j);
           fprintf(ficrespijb,"\n");
           for (h=0; h<=nhstepm; h++){
             /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
             fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
             /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
             fprintf(ficrespijb,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespijb,"\n");
         } /* end age deb */
       } /* end combination */
     } /* end nres */
     return 0;
    } /*  hBijx */
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
     int ncvyear=0; /* Number of years needed for the period prevalence to converge */
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int num_filled;
     int itimes;
     int NDIM=2;
     int vpopbased=0;
     int nres=0;
     int endishere=0;
     int noffset=0;
     int ncurrv=0; /* Temporary variable */
     
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb=0.;
   
     double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
     double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
   
     double fret;
     double dum=0.; /* Dummy variable */
     double ***p3mat;
     /* double ***mobaverage; */
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
   
     char  modeltemp[MAXLINE];
     char resultline[MAXLINE];
     
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt, c2;
     int jl=0;
     int i1, j1, jk, stepsize=0;
     int count=0;
   
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int backcast=0;
     int mobilav=0,popforecast=0;
     int hstepm=0, nhstepm=0;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage=0, fage=110., age, agelim=0., agebase=0.;
     double ftolpl=FTOL;
     double **prlim;
     double **bprlim;
     double ***param; /* Matrix of parameters */
     double ***paramstart; /* Matrix of starting parameter values */
     double  *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
     double **matcov; /* Matrix of covariance */
     double **hess; /* Hessian matrix */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
   
     double *epj, vepp;
   
     double dateprev1, dateprev2;
     double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0;
     double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0;
   
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
   #ifdef WIN32
     _getcwd(pathcd, size);
   #else
     getcwd(pathcd, size);
   #endif
     syscompilerinfo(0);
     printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       if(!fgets(pathr,FILENAMELENGTH,stdin)){
         printf("ERROR Empty parameter file name\n");
         goto end;
       }
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
       }
       i=strlen(pathr);
       if( i==0 ){
         printf("ERROR Empty parameter file name\n");
         goto end;
       }
       for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else if (argc<=2){
       strcpy(pathtot,argv[1]);
     }
     else{
       strcpy(pathtot,argv[1]);
       strcpy(z,argv[2]);
       printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   #ifdef WIN32
     _chdir(path); /* Can be a relative path */
     if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
   #else
     chdir(path); /* Can be a relative path */
     if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
   #endif
     printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Main Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"Version %s %s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     syscompilerinfo(1);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileresu, optionfilefiname); /* Without r in front */
     strcat(fileres,".txt");    /* Other files have txt extension */
     strcat(fileresu,".txt");    /* Other files have txt extension */
   
     /* Main ---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
     strcpy(filereso,"o");
     strcat(filereso,fileresu);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
         /*-------- Rewriting parameter file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name */
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", rfileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
       fflush(ficlog);
       goto end;
     }
     fprintf(ficres,"#IMaCh %s\n",version);
   
                                         
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     /* Is it a BOM UTF-8 Windows file? */
     /* First parameter line */
     while(fgets(line, MAXLINE, ficpar)) {
       noffset=0;
       if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
       {
         noffset=noffset+3;
         printf("# File is an UTF8 Bom.\n"); // 0xBF
       }
       else if( line[0] == (char)0xFE && line[1] == (char)0xFF)
       {
         noffset=noffset+2;
         printf("# File is an UTF16BE BOM file\n");
       }
       else if( line[0] == 0 && line[1] == 0)
       {
         if( line[2] == (char)0xFE && line[3] == (char)0xFF){
           noffset=noffset+4;
           printf("# File is an UTF16BE BOM file\n");
         }
       } else{
         ;/*printf(" Not a BOM file\n");*/
       }
     
       /* If line starts with a # it is a comment */
       if (line[noffset] == '#') {
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficres);
         fputs(line,ficlog);
         continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
                           title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
       if (num_filled != 5) {
         printf("Should be 5 parameters\n");
       }
       numlinepar++;
       printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
     }
     /* Second parameter line */
     while(fgets(line, MAXLINE, ficpar)) {
       /* If line starts with a # it is a comment */
       if (line[0] == '#') {
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficres);
         fputs(line,ficlog);
         continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
                           &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
       if (num_filled != 11) {
         printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
         printf("but line=%s\n",line);
       }
       printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
     }
     /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
     /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
     /* Third parameter line */
     while(fgets(line, MAXLINE, ficpar)) {
       /* If line starts with a # it is a comment */
       if (line[0] == '#') {
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficres);
         fputs(line,ficlog);
         continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
       if (num_filled != 1){
         printf("ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
         fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
         model[0]='\0';
         goto end;
       }
       else{
         if (model[0]=='+'){
           for(i=1; i<=strlen(model);i++)
             modeltemp[i-1]=model[i];
           strcpy(model,modeltemp); 
         }
       }
       /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
       printf("model=1+age+%s\n",model);fflush(stdout);
     }
     /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
     /* numlinepar=numlinepar+3; /\* In general *\/ */
     /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     /* if(model[0]=='#'|| model[0]== '\0'){ */
     if(model[0]=='#'){
       printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
    'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
    'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n");            \
       if(mle != -1){
         printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter vectors and subdiagonal covariance matrix.\n");
         exit(1);
       }
     }
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
         z[0]=line[1];
       }
       /* printf("****line [1] = %c \n",line[1]); */
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     if(nqv>=1)coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */
     if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,1,n);  /**< Time varying quantitative covariate */
     if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n);  /**< Time varying covariate (dummy and quantitative)*/
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7,age*age makes 3*/
     else
       ncovmodel=2; /* Constant and age */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
   /* We could also provide initial parameters values giving by simple logistic regression 
    * only one way, that is without matrix product. We will have nlstate maximizations */
         /* for(i=1;i<nlstate;i++){ */
         /*        /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
         /*    mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
         /* } */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }  else if(mle==-5) { /* Main Wizard */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
       hess=matrix(1,npar,1,npar);
     }  else{ /* Begin of mle != -1 or -5 */
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) || (j1 != jj)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,jj);
           fprintf(ficlog,"%1d%1d",i,jj);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
       
       /* Reads parameters values */
       p=param[1][1];
       pstart=paramstart[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ( (i1-i) * (j1-j) != 0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
       
       /* Reads covariance matrix */
       delti=delti3[1][1];
                   
                   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
                   
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
                   
       matcov=matrix(1,npar,1,npar);
       hess=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
                   
       /* Scans npar lines */
       for(i=1; i <=npar; i++){
         count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
         if(count != 3){
           printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
   This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
           fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
   This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
           exit(1);
         }else{
           if(mle==1)
             printf("%1d%1d%d",i1,j1,jk);
         }
         fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
         fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
                                   printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       /* End of read covariance matrix npar lines */
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
     }    /* End of mle != -3 */
     
     /*  Main data
      */
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     weight=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     for(i=1;i<=n;i++){
       num[i]=0;
       moisnais[i]=0;
       annais[i]=0;
       moisdc[i]=0;
       andc[i]=0;
       agedc[i]=0;
       cod[i]=0;
       weight[i]=1.0; /* Equal weights, 1 by default */
     }
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
     ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
     */
     
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     TvarsDind=ivector(1,NCOVMAX); /*  */
     TvarsD=ivector(1,NCOVMAX); /*  */
     TvarsQind=ivector(1,NCOVMAX); /*  */
     TvarsQ=ivector(1,NCOVMAX); /*  */
     TvarF=ivector(1,NCOVMAX); /*  */
     TvarFind=ivector(1,NCOVMAX); /*  */
     TvarV=ivector(1,NCOVMAX); /*  */
     TvarVind=ivector(1,NCOVMAX); /*  */
     TvarA=ivector(1,NCOVMAX); /*  */
     TvarAind=ivector(1,NCOVMAX); /*  */
     TvarFD=ivector(1,NCOVMAX); /*  */
     TvarFDind=ivector(1,NCOVMAX); /*  */
     TvarFQ=ivector(1,NCOVMAX); /*  */
     TvarFQind=ivector(1,NCOVMAX); /*  */
     TvarVD=ivector(1,NCOVMAX); /*  */
     TvarVDind=ivector(1,NCOVMAX); /*  */
     TvarVQ=ivector(1,NCOVMAX); /*  */
     TvarVQind=ivector(1,NCOVMAX); /*  */
   
     Tvalsel=vector(1,NCOVMAX); /*  */
     Tvarsel=ivector(1,NCOVMAX); /*  */
     Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
     Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
     Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
     Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
        Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2 
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
     Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
                                   * individual dummy, fixed or varying:
                                   * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
                                   * 3, 1, 0, 0, 0, 0, 0, 0},
                                   * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 , 
                                   * V1 df, V2 qf, V3 & V4 dv, V5 qv
                                   * Tmodelind[1]@9={9,0,3,2,}*/
     TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
     TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
                                   * individual quantitative, fixed or varying:
                                   * Tmodelqind[1]=1,Tvaraff[1]@9={4,
                                   * 3, 1, 0, 0, 0, 0, 0, 0},
                                   * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
   /* Main decodemodel */
   
   
     if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3  = {4, 3, 5}*/
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     /* free_vector(moisdc,1,n); */
     /* free_vector(andc,1,n); */
     /* */
     
     wav=ivector(1,imx);
     /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
     /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
     /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
     dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/
     bh=imatrix(1,lastpass-firstpass+2,1,imx);
     mw=imatrix(1,lastpass-firstpass+2,1,imx);
      
     /* Concatenates waves */
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        Death is a valid wave (if date is known).
        mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
        dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
     */
   
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* Concatenates waves */
    
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     cptcoveff=0;
     if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
       tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
     }
     
     ncovcombmax=pow(2,cptcoveff);
     invalidvarcomb=ivector(1, ncovcombmax); 
     for(i=1;i<ncovcombmax;i++)
       invalidvarcomb[i]=0;
     
     /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
        V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
     /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
     
     /*  codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
     /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
     /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j, 
      * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded 
      * (currently 0 or 1) in the data.
      * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of 
      * corresponding modality (h,j).
      */
   
     h=0;
     /*if (cptcovn > 0) */
     m=pow(2,cptcoveff);
    
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              * For k=4 covariates, h goes from 1 to m=2**k
              * codtabm(h,k)=  (1 & (h-1) >> (k-1)) + 1;
              * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
              *     h\k   1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     2
              *    10     2     1     1     2
              *    11 i=6 1     2     1     2
              *    12     2     2     1     2
              *    13 i=7 1 i=4 1     2     2    
              *    14     2     1     2     2
              *    15 i=8 1     2     2     2
              *    16     2     2     2     2
              */
     /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
        /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
        * and the value of each covariate?
        * V1=1, V2=1, V3=2, V4=1 ?
        * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
        * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
        * In order to get the real value in the data, we use nbcode
        * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
        * We are keeping this crazy system in order to be able (in the future?) 
        * to have more than 2 values (0 or 1) for a covariate.
        * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
        * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
        *              bbbbbbbb
        *              76543210     
        *   h-1        00000101 (6-1=5)
        *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
        *           &
        *     1        00000001 (1)
        *              00000000        = 1 & ((h-1) >> (k-1))
        *          +1= 00000001 =1 
        *
        * h=14, k=3 => h'=h-1=13, k'=k-1=2
        *          h'      1101 =2^3+2^2+0x2^1+2^0
        *    >>k'            11
        *          &   00000001
        *            = 00000001
        *      +1    = 00000010=2    =  codtabm(14,3)   
        * Reverse h=6 and m=16?
        * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
        * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
        * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1 
        * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
        * V3=decodtabm(14,3,2**4)=2
        *          h'=13   1101 =2^3+2^2+0x2^1+2^0
        *(h-1) >> (j-1)    0011 =13 >> 2
        *          &1 000000001
        *           = 000000001
        *         +1= 000000010 =2
        *                  2211
        *                  V1=1+1, V2=0+1, V3=1+1, V4=1+1
        *                  V3=2
                    * codtabm and decodtabm are identical
        */
   
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /* Initialisation of ----------- gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-MORT_");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# IMaCh-%s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
   
   
     /* Initialisation of --------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-MORT_");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C)  2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br>  \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   <font size=\"2\">IMaCh-%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
   #ifdef WIN32
     _chdir(optionfilefiname); /* Move to directory named optionfile */
   #else
     chdir(optionfilefiname); /* Move to directory named optionfile */
   #endif
             
     
     /* Calculates basic frequencies. Computes observed prevalence at single age 
                    and for any valid combination of covariates
        and prints on file fileres'p'. */
     freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
                 firstpass, lastpass,  stepm,  weightopt, model);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<h4>Parameter line 2</h4><ul><li>Tolerance for the convergence of the likelihood: ftol=%f \n<li>Interval for the elementary matrix (in month): stepm=%d",\
             ftol, stepm);
     fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
     ncurrv=1;
     for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
     fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv); 
     ncurrv=i;
     for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
     fprintf(fichtm,"\n<li> Number of time varying (wave varying) covariates: ntv=%d ", ntv);
     ncurrv=i;
     for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
     fprintf(fichtm,"\n<li>Number of quantitative time varying covariates: nqtv=%d ", nqtv);
     ncurrv=i;
     for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
     fprintf(fichtm,"\n<li>Weights column \n<br>Number of alive states: nlstate=%d <br>Number of death states (not really implemented): ndeath=%d \n<li>Number of waves: maxwav=%d \n<li>Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n<li>Does the weight column be taken into account (1), or not (0): weight=%d</ul>\n", \
              nlstate, ndeath, maxwav, mle, weightopt);
   
     fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
   <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
   
     
     fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
     imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
   
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     /* For mortality only */
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
       for(i=1;i<=NDIM;i++)
         for(j=1;j<=NDIM;j++)
           ximort[i][j]=0.;
       /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
                   
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
       
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
           
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"POW-MORT_"); 
       strcat(filerespow,fileresu);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
       /*     gsl_vector_set(x, 0, 0.0268); */
       /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
                                   matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       fprintf(ficlog,"\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
                                   printf("%f ",matcov[i][j]);
                                   fprintf(ficlog,"%f ",matcov[i][j]);
         }
         printf("\n ");  fprintf(ficlog,"\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) {
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
         fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
       }
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
                   ageminpar=50;
                   agemaxpar=100;
       if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
           printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
   This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
           fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
   This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
       }else{
                           printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
                           fprintf(ficlog,"Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
         printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
                   }
       printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
       free_matrix(ximort,1,NDIM,1,NDIM);
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
   #ifdef GSL
   #endif
     } /* Endof if mle==-3 mortality only */
     /* Standard  */
     else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
       globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
       /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2, Real Maximization */
         /* mlikeli uses func not funcone */
         /* for(i=1;i<nlstate;i++){ */
         /*        /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
         /*    mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
         /* } */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
         globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
         /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
         likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       }
       globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%12.7f ",p[jk]);
               fprintf(ficlog,"%12.7f ",p[jk]);
               fprintf(ficres,"%12.7f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle != 0){
         /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, hess, p, npar, delti, ftolhess, func);
         printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
         fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n  It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
         for(i=1,jk=1; i <=nlstate; i++){
           for(k=1; k <=(nlstate+ndeath); k++){
             if (k != i) {
               printf("%d%d ",i,k);
               fprintf(ficlog,"%d%d ",i,k);
               for(j=1; j <=ncovmodel; j++){
                 printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
                 fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
                 jk++; 
               }
               printf("\n");
               fprintf(ficlog,"\n");
             }
           }
         }
       } /* end of hesscov and Wald tests */
       
       /*  */
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle >= 1) /* To big for the screen */
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.7e",matcov[jj][ll]); 
                           fprintf(ficlog," %.7e",matcov[jj][ll]); 
                           fprintf(ficres," %.7e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       while(fgets(line, MAXLINE, ficpar)) {
         /* If line starts with a # it is a comment */
         if (line[0] == '#') {
           numlinepar++;
           fputs(line,stdout);
           fputs(line,ficparo);
           fputs(line,ficlog);
           continue;
         }else
           break;
       }
       
       /* while((c=getc(ficpar))=='#' && c!= EOF){ */
       /*   ungetc(c,ficpar); */
       /*   fgets(line, MAXLINE, ficpar); */
       /*   fputs(line,stdout); */
       /*   fputs(line,ficparo); */
       /* } */
       /* ungetc(c,ficpar); */
       
       estepm=0;
       if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){
         
         if (num_filled != 6) {
           printf("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
           fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
           goto end;
         }
         printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
       }
       /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
       /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
       
       /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
                   
       /* Other stuffs, more or less useful */    
       while(fgets(line, MAXLINE, ficpar)) {
         /* If line starts with a # it is a comment */
         if (line[0] == '#') {
           numlinepar++;
           fputs(line,stdout);
           fputs(line,ficparo);
           fputs(line,ficlog);
           continue;
         }else
           break;
       }
   
       if((num_filled=sscanf(line,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav)) !=EOF){
         
         if (num_filled != 7) {
           printf("Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
           fprintf(ficlog,"Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
           goto end;
         }
         printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
         fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
         fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
         fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       }
   
       while(fgets(line, MAXLINE, ficpar)) {
         /* If line starts with a # it is a comment */
         if (line[0] == '#') {
           numlinepar++;
           fputs(line,stdout);
           fputs(line,ficparo);
           fputs(line,ficlog);
           continue;
         }else
           break;
       }
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
         if (num_filled != 1) {
           printf("Error: Not 1 (data)parameters in line but %d, for example:pop_based=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
           fprintf(ficlog,"Error: Not 1 (data)parameters in line but %d, for example: pop_based=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
           goto end;
         }
         printf("pop_based=%d\n",popbased);
         fprintf(ficlog,"pop_based=%d\n",popbased);
         fprintf(ficparo,"pop_based=%d\n",popbased);   
         fprintf(ficres,"pop_based=%d\n",popbased);   
       }
        
       /* Results */
       nresult=0;
       do{
         if(!fgets(line, MAXLINE, ficpar)){
           endishere=1;
           parameterline=14;
         }else if (line[0] == '#') {
           /* If line starts with a # it is a comment */
           numlinepar++;
           fputs(line,stdout);
           fputs(line,ficparo);
           fputs(line,ficlog);
           continue;
         }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
           parameterline=11;
         else if(sscanf(line,"backcast=%[^\n]\n",modeltemp))
           parameterline=12;
         else if(sscanf(line,"result:%[^\n]\n",modeltemp))
           parameterline=13;
         else{
           parameterline=14;
         }
         switch (parameterline){ 
         case 11:
           if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF){
             if (num_filled != 8) {
               printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
               fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
               goto end;
             }
             fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
             printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
             fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
             fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
             /* day and month of proj2 are not used but only year anproj2.*/
             dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
             dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
   
           }
           break;
         case 12:
           /*fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);*/
           if((num_filled=sscanf(line,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF){
             if (num_filled != 8) {
               printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
               fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
               goto end;
             }
             printf("backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
             fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
             fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
             fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
             /* day and month of proj2 are not used but only year anproj2.*/
             dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
             dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
           }
           break;
         case 13:
           if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
             if (num_filled == 0){
               resultline[0]='\0';
               printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
               fprintf(ficlog,"Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
               break;
             } else if (num_filled != 1){
               printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
               fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
             }
             nresult++; /* Sum of resultlines */
             printf("Result %d: result=%s\n",nresult, resultline);
             if(nresult > MAXRESULTLINES){
               printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
               fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
               goto end;
             }
             decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
             fprintf(ficparo,"result: %s\n",resultline);
             fprintf(ficres,"result: %s\n",resultline);
             fprintf(ficlog,"result: %s\n",resultline);
             break;
           case 14: 
             if(ncovmodel >2 && nresult==0 ){
               printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
               goto end;
             }
             break;
           default:
             nresult=1;
             decoderesult(".",nresult ); /* No covariate */
           }
         } /* End switch parameterline */
       }while(endishere==0); /* End do */
       
       /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
         printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
   This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
         fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
   This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
       }else{
         /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
         printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, backcast, pathc,p, (int)anproj1-bage, (int)anback1-fage);
       }
       printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \
                    jprev1,mprev1,anprev1,dateprev1, dateproj1, dateback1,jprev2,mprev2,anprev2,dateprev2,dateproj2, dateback2);
                   
       /*------------ free_vector  -------------*/
       /*  chdir(path); */
                   
       /* free_ivector(wav,1,imx); */  /* Moved after last prevalence call */
       /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
       /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
       /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx);    */
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
                   
                   
       /* Other results (useful)*/
                   
                   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
       /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
       prlim=matrix(1,nlstate,1,nlstate);
       prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
       /*#include "hpijx.h"*/
       hPijx(p, bage, fage);
       fclose(ficrespij);
       
       /* ncovcombmax=  pow(2,cptcoveff); */
       /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
       
       /* Prevalence for each covariate combination in probs[age][status][cov] */
       probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
       for(i=AGEINF;i<=AGESUP;i++)
         for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
           for(k=1;k<=ncovcombmax;k++)
             probs[i][j][k]=0.;
       prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, 
                  ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       if (mobilav!=0 ||mobilavproj !=0 ) {
         mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
         for(i=AGEINF;i<=AGESUP;i++)
           for(j=1;j<=nlstate+ndeath;j++)
             for(k=1;k<=ncovcombmax;k++)
               mobaverages[i][j][k]=0.;
         mobaverage=mobaverages;
         if (mobilav!=0) {
           printf("Movingaveraging observed prevalence\n");
           fprintf(ficlog,"Movingaveraging observed prevalence\n");
           if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
             fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
             printf(" Error in movingaverage mobilav=%d\n",mobilav);
           }
         } else if (mobilavproj !=0) {
           printf("Movingaveraging projected observed prevalence\n");
           fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
           if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
             fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
             printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
           }
         }else{
           printf("Internal error moving average\n");
           fflush(stdout);
           exit(1);
         }
       }/* end if moving average */
       
       /*---------- Forecasting ------------------*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
       }
   
       /* Backcasting */
       if(backcast==1){
         ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        
         ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        
         ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
   
         /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
   
         bprlim=matrix(1,nlstate,1,nlstate);
   
         back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
         fclose(ficresplb);
   
         hBijx(p, bage, fage, mobaverage);
         fclose(ficrespijb);
   
         prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2,
                          mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff);
         varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
   
         
         free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
         free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
         free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
         free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
       }    /* end  Backcasting */
    
    
       /* ------ Other prevalence ratios------------ */
   
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+2,1,imx);   
                   
                   
       /*---------- Health expectancies, no variances ------------*/
                   
       strcpy(filerese,"E_");
       strcat(filerese,fileresu);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
   
       pstamp(ficreseij);
                   
       i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
       if (cptcovn < 1){i1=1;}
       
       for(nres=1; nres <= nresult; nres++) /* For each resultline */
       for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
         if(i1 != 1 && TKresult[nres]!= k)
           continue;
         fprintf(ficreseij,"\n#****** ");
         printf("\n#****** ");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
         }
         fprintf(ficreseij,"******\n");
         printf("******\n");
         
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);  
         
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
       }
       fclose(ficreseij);
       printf("done evsij\n");fflush(stdout);
       fprintf(ficlog,"done evsij\n");fflush(ficlog);
   
                   
       /*---------- State-specific expectancies and variances ------------*/
                   
       strcpy(filerest,"T_");
       strcat(filerest,fileresu);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
       strcpy(fileresstde,"STDE_");
       strcat(fileresstde,fileresu);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("  Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"  Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"CVE_");
       strcat(filerescve,fileresu);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"V_");
       strcat(fileresv,fileresu);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
       fprintf(ficlog,"      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
   
       i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
       if (cptcovn < 1){i1=1;}
       
       for(nres=1; nres <= nresult; nres++) /* For each resultline */
       for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
         if(i1 != 1 && TKresult[nres]!= k)
           continue;
         printf("\n#****** Result for:");
         fprintf(ficrest,"\n#****** Result for:");
         fprintf(ficlog,"\n#****** Result for:");
         for(j=1;j<=cptcoveff;j++){ 
           printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
         } 
         fprintf(ficrest,"******\n");
         fprintf(ficlog,"******\n");
         printf("******\n");
         
         fprintf(ficresstdeij,"\n#****** ");
         fprintf(ficrescveij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
         } 
         fprintf(ficresstdeij,"******\n");
         fprintf(ficrescveij,"******\n");
         
         fprintf(ficresvij,"\n#****** ");
         /* pstamp(ficresvij); */
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
         } 
         fprintf(ficresvij,"******\n");
         
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         printf(" cvevsij ");
         fprintf(ficlog, " cvevsij ");
         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
         printf(" end cvevsij \n ");
         fprintf(ficlog, " end cvevsij \n ");
         
         /*
          */
         /* goto endfree; */
         
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         pstamp(ficrest);
         
         epj=vector(1,nlstate+1);
         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
           oldm=oldms;savm=savms; /* ZZ Segmentation fault */
           cptcod= 0; /* To be deleted */
           printf("varevsij vpopbased=%d \n",vpopbased);
           fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart, nres); /* cptcod not initialized Intel */
           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
           if(vpopbased==1)
             fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
           else
             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
           fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
           /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
           printf("Computing age specific period (stable) prevalences in each health state \n");
           fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
             if (vpopbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
             
             fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
             /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
             /* printf(" age %4.0f ",age); */
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
               }
               epj[nlstate+1] +=epj[j];
             }
             /* printf(" age %4.0f \n",age); */
             
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
         } /* End vpopbased */
         free_vector(epj,1,nlstate+1);
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         printf("done selection\n");fflush(stdout);
         fprintf(ficlog,"done selection\n");fflush(ficlog);
         
       } /* End k selection */
   
       printf("done State-specific expectancies\n");fflush(stdout);
       fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
   
       /* variance-covariance of period prevalence*/
       varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
   
       
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
       
       
       /*---------- End : free ----------------*/
       if (mobilav!=0 ||mobilavproj !=0)
         free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
       free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     }  /* mle==-3 arrives here for freeing */
     /* endfree:*/
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);
     if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
     if(nqv>=1)free_matrix(coqvar,1,nqv,1,n);
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     free_matrix(hess,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     
     free_ivector(ncodemax,1,NCOVMAX);
     free_ivector(ncodemaxwundef,1,NCOVMAX);
     free_ivector(Dummy,-1,NCOVMAX);
     free_ivector(Fixed,-1,NCOVMAX);
     free_ivector(DummyV,1,NCOVMAX);
     free_ivector(FixedV,1,NCOVMAX);
     free_ivector(Typevar,-1,NCOVMAX);
     free_ivector(Tvar,1,NCOVMAX);
     free_ivector(TvarsQ,1,NCOVMAX);
     free_ivector(TvarsQind,1,NCOVMAX);
     free_ivector(TvarsD,1,NCOVMAX);
     free_ivector(TvarsDind,1,NCOVMAX);
     free_ivector(TvarFD,1,NCOVMAX);
     free_ivector(TvarFDind,1,NCOVMAX);
     free_ivector(TvarF,1,NCOVMAX);
     free_ivector(TvarFind,1,NCOVMAX);
     free_ivector(TvarV,1,NCOVMAX);
     free_ivector(TvarVind,1,NCOVMAX);
     free_ivector(TvarA,1,NCOVMAX);
     free_ivector(TvarAind,1,NCOVMAX);
     free_ivector(TvarFQ,1,NCOVMAX);
     free_ivector(TvarFQind,1,NCOVMAX);
     free_ivector(TvarVD,1,NCOVMAX);
     free_ivector(TvarVDind,1,NCOVMAX);
     free_ivector(TvarVQ,1,NCOVMAX);
     free_ivector(TvarVQind,1,NCOVMAX);
     free_ivector(Tvarsel,1,NCOVMAX);
     free_vector(Tvalsel,1,NCOVMAX);
     free_ivector(Tposprod,1,NCOVMAX);
     free_ivector(Tprod,1,NCOVMAX);
     free_ivector(Tvaraff,1,NCOVMAX);
     free_ivector(invalidvarcomb,1,ncovcombmax);
     free_ivector(Tage,1,NCOVMAX);
     free_ivector(Tmodelind,1,NCOVMAX);
     free_ivector(TmodelInvind,1,NCOVMAX);
     free_ivector(TmodelInvQind,1,NCOVMAX);
     
     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
     /* free_imatrix(codtab,1,100,1,10); */
     fflush(fichtm);
     fflush(ficgp);
     
     
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
     
   
   /* Executes gnuplot */
     
     printf("Before Current directory %s!\n",pathcd);
   #ifdef WIN32
     if (_chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(_getcwd(pathcd,MAXLINE) > 0)
   #else
       if(chdir(pathcd) != 0)
         printf("Can't move to directory %s!\n", path);
     if (getcwd(pathcd, MAXLINE) > 0)
   #endif 
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
     
     if((outcmd=system(plotcmd)) != 0){
       printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
   end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: "); fflush(stdout);
       scanf("%s",z);
     }
     exit(0);
   }

Removed from v.1.46  
changed lines
  Added in v.1.282


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