Diff for /imach/src/imach.c between versions 1.32 and 1.201

version 1.32, 2002/03/11 14:17:15 version 1.201, 2015/09/15 17:34:58
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.201  2015/09/15 17:34:58  brouard
      Summary: 0.98r0
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    - Some new graphs like suvival functions
   first survey ("cross") where individuals from different ages are    - Some bugs fixed like model=1+age+V2.
   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 1.200  2015/09/09 16:53:55  brouard
   second wave of interviews ("longitudinal") which measure each change    Summary: Big bug thanks to Flavia
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Even model=1+age+V2. did not work anymore
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.199  2015/09/07 14:09:23  brouard
   simplest model is the multinomial logistic model where pij is the    Summary: 0.98q6 changing default small png format for graph to vectorized svg.
   probabibility to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.198  2015/09/03 07:14:39  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Summary: 0.98q5 Flavia
   '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 1.197  2015/09/01 18:24:39  brouard
   where the markup *Covariates have to be included here again* invites    *** empty log message ***
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.196  2015/08/18 23:17:52  brouard
     Summary: 0.98q5
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.195  2015/08/18 16:28:39  brouard
   identical for each individual. Also, if a individual missed an    Summary: Adding a hack for testing purpose
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      After reading the title, ftol and model lines, if the comment line has
     a q, starting with #q, the answer at the end of the run is quit. It
   hPijx is the probability to be observed in state i at age x+h    permits to run test files in batch with ctest. The former workaround was
   conditional to the observed state i at age x. The delay 'h' can be    $ echo q | imach foo.imach
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    Revision 1.194  2015/08/18 13:32:00  brouard
   semester or year) is model as a multinomial logistic.  The hPx    Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.193  2015/08/04 07:17:42  brouard
   hPijx.    Summary: 0.98q4
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.192  2015/07/16 16:49:02  brouard
   of the life expectancies. It also computes the prevalence limits.    Summary: Fixing some outputs
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.191  2015/07/14 10:00:33  brouard
            Institut national d'études démographiques, Paris.    Summary: Some fixes
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.190  2015/05/05 08:51:13  brouard
   It is copyrighted identically to a GNU software product, ie programme and    Summary: Adding digits in output parameters (7 digits instead of 6)
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Fix 1+age+.
   **********************************************************************/  
      Revision 1.189  2015/04/30 14:45:16  brouard
 #include <math.h>    Summary: 0.98q2
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.188  2015/04/30 08:27:53  brouard
 #include <unistd.h>    *** empty log message ***
   
 #define MAXLINE 256    Revision 1.187  2015/04/29 09:11:15  brouard
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    *** empty log message ***
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.186  2015/04/23 12:01:52  brouard
 #define windows    Summary: V1*age is working now, version 0.98q1
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Some codes had been disabled in order to simplify and Vn*age was
     working in the optimization phase, ie, giving correct MLE parameters,
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    but, as usual, outputs were not correct and program core dumped.
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.185  2015/03/11 13:26:42  brouard
 #define NINTERVMAX 8    Summary: Inclusion of compile and links command line for Intel Compiler
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.184  2015/03/11 11:52:39  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    Summary: Back from Windows 8. Intel Compiler
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.183  2015/03/10 20:34:32  brouard
 #define AGESUP 130    Summary: 0.98q0, trying with directest, mnbrak fixed
 #define AGEBASE 40  
     We use directest instead of original Powell test; probably no
     incidence on the results, but better justifications;
 int erreur; /* Error number */    We fixed Numerical Recipes mnbrak routine which was wrong and gave
 int nvar;    wrong results.
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.182  2015/02/12 08:19:57  brouard
 int nlstate=2; /* Number of live states */    Summary: Trying to keep directest which seems simpler and more general
 int ndeath=1; /* Number of dead states */    Author: Nicolas Brouard
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.181  2015/02/11 23:22:24  brouard
     Summary: Comments on Powell added
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Author:
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.180  2015/02/11 17:33:45  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Summary: Finishing move from main to function (hpijx and prevalence_limit)
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Revision 1.179  2015/01/04 09:57:06  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Summary: back to OS/X
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Revision 1.178  2015/01/04 09:35:48  brouard
 FILE *ficgp,*ficresprob,*ficpop;    *** empty log message ***
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.177  2015/01/03 18:40:56  brouard
  FILE  *ficresvij;    Summary: Still testing ilc32 on OSX
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.176  2015/01/03 16:45:04  brouard
   char fileresvpl[FILENAMELENGTH];    *** empty log message ***
   
 #define NR_END 1    Revision 1.175  2015/01/03 16:33:42  brouard
 #define FREE_ARG char*    *** empty log message ***
 #define FTOL 1.0e-10  
     Revision 1.174  2015/01/03 16:15:49  brouard
 #define NRANSI    Summary: Still in cross-compilation
 #define ITMAX 200  
     Revision 1.173  2015/01/03 12:06:26  brouard
 #define TOL 2.0e-4    Summary: trying to detect cross-compilation
   
 #define CGOLD 0.3819660    Revision 1.172  2014/12/27 12:07:47  brouard
 #define ZEPS 1.0e-10    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.171  2014/12/23 13:26:59  brouard
 #define GOLD 1.618034    Summary: Back from Visual C
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Still problem with utsname.h on Windows
   
 static double maxarg1,maxarg2;    Revision 1.170  2014/12/23 11:17:12  brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Summary: Cleaning some \%% back to %%
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      The escape was mandatory for a specific compiler (which one?), but too many warnings.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.169  2014/12/22 23:08:31  brouard
     Summary: 0.98p
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Outputs some informations on compiler used, OS etc. Testing on different platforms.
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.168  2014/12/22 15:17:42  brouard
 int imx;    Summary: update
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.167  2014/12/22 13:50:56  brouard
     Summary: Testing uname and compiler version and if compiled 32 or 64
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Testing on Linux 64
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.166  2014/12/22 11:40:47  brouard
 double dateintmean=0;    *** empty log message ***
   
 double *weight;    Revision 1.165  2014/12/16 11:20:36  brouard
 int **s; /* Status */    Summary: After compiling on Visual C
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    * imach.c (Module): Merging 1.61 to 1.162
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Revision 1.164  2014/12/16 10:52:11  brouard
 double ftolhess; /* Tolerance for computing hessian */    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
   
 /**************** split *************************/    * imach.c (Module): Merging 1.61 to 1.162
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    Revision 1.163  2014/12/16 10:30:11  brouard
    char *s;                             /* pointer */    * imach.c (Module): Merging 1.61 to 1.162
    int  l1, l2;                         /* length counters */  
     Revision 1.162  2014/09/25 11:43:39  brouard
    l1 = strlen( path );                 /* length of path */    Summary: temporary backup 0.99!
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows    Revision 1.1  2014/09/16 11:06:58  brouard
    s = strrchr( path, '\\' );           /* find last / */    Summary: With some code (wrong) for nlopt
 #else  
    s = strrchr( path, '/' );            /* find last / */    Author:
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */    Revision 1.161  2014/09/15 20:41:41  brouard
 #if     defined(__bsd__)                /* get current working directory */    Summary: Problem with macro SQR on Intel compiler
       extern char       *getwd( );  
     Revision 1.160  2014/09/02 09:24:05  brouard
       if ( getwd( dirc ) == NULL ) {    *** empty log message ***
 #else  
       extern char       *getcwd( );    Revision 1.159  2014/09/01 10:34:10  brouard
     Summary: WIN32
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Author: Brouard
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.158  2014/08/27 17:11:51  brouard
       }    *** empty log message ***
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.157  2014/08/27 16:26:55  brouard
       s++;                              /* after this, the filename */    Summary: Preparing windows Visual studio version
       l2 = strlen( s );                 /* length of filename */    Author: Brouard
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    In order to compile on Visual studio, time.h is now correct and time_t
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    and tm struct should be used. difftime should be used but sometimes I
       dirc[l1-l2] = 0;                  /* add zero */    just make the differences in raw time format (time(&now).
    }    Trying to suppress #ifdef LINUX
    l1 = strlen( dirc );                 /* length of directory */    Add xdg-open for __linux in order to open default browser.
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.156  2014/08/25 20:10:10  brouard
 #else    *** empty log message ***
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif    Revision 1.155  2014/08/25 18:32:34  brouard
    s = strrchr( name, '.' );            /* find last / */    Summary: New compile, minor changes
    s++;    Author: Brouard
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);    Revision 1.154  2014/06/20 17:32:08  brouard
    l2= strlen( s)+1;    Summary: Outputs now all graphs of convergence to period prevalence
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    Revision 1.153  2014/06/20 16:45:46  brouard
    return( 0 );                         /* we're done */    Summary: If 3 live state, convergence to period prevalence on same graph
 }    Author: Brouard
   
     Revision 1.152  2014/06/18 17:54:09  brouard
 /******************************************/    Summary: open browser, use gnuplot on same dir than imach if not found in the path
   
 void replace(char *s, char*t)    Revision 1.151  2014/06/18 16:43:30  brouard
 {    *** empty log message ***
   int i;  
   int lg=20;    Revision 1.150  2014/06/18 16:42:35  brouard
   i=0;    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
   lg=strlen(t);    Author: brouard
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.149  2014/06/18 15:51:14  brouard
     if (t[i]== '\\') s[i]='/';    Summary: Some fixes in parameter files errors
   }    Author: Nicolas Brouard
 }  
     Revision 1.148  2014/06/17 17:38:48  brouard
 int nbocc(char *s, char occ)    Summary: Nothing new
 {    Author: Brouard
   int i,j=0;  
   int lg=20;    Just a new packaging for OS/X version 0.98nS
   i=0;  
   lg=strlen(s);    Revision 1.147  2014/06/16 10:33:11  brouard
   for(i=0; i<= lg; i++) {    *** empty log message ***
   if  (s[i] == occ ) j++;  
   }    Revision 1.146  2014/06/16 10:20:28  brouard
   return j;    Summary: Merge
 }    Author: Brouard
   
 void cutv(char *u,char *v, char*t, char occ)    Merge, before building revised version.
 {  
   int i,lg,j,p=0;    Revision 1.145  2014/06/10 21:23:15  brouard
   i=0;    Summary: Debugging with valgrind
   for(j=0; j<=strlen(t)-1; j++) {    Author: Nicolas Brouard
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    Lot of changes in order to output the results with some covariates
     After the Edimburgh REVES conference 2014, it seems mandatory to
   lg=strlen(t);    improve the code.
   for(j=0; j<p; j++) {    No more memory valgrind error but a lot has to be done in order to
     (u[j] = t[j]);    continue the work of splitting the code into subroutines.
   }    Also, decodemodel has been improved. Tricode is still not
      u[p]='\0';    optimal. nbcode should be improved. Documentation has been added in
     the source code.
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    Revision 1.143  2014/01/26 09:45:38  brouard
   }    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 }  
     * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 /********************** nrerror ********************/    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   
 void nrerror(char error_text[])    Revision 1.142  2014/01/26 03:57:36  brouard
 {    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   exit(1);  
 }    Revision 1.141  2014/01/26 02:42:01  brouard
 /*********************** vector *******************/    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 double *vector(int nl, int nh)  
 {    Revision 1.140  2011/09/02 10:37:54  brouard
   double *v;    Summary: times.h is ok with mingw32 now.
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    Revision 1.139  2010/06/14 07:50:17  brouard
   return v-nl+NR_END;    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 }    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   
 /************************ free vector ******************/    Revision 1.138  2010/04/30 18:19:40  brouard
 void free_vector(double*v, int nl, int nh)    *** empty log message ***
 {  
   free((FREE_ARG)(v+nl-NR_END));    Revision 1.137  2010/04/29 18:11:38  brouard
 }    (Module): Checking covariates for more complex models
     than V1+V2. A lot of change to be done. Unstable.
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    Revision 1.136  2010/04/26 20:30:53  brouard
 {    (Module): merging some libgsl code. Fixing computation
   int *v;    of likelione (using inter/intrapolation if mle = 0) in order to
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    get same likelihood as if mle=1.
   if (!v) nrerror("allocation failure in ivector");    Some cleaning of code and comments added.
   return v-nl+NR_END;  
 }    Revision 1.135  2009/10/29 15:33:14  brouard
     (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)    Revision 1.134  2009/10/29 13:18:53  brouard
 {    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.133  2009/07/06 10:21:25  brouard
     just nforces
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)    Revision 1.132  2009/07/06 08:22:05  brouard
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Many tings
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Revision 1.131  2009/06/20 16:22:47  brouard
   int **m;    Some dimensions resccaled
    
   /* allocate pointers to rows */    Revision 1.130  2009/05/26 06:44:34  brouard
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    (Module): Max Covariate is now set to 20 instead of 8. A
   if (!m) nrerror("allocation failure 1 in matrix()");    lot of cleaning with variables initialized to 0. Trying to make
   m += NR_END;    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   m -= nrl;  
      Revision 1.129  2007/08/31 13:49:27  lievre
      Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    Revision 1.128  2006/06/30 13:02:05  brouard
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    (Module): Clarifications on computing e.j
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.127  2006/04/28 18:11:50  brouard
      (Module): Yes the sum of survivors was wrong since
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    imach-114 because nhstepm was no more computed in the age
      loop. Now we define nhstepma in the age loop.
   /* return pointer to array of pointers to rows */    (Module): In order to speed up (in case of numerous covariates) we
   return m;    compute health expectancies (without variances) in a first step
 }    and then all the health expectancies with variances or standard
     deviation (needs data from the Hessian matrices) which slows the
 /****************** free_imatrix *************************/    computation.
 void free_imatrix(m,nrl,nrh,ncl,nch)    In the future we should be able to stop the program is only health
       int **m;    expectancies and graph are needed without standard deviations.
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */    Revision 1.126  2006/04/28 17:23:28  brouard
 {    (Module): Yes the sum of survivors was wrong since
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    imach-114 because nhstepm was no more computed in the age
   free((FREE_ARG) (m+nrl-NR_END));    loop. Now we define nhstepma in the age loop.
 }    Version 0.98h
   
 /******************* matrix *******************************/    Revision 1.125  2006/04/04 15:20:31  lievre
 double **matrix(long nrl, long nrh, long ncl, long nch)    Errors in calculation of health expectancies. Age was not initialized.
 {    Forecasting file added.
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Revision 1.124  2006/03/22 17:13:53  lievre
     Parameters are printed with %lf instead of %f (more numbers after the comma).
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    The log-likelihood is printed in the log file
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.123  2006/03/20 10:52:43  brouard
   m -= nrl;    * imach.c (Module): <title> changed, corresponds to .htm file
     name. <head> headers where missing.
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    * imach.c (Module): Weights can have a decimal point as for
   m[nrl] += NR_END;    English (a comma might work with a correct LC_NUMERIC environment,
   m[nrl] -= ncl;    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    1.
   return m;    Version 0.98g
 }  
     Revision 1.122  2006/03/20 09:45:41  brouard
 /*************************free matrix ************************/    (Module): Weights can have a decimal point as for
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    English (a comma might work with a correct LC_NUMERIC environment,
 {    otherwise the weight is truncated).
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Modification of warning when the covariates values are not 0 or
   free((FREE_ARG)(m+nrl-NR_END));    1.
 }    Version 0.98g
   
 /******************* ma3x *******************************/    Revision 1.121  2006/03/16 17:45:01  lievre
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    * imach.c (Module): Comments concerning covariates added
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    * imach.c (Module): refinements in the computation of lli if
   double ***m;    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.120  2006/03/16 15:10:38  lievre
   m += NR_END;    (Module): refinements in the computation of lli if
   m -= nrl;    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.119  2006/03/15 17:42:26  brouard
   m[nrl] += NR_END;    (Module): Bug if status = -2, the loglikelihood was
   m[nrl] -= ncl;    computed as likelihood omitting the logarithm. Version O.98e
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Revision 1.118  2006/03/14 18:20:07  brouard
     (Module): varevsij Comments added explaining the second
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    table of variances if popbased=1 .
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   m[nrl][ncl] += NR_END;    (Module): Function pstamp added
   m[nrl][ncl] -= nll;    (Module): Version 0.98d
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;    Revision 1.117  2006/03/14 17:16:22  brouard
      (Module): varevsij Comments added explaining the second
   for (i=nrl+1; i<=nrh; i++) {    table of variances if popbased=1 .
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     for (j=ncl+1; j<=nch; j++)    (Module): Function pstamp added
       m[i][j]=m[i][j-1]+nlay;    (Module): Version 0.98d
   }  
   return m;    Revision 1.116  2006/03/06 10:29:27  brouard
 }    (Module): Variance-covariance wrong links and
     varian-covariance of ej. is needed (Saito).
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    Revision 1.115  2006/02/27 12:17:45  brouard
 {    (Module): One freematrix added in mlikeli! 0.98c
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Revision 1.114  2006/02/26 12:57:58  brouard
   free((FREE_ARG)(m+nrl-NR_END));    (Module): Some improvements in processing parameter
 }    filename with strsep.
   
 /***************** f1dim *************************/    Revision 1.113  2006/02/24 14:20:24  brouard
 extern int ncom;    (Module): Memory leaks checks with valgrind and:
 extern double *pcom,*xicom;    datafile was not closed, some imatrix were not freed and on matrix
 extern double (*nrfunc)(double []);    allocation too.
    
 double f1dim(double x)    Revision 1.112  2006/01/30 09:55:26  brouard
 {    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   int j;  
   double f;    Revision 1.111  2006/01/25 20:38:18  brouard
   double *xt;    (Module): Lots of cleaning and bugs added (Gompertz)
      (Module): Comments can be added in data file. Missing date values
   xt=vector(1,ncom);    can be a simple dot '.'.
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);    Revision 1.110  2006/01/25 00:51:50  brouard
   free_vector(xt,1,ncom);    (Module): Lots of cleaning and bugs added (Gompertz)
   return f;  
 }    Revision 1.109  2006/01/24 19:37:15  brouard
     (Module): Comments (lines starting with a #) are allowed in data.
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    Revision 1.108  2006/01/19 18:05:42  lievre
 {    Gnuplot problem appeared...
   int iter;    To be fixed
   double a,b,d,etemp;  
   double fu,fv,fw,fx;    Revision 1.107  2006/01/19 16:20:37  brouard
   double ftemp;    Test existence of gnuplot in imach path
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;    Revision 1.106  2006/01/19 13:24:36  brouard
      Some cleaning and links added in html output
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);    Revision 1.105  2006/01/05 20:23:19  lievre
   x=w=v=bx;    *** empty log message ***
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {    Revision 1.104  2005/09/30 16:11:43  lievre
     xm=0.5*(a+b);    (Module): sump fixed, loop imx fixed, and simplifications.
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    (Module): If the status is missing at the last wave but we know
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    that the person is alive, then we can code his/her status as -2
     printf(".");fflush(stdout);    (instead of missing=-1 in earlier versions) and his/her
 #ifdef DEBUG    contributions to the likelihood is 1 - Prob of dying from last
     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);    health status (= 1-p13= p11+p12 in the easiest case of somebody in
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    the healthy state at last known wave). Version is 0.98
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    Revision 1.103  2005/09/30 15:54:49  lievre
       *xmin=x;    (Module): sump fixed, loop imx fixed, and simplifications.
       return fx;  
     }    Revision 1.102  2004/09/15 17:31:30  brouard
     ftemp=fu;    Add the possibility to read data file including tab characters.
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);    Revision 1.101  2004/09/15 10:38:38  brouard
       q=(x-v)*(fx-fw);    Fix on curr_time
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);    Revision 1.100  2004/07/12 18:29:06  brouard
       if (q > 0.0) p = -p;    Add version for Mac OS X. Just define UNIX in Makefile
       q=fabs(q);  
       etemp=e;    Revision 1.99  2004/06/05 08:57:40  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 1.98  2004/05/16 15:05:56  brouard
       else {    New version 0.97 . First attempt to estimate force of mortality
         d=p/q;    directly from the data i.e. without the need of knowing the health
         u=x+d;    state at each age, but using a Gompertz model: log u =a + b*age .
         if (u-a < tol2 || b-u < tol2)    This is the basic analysis of mortality and should be done before any
           d=SIGN(tol1,xm-x);    other analysis, in order to test if the mortality estimated from the
       }    cross-longitudinal survey is different from the mortality estimated
     } else {    from other sources like vital statistic data.
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }    The same imach parameter file can be used but the option for mle should be -3.
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);    Agnès, who wrote this part of the code, tried to keep most of the
     if (fu <= fx) {    former routines in order to include the new code within the former code.
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)    The output is very simple: only an estimate of the intercept and of
         SHFT(fv,fw,fx,fu)    the slope with 95% confident intervals.
         } else {  
           if (u < x) a=u; else b=u;    Current limitations:
           if (fu <= fw || w == x) {    A) Even if you enter covariates, i.e. with the
             v=w;    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
             w=u;    B) There is no computation of Life Expectancy nor Life Table.
             fv=fw;  
             fw=fu;    Revision 1.97  2004/02/20 13:25:42  lievre
           } else if (fu <= fv || v == x || v == w) {    Version 0.96d. Population forecasting command line is (temporarily)
             v=u;    suppressed.
             fv=fu;  
           }    Revision 1.96  2003/07/15 15:38:55  brouard
         }    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   }    rewritten within the same printf. Workaround: many printfs.
   nrerror("Too many iterations in brent");  
   *xmin=x;    Revision 1.95  2003/07/08 07:54:34  brouard
   return fx;    * imach.c (Repository):
 }    (Repository): Using imachwizard code to output a more meaningful covariance
     matrix (cov(a12,c31) instead of numbers.
 /****************** mnbrak ***********************/  
     Revision 1.94  2003/06/27 13:00:02  brouard
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    Just cleaning
             double (*func)(double))  
 {    Revision 1.93  2003/06/25 16:33:55  brouard
   double ulim,u,r,q, dum;    (Module): On windows (cygwin) function asctime_r doesn't
   double fu;    exist so I changed back to asctime which exists.
      (Module): Version 0.96b
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);    Revision 1.92  2003/06/25 16:30:45  brouard
   if (*fb > *fa) {    (Module): On windows (cygwin) function asctime_r doesn't
     SHFT(dum,*ax,*bx,dum)    exist so I changed back to asctime which exists.
       SHFT(dum,*fb,*fa,dum)  
       }    Revision 1.91  2003/06/25 15:30:29  brouard
   *cx=(*bx)+GOLD*(*bx-*ax);    * imach.c (Repository): Duplicated warning errors corrected.
   *fc=(*func)(*cx);    (Repository): Elapsed time after each iteration is now output. It
   while (*fb > *fc) {    helps to forecast when convergence will be reached. Elapsed time
     r=(*bx-*ax)*(*fb-*fc);    is stamped in powell.  We created a new html file for the graphs
     q=(*bx-*cx)*(*fb-*fa);    concerning matrix of covariance. It has extension -cov.htm.
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    Revision 1.90  2003/06/24 12:34:15  brouard
     ulim=(*bx)+GLIMIT*(*cx-*bx);    (Module): Some bugs corrected for windows. Also, when
     if ((*bx-u)*(u-*cx) > 0.0) {    mle=-1 a template is output in file "or"mypar.txt with the design
       fu=(*func)(u);    of the covariance matrix to be input.
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);    Revision 1.89  2003/06/24 12:30:52  brouard
       if (fu < *fc) {    (Module): Some bugs corrected for windows. Also, when
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    mle=-1 a template is output in file "or"mypar.txt with the design
           SHFT(*fb,*fc,fu,(*func)(u))    of the covariance matrix to be input.
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    Revision 1.88  2003/06/23 17:54:56  brouard
       u=ulim;    * 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.
       fu=(*func)(u);  
     } else {    Revision 1.87  2003/06/18 12:26:01  brouard
       u=(*cx)+GOLD*(*cx-*bx);    Version 0.96
       fu=(*func)(u);  
     }    Revision 1.86  2003/06/17 20:04:08  brouard
     SHFT(*ax,*bx,*cx,u)    (Module): Change position of html and gnuplot routines and added
       SHFT(*fa,*fb,*fc,fu)    routine fileappend.
       }  
 }    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
 /*************** linmin ************************/    current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
 int ncom;    was wrong (infinity). We still send an "Error" but patch by
 double *pcom,*xicom;    assuming that the date of death was just one stepm after the
 double (*nrfunc)(double []);    interview.
      (Repository): Because some people have very long ID (first column)
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    we changed int to long in num[] and we added a new lvector for
 {    memory allocation. But we also truncated to 8 characters (left
   double brent(double ax, double bx, double cx,    truncation)
                double (*f)(double), double tol, double *xmin);    (Repository): No more line truncation errors.
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    Revision 1.84  2003/06/13 21:44:43  brouard
               double *fc, double (*func)(double));    * imach.c (Repository): Replace "freqsummary" at a correct
   int j;    place. It differs from routine "prevalence" which may be called
   double xx,xmin,bx,ax;    many times. Probs is memory consuming and must be used with
   double fx,fb,fa;    parcimony.
      Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   ncom=n;  
   pcom=vector(1,n);    Revision 1.83  2003/06/10 13:39:11  lievre
   xicom=vector(1,n);    *** empty log message ***
   nrfunc=func;  
   for (j=1;j<=n;j++) {    Revision 1.82  2003/06/05 15:57:20  brouard
     pcom[j]=p[j];    Add log in  imach.c and  fullversion number is now printed.
     xicom[j]=xi[j];  
   }  */
   ax=0.0;  /*
   xx=1.0;     Interpolated Markov Chain
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    Short summary of the programme:
 #ifdef DEBUG    
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    This program computes Healthy Life Expectancies from
 #endif    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   for (j=1;j<=n;j++) {    first survey ("cross") where individuals from different ages are
     xi[j] *= xmin;    interviewed on their health status or degree of disability (in the
     p[j] += xi[j];    case of a health survey which is our main interest) -2- at least a
   }    second wave of interviews ("longitudinal") which measure each change
   free_vector(xicom,1,n);    (if any) in individual health status.  Health expectancies are
   free_vector(pcom,1,n);    computed from the time spent in each health state according to a
 }    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
 /*************** powell ************************/    simplest model is the multinomial logistic model where pij is the
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    probability to be observed in state j at the second wave
             double (*func)(double []))    conditional to be observed in state i at the first wave. Therefore
 {    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   void linmin(double p[], double xi[], int n, double *fret,    'age' is age and 'sex' is a covariate. If you want to have a more
               double (*func)(double []));    complex model than "constant and age", you should modify the program
   int i,ibig,j;    where the markup *Covariates have to be included here again* invites
   double del,t,*pt,*ptt,*xit;    you to do it.  More covariates you add, slower the
   double fp,fptt;    convergence.
   double *xits;  
   pt=vector(1,n);    The advantage of this computer programme, compared to a simple
   ptt=vector(1,n);    multinomial logistic model, is clear when the delay between waves is not
   xit=vector(1,n);    identical for each individual. Also, if a individual missed an
   xits=vector(1,n);    intermediate interview, the information is lost, but taken into
   *fret=(*func)(p);    account using an interpolation or extrapolation.  
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {    hPijx is the probability to be observed in state i at age x+h
     fp=(*fret);    conditional to the observed state i at age x. The delay 'h' can be
     ibig=0;    split into an exact number (nh*stepm) of unobserved intermediate
     del=0.0;    states. This elementary transition (by month, quarter,
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    semester or year) is modelled as a multinomial logistic.  The hPx
     for (i=1;i<=n;i++)    matrix is simply the matrix product of nh*stepm elementary matrices
       printf(" %d %.12f",i, p[i]);    and the contribution of each individual to the likelihood is simply
     printf("\n");    hPijx.
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    Also this programme outputs the covariance matrix of the parameters but also
       fptt=(*fret);    of the life expectancies. It also computes the period (stable) prevalence. 
 #ifdef DEBUG    
       printf("fret=%lf \n",*fret);    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #endif             Institut national d'études démographiques, Paris.
       printf("%d",i);fflush(stdout);    This software have been partly granted by Euro-REVES, a concerted action
       linmin(p,xit,n,fret,func);    from the European Union.
       if (fabs(fptt-(*fret)) > del) {    It is copyrighted identically to a GNU software product, ie programme and
         del=fabs(fptt-(*fret));    software can be distributed freely for non commercial use. Latest version
         ibig=i;    can be accessed at http://euroreves.ined.fr/imach .
       }  
 #ifdef DEBUG    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
       printf("%d %.12e",i,(*fret));    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
       for (j=1;j<=n;j++) {    
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    **********************************************************************/
         printf(" x(%d)=%.12e",j,xit[j]);  /*
       }    main
       for(j=1;j<=n;j++)    read parameterfile
         printf(" p=%.12e",p[j]);    read datafile
       printf("\n");    concatwav
 #endif    freqsummary
     }    if (mle >= 1)
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      mlikeli
 #ifdef DEBUG    print results files
       int k[2],l;    if mle==1 
       k[0]=1;       computes hessian
       k[1]=-1;    read end of parameter file: agemin, agemax, bage, fage, estepm
       printf("Max: %.12e",(*func)(p));        begin-prev-date,...
       for (j=1;j<=n;j++)    open gnuplot file
         printf(" %.12e",p[j]);    open html file
       printf("\n");    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
       for(l=0;l<=1;l++) {     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
         for (j=1;j<=n;j++) {                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      freexexit2 possible for memory heap.
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  
         }    h Pij x                         | pij_nom  ficrestpij
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));     # 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
 #endif         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
   
          1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
       free_vector(xit,1,n);         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
       free_vector(xits,1,n);    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
       free_vector(ptt,1,n);     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
       free_vector(pt,1,n);     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
       return;  
     }    forecasting if prevfcast==1 prevforecast call prevalence()
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    health expectancies
     for (j=1;j<=n;j++) {    Variance-covariance of DFLE
       ptt[j]=2.0*p[j]-pt[j];    prevalence()
       xit[j]=p[j]-pt[j];     movingaverage()
       pt[j]=p[j];    varevsij() 
     }    if popbased==1 varevsij(,popbased)
     fptt=(*func)(ptt);    total life expectancies
     if (fptt < fp) {    Variance of period (stable) prevalence
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);   end
       if (t < 0.0) {  */
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {  /* #define DEBUG */
           xi[j][ibig]=xi[j][n];  /* #define DEBUGBRENT */
           xi[j][n]=xit[j];  #define POWELL /* Instead of NLOPT */
         }  #define POWELLF1F3 /* Skip test */
 #ifdef DEBUG  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
         for(j=1;j<=n;j++)  
           printf(" %.12e",xit[j]);  #include <math.h>
         printf("\n");  #include <stdio.h>
 #endif  #include <stdlib.h>
       }  #include <string.h>
     }  
   }  #ifdef _WIN32
 }  #include <io.h>
   #include <windows.h>
 /**** Prevalence limit ****************/  #include <tchar.h>
   #else
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  #include <unistd.h>
 {  #endif
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  
      matrix by transitions matrix until convergence is reached */  #include <limits.h>
   #include <sys/types.h>
   int i, ii,j,k;  
   double min, max, maxmin, maxmax,sumnew=0.;  #if defined(__GNUC__)
   double **matprod2();  #include <sys/utsname.h> /* Doesn't work on Windows */
   double **out, cov[NCOVMAX], **pmij();  #endif
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */  #include <sys/stat.h>
   #include <errno.h>
   for (ii=1;ii<=nlstate+ndeath;ii++)  /* extern int errno; */
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /* #ifdef LINUX */
     }  /* #include <time.h> */
   /* #include "timeval.h" */
    cov[1]=1.;  /* #else */
    /* #include <sys/time.h> */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /* #endif */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  
     newm=savm;  #include <time.h>
     /* Covariates have to be included here again */  
      cov[2]=agefin;  #ifdef GSL
    #include <gsl/gsl_errno.h>
       for (k=1; k<=cptcovn;k++) {  #include <gsl/gsl_multimin.h>
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  #endif
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  
       }  
       for (k=1; k<=cptcovage;k++)  #ifdef NLOPT
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  #include <nlopt.h>
       for (k=1; k<=cptcovprod;k++)  typedef struct {
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    double (* function)(double [] );
   } myfunc_data ;
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  #endif
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  
   /* #include <libintl.h> */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  /* #define _(String) gettext (String) */
   
     savm=oldm;  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
     oldm=newm;  
     maxmax=0.;  #define GNUPLOTPROGRAM "gnuplot"
     for(j=1;j<=nlstate;j++){  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       min=1.;  #define FILENAMELENGTH 132
       max=0.;  
       for(i=1; i<=nlstate; i++) {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
         sumnew=0;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
         max=FMAX(max,prlim[i][j]);  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
         min=FMIN(min,prlim[i][j]);  
       }  #define NINTERVMAX 8
       maxmin=max-min;  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
       maxmax=FMAX(maxmax,maxmin);  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
     }  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
     if(maxmax < ftolpl){  #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
       return prlim;  #define MAXN 20000
     }  #define YEARM 12. /**< Number of months per year */
   }  #define AGESUP 130
 }  #define AGEBASE 40
   #define AGEOVERFLOW 1.e20
 /*************** transition probabilities ***************/  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
   #ifdef _WIN32
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  #define DIRSEPARATOR '\\'
 {  #define CHARSEPARATOR "\\"
   double s1, s2;  #define ODIRSEPARATOR '/'
   /*double t34;*/  #else
   int i,j,j1, nc, ii, jj;  #define DIRSEPARATOR '/'
   #define CHARSEPARATOR "/"
     for(i=1; i<= nlstate; i++){  #define ODIRSEPARATOR '\\'
     for(j=1; j<i;j++){  #endif
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         /*s2 += param[i][j][nc]*cov[nc];*/  /* $Id$ */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /* $State$ */
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  #include "version.h"
       }  char version[]=__IMACH_VERSION__;
       ps[i][j]=s2;  char copyright[]="September 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  char fullversion[]="$Revision$ $Date$"; 
     }  char strstart[80];
     for(j=i+1; j<=nlstate+ndeath;j++){  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  /* 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) */
       ps[i][j]=s2;  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
     }  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
   }  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
     /*ps[3][2]=1;*/  int cptcovprodnoage=0; /**< Number of covariate products without age */   
   int cptcoveff=0; /* Total number of covariates to vary for printing results */
   for(i=1; i<= nlstate; i++){  int cptcov=0; /* Working variable */
      s1=0;  int npar=NPARMAX;
     for(j=1; j<i; j++)  int nlstate=2; /* Number of live states */
       s1+=exp(ps[i][j]);  int ndeath=1; /* Number of dead states */
     for(j=i+1; j<=nlstate+ndeath; j++)  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       s1+=exp(ps[i][j]);  int popbased=0;
     ps[i][i]=1./(s1+1.);  
     for(j=1; j<i; j++)  int *wav; /* Number of waves for this individuual 0 is possible */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  int maxwav=0; /* Maxim number of waves */
     for(j=i+1; j<=nlstate+ndeath; j++)  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
   } /* end i */                     to the likelihood and the sum of weights (done by funcone)*/
   int mle=1, weightopt=0;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
     for(jj=1; jj<= nlstate+ndeath; jj++){  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       ps[ii][jj]=0;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       ps[ii][ii]=1;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     }  int countcallfunc=0;  /* Count the number of calls to func */
   }  double jmean=1; /* Mean space between 2 waves */
   double **matprod2(); /* test */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     for(jj=1; jj<= nlstate+ndeath; jj++){  /*FILE *fic ; */ /* Used in readdata only */
      printf("%lf ",ps[ii][jj]);  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
    }  FILE *ficlog, *ficrespow;
     printf("\n ");  int globpr=0; /* Global variable for printing or not */
     }  double fretone; /* Only one call to likelihood */
     printf("\n ");printf("%lf ",cov[2]);*/  long ipmx=0; /* Number of contributions */
 /*  double sw; /* Sum of weights */
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  char filerespow[FILENAMELENGTH];
   goto end;*/  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
     return ps;  FILE *ficresilk;
 }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 /**************** Product of 2 matrices ******************/  FILE *fichtm, *fichtmcov; /* Html File */
   FILE *ficreseij;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  char filerese[FILENAMELENGTH];
 {  FILE *ficresstdeij;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  char fileresstde[FILENAMELENGTH];
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  FILE *ficrescveij;
   /* in, b, out are matrice of pointers which should have been initialized  char filerescve[FILENAMELENGTH];
      before: only the contents of out is modified. The function returns  FILE  *ficresvij;
      a pointer to pointers identical to out */  char fileresv[FILENAMELENGTH];
   long i, j, k;  FILE  *ficresvpl;
   for(i=nrl; i<= nrh; i++)  char fileresvpl[FILENAMELENGTH];
     for(k=ncolol; k<=ncoloh; k++)  char title[MAXLINE];
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
         out[i][k] +=in[i][j]*b[j][k];  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   return out;  char command[FILENAMELENGTH];
 }  int  outcmd=0;
   
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 /************* Higher Matrix Product ***************/  char fileresu[FILENAMELENGTH]; /* Without r in front */
   char filelog[FILENAMELENGTH]; /* Log file */
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  char filerest[FILENAMELENGTH];
 {  char fileregp[FILENAMELENGTH];
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  char popfile[FILENAMELENGTH];
      duration (i.e. until  
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
      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).  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
      Model is determined by parameters x and covariates have to be  /* struct timezone tzp; */
      included manually here.  /* extern int gettimeofday(); */
   struct tm tml, *gmtime(), *localtime();
      */  
   extern time_t time();
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];  struct tm start_time, end_time, curr_time, last_time, forecast_time;
   double **newm;  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
   struct tm tm;
   /* Hstepm could be zero and should return the unit matrix */  
   for (i=1;i<=nlstate+ndeath;i++)  char strcurr[80], strfor[80];
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);  char *endptr;
       po[i][j][0]=(i==j ? 1.0 : 0.0);  long lval;
     }  double dval;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(h=1; h <=nhstepm; h++){  #define NR_END 1
     for(d=1; d <=hstepm; d++){  #define FREE_ARG char*
       newm=savm;  #define FTOL 1.0e-10
       /* Covariates have to be included here again */  
       cov[1]=1.;  #define NRANSI 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  #define ITMAX 200 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
       for (k=1; k<=cptcovage;k++)  #define TOL 2.0e-4 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)  #define CGOLD 0.3819660 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  #define GOLD 1.618034 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  #define GLIMIT 100.0 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  #define TINY 1.0e-20 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;  static double maxarg1,maxarg2;
       oldm=newm;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     }  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     for(i=1; i<=nlstate+ndeath; i++)    
       for(j=1;j<=nlstate+ndeath;j++) {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
         po[i][j][h]=newm[i][j];  #define rint(a) floor(a+0.5)
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
          */  #define mytinydouble 1.0e-16
       }  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
   } /* end h */  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
   return po;  /* static double dsqrarg; */
 }  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
   static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 /*************** log-likelihood *************/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 double func( double *x)  int agegomp= AGEGOMP;
 {  
   int i, ii, j, k, mi, d, kk;  int imx; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  int stepm=1;
   double **out;  /* Stepm, step in month: minimum step interpolation*/
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */  int estepm;
   long ipmx;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   /*extern weight */  
   /* We are differentiating ll according to initial status */  int m,nb;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  long *num;
   /*for(i=1;i<imx;i++)  int firstpass=0, lastpass=4,*cod, *cens;
     printf(" %d\n",s[4][i]);  int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
   */                     covariate for which somebody answered excluding 
   cov[1]=1.;                     undefined. Usually 2: 0 and 1. */
   int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
   for(k=1; k<=nlstate; k++) ll[k]=0.;                               covariate for which somebody answered including 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){                               undefined. Usually 3: -1, 0 and 1. */
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     for(mi=1; mi<= wav[i]-1; mi++){  double **pmmij, ***probs;
       for (ii=1;ii<=nlstate+ndeath;ii++)  double *ageexmed,*agecens;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  double dateintmean=0;
       for(d=0; d<dh[mi][i]; d++){  
         newm=savm;  double *weight;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  int **s; /* Status */
         for (kk=1; kk<=cptcovage;kk++) {  double *agedc;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
         }                    * covar=matrix(0,NCOVMAX,1,n); 
                            * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  double  idx; 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
         savm=oldm;  int *Tage;
         oldm=newm;  int *Ndum; /** Freq of modality (tricode */
          /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
          int **Tvard, *Tprod, cptcovprod, *Tvaraff;
       } /* end mult */  double *lsurv, *lpop, *tpop;
        
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  double ftolhess; /**< Tolerance for computing hessian */
       ipmx +=1;  
       sw += weight[i];  /**************** split *************************/
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     } /* end of wave */  {
   } /* end of individual */    /* 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(k=1,l=0.; k<=nlstate; k++) l += ll[k];    */ 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    char  *ss;                            /* pointer */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    int   l1=0, l2=0;                             /* length counters */
   return -l;  
 }    l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 /*********** Maximum Likelihood Estimation ***************/    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       strcpy( name, path );               /* we got the fullname name because no directory */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   int i,j, iter;      /* get current working directory */
   double **xi,*delti;      /*    extern  char* getcwd ( char *buf , int len);*/
   double fret;  #ifdef WIN32
   xi=matrix(1,npar,1,npar);      if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
   for (i=1;i<=npar;i++)  #else
     for (j=1;j<=npar;j++)          if (getcwd(dirc, FILENAME_MAX) == NULL) {
       xi[i][j]=(i==j ? 1.0 : 0.0);  #endif
   printf("Powell\n");        return( GLOCK_ERROR_GETCWD );
   powell(p,xi,npar,ftol,&iter,&fret,func);      }
       /* got dirc from getcwd*/
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      printf(" DIRC = %s \n",dirc);
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
 }      l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 /**** Computes Hessian and covariance matrix ***/      strcpy( name, ss );         /* save file name */
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 {      dirc[l1-l2] = '\0';                 /* add zero */
   double  **a,**y,*x,pd;      printf(" DIRC2 = %s \n",dirc);
   double **hess;    }
   int i, j,jk;    /* We add a separator at the end of dirc if not exists */
   int *indx;    l1 = strlen( dirc );                  /* length of directory */
     if( dirc[l1-1] != DIRSEPARATOR ){
   double hessii(double p[], double delta, int theta, double delti[]);      dirc[l1] =  DIRSEPARATOR;
   double hessij(double p[], double delti[], int i, int j);      dirc[l1+1] = 0; 
   void lubksb(double **a, int npar, int *indx, double b[]) ;      printf(" DIRC3 = %s \n",dirc);
   void ludcmp(double **a, int npar, int *indx, double *d) ;    }
     ss = strrchr( name, '.' );            /* find last / */
   hess=matrix(1,npar,1,npar);    if (ss >0){
       ss++;
   printf("\nCalculation of the hessian matrix. Wait...\n");      strcpy(ext,ss);                     /* save extension */
   for (i=1;i<=npar;i++){      l1= strlen( name);
     printf("%d",i);fflush(stdout);      l2= strlen(ss)+1;
     hess[i][i]=hessii(p,ftolhess,i,delti);      strncpy( finame, name, l1-l2);
     /*printf(" %f ",p[i]);*/      finame[l1-l2]= 0;
     /*printf(" %lf ",hess[i][i]);*/    }
   }  
      return( 0 );                          /* we're done */
   for (i=1;i<=npar;i++) {  }
     for (j=1;j<=npar;j++)  {  
       if (j>i) {  
         printf(".%d%d",i,j);fflush(stdout);  /******************************************/
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];      void replace_back_to_slash(char *s, char*t)
         /*printf(" %lf ",hess[i][j]);*/  {
       }    int i;
     }    int lg=0;
   }    i=0;
   printf("\n");    lg=strlen(t);
     for(i=0; i<= lg; i++) {
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      (s[i] = t[i]);
        if (t[i]== '\\') s[i]='/';
   a=matrix(1,npar,1,npar);    }
   y=matrix(1,npar,1,npar);  }
   x=vector(1,npar);  
   indx=ivector(1,npar);  char *trimbb(char *out, char *in)
   for (i=1;i<=npar;i++)  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    char *s;
   ludcmp(a,npar,indx,&pd);    s=out;
     while (*in != '\0'){
   for (j=1;j<=npar;j++) {      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
     for (i=1;i<=npar;i++) x[i]=0;        in++;
     x[j]=1;      }
     lubksb(a,npar,indx,x);      *out++ = *in++;
     for (i=1;i<=npar;i++){    }
       matcov[i][j]=x[i];    *out='\0';
     }    return s;
   }  }
   
   printf("\n#Hessian matrix#\n");  /* char *substrchaine(char *out, char *in, char *chain) */
   for (i=1;i<=npar;i++) {  /* { */
     for (j=1;j<=npar;j++) {  /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
       printf("%.3e ",hess[i][j]);  /*   char *s, *t; */
     }  /*   t=in;s=out; */
     printf("\n");  /*   while ((*in != *chain) && (*in != '\0')){ */
   }  /*     *out++ = *in++; */
   /*   } */
   /* Recompute Inverse */  
   for (i=1;i<=npar;i++)  /*   /\* *in matches *chain *\/ */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  /*   while ((*in++ == *chain++) && (*in != '\0')){ */
   ludcmp(a,npar,indx,&pd);  /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   /*   } */
   /*  printf("\n#Hessian matrix recomputed#\n");  /*   in--; chain--; */
   /*   while ( (*in != '\0')){ */
   for (j=1;j<=npar;j++) {  /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
     for (i=1;i<=npar;i++) x[i]=0;  /*     *out++ = *in++; */
     x[j]=1;  /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
     lubksb(a,npar,indx,x);  /*   } */
     for (i=1;i<=npar;i++){  /*   *out='\0'; */
       y[i][j]=x[i];  /*   out=s; */
       printf("%.3e ",y[i][j]);  /*   return out; */
     }  /* } */
     printf("\n");  char *substrchaine(char *out, char *in, char *chain)
   }  {
   */    /* Substract chain 'chain' from 'in', return and output 'out' */
     /* in="V1+V1*age+age*age+V2", chain="age*age" */
   free_matrix(a,1,npar,1,npar);  
   free_matrix(y,1,npar,1,npar);    char *strloc;
   free_vector(x,1,npar);  
   free_ivector(indx,1,npar);    strcpy (out, in); 
   free_matrix(hess,1,npar,1,npar);    strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
     printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
     if(strloc != NULL){ 
 }      /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
       memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
 /*************** hessian matrix ****************/      /* strcpy (strloc, strloc +strlen(chain));*/
 double hessii( double x[], double delta, int theta, double delti[])    }
 {    printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
   int i;    return out;
   int l=1, lmax=20;  }
   double k1,k2;  
   double p2[NPARMAX+1];  
   double res;  char *cutl(char *blocc, char *alocc, char *in, char occ)
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  {
   double fx;    /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' 
   int k=0,kmax=10;       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   double l1;       gives blocc="abcdef" and alocc="ghi2j".
        If occ is not found blocc is null and alocc is equal to in. Returns blocc
   fx=func(x);    */
   for (i=1;i<=npar;i++) p2[i]=x[i];    char *s, *t;
   for(l=0 ; l <=lmax; l++){    t=in;s=in;
     l1=pow(10,l);    while ((*in != occ) && (*in != '\0')){
     delts=delt;      *alocc++ = *in++;
     for(k=1 ; k <kmax; k=k+1){    }
       delt = delta*(l1*k);    if( *in == occ){
       p2[theta]=x[theta] +delt;      *(alocc)='\0';
       k1=func(p2)-fx;      s=++in;
       p2[theta]=x[theta]-delt;    }
       k2=func(p2)-fx;   
       /*res= (k1-2.0*fx+k2)/delt/delt; */    if (s == t) {/* occ not found */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      *(alocc-(in-s))='\0';
            in=s;
 #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);    while ( *in != '\0'){
 #endif      *blocc++ = *in++;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    }
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  
         k=kmax;    *blocc='\0';
       }    return t;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  }
         k=kmax; l=lmax*10.;  char *cutv(char *blocc, char *alocc, char *in, char occ)
       }  {
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' 
         delts=delt;       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       }       gives blocc="abcdef2ghi" and alocc="j".
     }       If occ is not found blocc is null and alocc is equal to in. Returns alocc
   }    */
   delti[theta]=delts;    char *s, *t;
   return res;    t=in;s=in;
      while (*in != '\0'){
 }      while( *in == occ){
         *blocc++ = *in++;
 double hessij( double x[], double delti[], int thetai,int thetaj)        s=in;
 {      }
   int i;      *blocc++ = *in++;
   int l=1, l1, lmax=20;    }
   double k1,k2,k3,k4,res,fx;    if (s == t) /* occ not found */
   double p2[NPARMAX+1];      *(blocc-(in-s))='\0';
   int k;    else
       *(blocc-(in-s)-1)='\0';
   fx=func(x);    in=s;
   for (k=1; k<=2; k++) {    while ( *in != '\0'){
     for (i=1;i<=npar;i++) p2[i]=x[i];      *alocc++ = *in++;
     p2[thetai]=x[thetai]+delti[thetai]/k;    }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k1=func(p2)-fx;    *alocc='\0';
      return s;
     p2[thetai]=x[thetai]+delti[thetai]/k;  }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k2=func(p2)-fx;  int nbocc(char *s, char occ)
    {
     p2[thetai]=x[thetai]-delti[thetai]/k;    int i,j=0;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    int lg=20;
     k3=func(p2)-fx;    i=0;
      lg=strlen(s);
     p2[thetai]=x[thetai]-delti[thetai]/k;    for(i=0; i<= lg; i++) {
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    if  (s[i] == occ ) j++;
     k4=func(p2)-fx;    }
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    return j;
 #ifdef DEBUG  }
     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);  
 #endif  /* void cutv(char *u,char *v, char*t, char occ) */
   }  /* { */
   return res;  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
 }  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   /*      gives u="abcdef2ghi" and v="j" *\/ */
 /************** Inverse of matrix **************/  /*   int i,lg,j,p=0; */
 void ludcmp(double **a, int n, int *indx, double *d)  /*   i=0; */
 {  /*   lg=strlen(t); */
   int i,imax,j,k;  /*   for(j=0; j<=lg-1; j++) { */
   double big,dum,sum,temp;  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   double *vv;  /*   } */
    
   vv=vector(1,n);  /*   for(j=0; j<p; j++) { */
   *d=1.0;  /*     (u[j] = t[j]); */
   for (i=1;i<=n;i++) {  /*   } */
     big=0.0;  /*      u[p]='\0'; */
     for (j=1;j<=n;j++)  
       if ((temp=fabs(a[i][j])) > big) big=temp;  /*    for(j=0; j<= lg; j++) { */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
     vv[i]=1.0/big;  /*   } */
   }  /* } */
   for (j=1;j<=n;j++) {  
     for (i=1;i<j;i++) {  #ifdef _WIN32
       sum=a[i][j];  char * strsep(char **pp, const char *delim)
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  {
       a[i][j]=sum;    char *p, *q;
     }           
     big=0.0;    if ((p = *pp) == NULL)
     for (i=j;i<=n;i++) {      return 0;
       sum=a[i][j];    if ((q = strpbrk (p, delim)) != NULL)
       for (k=1;k<j;k++)    {
         sum -= a[i][k]*a[k][j];      *pp = q + 1;
       a[i][j]=sum;      *q = '\0';
       if ( (dum=vv[i]*fabs(sum)) >= big) {    }
         big=dum;    else
         imax=i;      *pp = 0;
       }    return p;
     }  }
     if (j != imax) {  #endif
       for (k=1;k<=n;k++) {  
         dum=a[imax][k];  /********************** nrerror ********************/
         a[imax][k]=a[j][k];  
         a[j][k]=dum;  void nrerror(char error_text[])
       }  {
       *d = -(*d);    fprintf(stderr,"ERREUR ...\n");
       vv[imax]=vv[j];    fprintf(stderr,"%s\n",error_text);
     }    exit(EXIT_FAILURE);
     indx[j]=imax;  }
     if (a[j][j] == 0.0) a[j][j]=TINY;  /*********************** vector *******************/
     if (j != n) {  double *vector(int nl, int nh)
       dum=1.0/(a[j][j]);  {
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    double *v;
     }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   }    if (!v) nrerror("allocation failure in vector");
   free_vector(vv,1,n);  /* Doesn't work */    return v-nl+NR_END;
 ;  }
 }  
   /************************ free vector ******************/
 void lubksb(double **a, int n, int *indx, double b[])  void free_vector(double*v, int nl, int nh)
 {  {
   int i,ii=0,ip,j;    free((FREE_ARG)(v+nl-NR_END));
   double sum;  }
    
   for (i=1;i<=n;i++) {  /************************ivector *******************************/
     ip=indx[i];  int *ivector(long nl,long nh)
     sum=b[ip];  {
     b[ip]=b[i];    int *v;
     if (ii)    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    if (!v) nrerror("allocation failure in ivector");
     else if (sum) ii=i;    return v-nl+NR_END;
     b[i]=sum;  }
   }  
   for (i=n;i>=1;i--) {  /******************free ivector **************************/
     sum=b[i];  void free_ivector(int *v, long nl, long nh)
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  {
     b[i]=sum/a[i][i];    free((FREE_ARG)(v+nl-NR_END));
   }  }
 }  
   /************************lvector *******************************/
 /************ Frequencies ********************/  long *lvector(long nl,long nh)
 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)  {
 {  /* Some frequencies */    long *v;
      v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    if (!v) nrerror("allocation failure in ivector");
   double ***freq; /* Frequencies */    return v-nl+NR_END;
   double *pp;  }
   double pos, k2, dateintsum=0,k2cpt=0;  
   FILE *ficresp;  /******************free lvector **************************/
   char fileresp[FILENAMELENGTH];  void free_lvector(long *v, long nl, long nh)
    {
   pp=vector(1,nlstate);    free((FREE_ARG)(v+nl-NR_END));
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  }
   strcpy(fileresp,"p");  
   strcat(fileresp,fileres);  /******************* imatrix *******************************/
   if((ficresp=fopen(fileresp,"w"))==NULL) {  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     printf("Problem with prevalence resultfile: %s\n", fileresp);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     exit(0);  { 
   }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    int **m; 
   j1=0;    
     /* allocate pointers to rows */ 
   j=cptcoveff;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
   for(k1=1; k1<=j;k1++){    m -= nrl; 
    for(i1=1; i1<=ncodemax[k1];i1++){    
        j1++;    
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    /* allocate rows and set pointers to them */ 
          scanf("%d", i);*/    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
         for (i=-1; i<=nlstate+ndeath; i++)      if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
          for (jk=-1; jk<=nlstate+ndeath; jk++)      m[nrl] += NR_END; 
            for(m=agemin; m <= agemax+3; m++)    m[nrl] -= ncl; 
              freq[i][jk][m]=0;    
     for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
         dateintsum=0;    
         k2cpt=0;    /* return pointer to array of pointers to rows */ 
        for (i=1; i<=imx; i++) {    return m; 
          bool=1;  } 
          if  (cptcovn>0) {  
            for (z1=1; z1<=cptcoveff; z1++)  /****************** free_imatrix *************************/
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  void free_imatrix(m,nrl,nrh,ncl,nch)
                bool=0;        int **m;
          }        long nch,ncl,nrh,nrl; 
          if (bool==1) {       /* free an int matrix allocated by imatrix() */ 
            for(m=firstpass; m<=lastpass; m++){  { 
              k2=anint[m][i]+(mint[m][i]/12.);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
              if ((k2>=dateprev1) && (k2<=dateprev2)) {    free((FREE_ARG) (m+nrl-NR_END)); 
                if(agev[m][i]==0) agev[m][i]=agemax+1;  } 
                if(agev[m][i]==1) agev[m][i]=agemax+2;  
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  /******************* matrix *******************************/
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  double **matrix(long nrl, long nrh, long ncl, long nch)
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  {
                  dateintsum=dateintsum+k2;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
                  k2cpt++;    double **m;
                }  
     m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
              }    if (!m) nrerror("allocation failure 1 in matrix()");
            }    m += NR_END;
          }    m -= nrl;
        }  
            m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
         if  (cptcovn>0) {    m[nrl] -= ncl;
          fprintf(ficresp, "\n#********** Variable ");  
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
        fprintf(ficresp, "**********\n#");    return m;
         }    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
        for(i=1; i<=nlstate;i++)  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
        fprintf(ficresp, "\n");     */
          }
   for(i=(int)agemin; i <= (int)agemax+3; i++){  
     if(i==(int)agemax+3)  /*************************free matrix ************************/
       printf("Total");  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     else  {
       printf("Age %d", i);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     for(jk=1; jk <=nlstate ; jk++){    free((FREE_ARG)(m+nrl-NR_END));
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  }
         pp[jk] += freq[jk][m][i];  
     }  /******************* ma3x *******************************/
     for(jk=1; jk <=nlstate ; jk++){  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       for(m=-1, pos=0; m <=0 ; m++)  {
         pos += freq[jk][m][i];    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       if(pp[jk]>=1.e-10)    double ***m;
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  
       else    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    if (!m) nrerror("allocation failure 1 in matrix()");
     }    m += NR_END;
     m -= nrl;
      for(jk=1; jk <=nlstate ; jk++){  
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         pp[jk] += freq[jk][m][i];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
      }    m[nrl] += NR_END;
     m[nrl] -= ncl;
     for(jk=1,pos=0; jk <=nlstate ; jk++)  
       pos += pp[jk];    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     for(jk=1; jk <=nlstate ; jk++){  
       if(pos>=1.e-5)    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       else    m[nrl][ncl] += NR_END;
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    m[nrl][ncl] -= nll;
       if( i <= (int) agemax){    for (j=ncl+1; j<=nch; j++) 
         if(pos>=1.e-5){      m[nrl][j]=m[nrl][j-1]+nlay;
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    
           probs[i][jk][j1]= pp[jk]/pos;    for (i=nrl+1; i<=nrh; i++) {
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         }      for (j=ncl+1; j<=nch; j++) 
       else        m[i][j]=m[i][j-1]+nlay;
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    }
       }    return m; 
     }    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     for(jk=-1; jk <=nlstate+ndeath; jk++)             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       for(m=-1; m <=nlstate+ndeath; m++)    */
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  }
     if(i <= (int) agemax)  
       fprintf(ficresp,"\n");  /*************************free ma3x ************************/
     printf("\n");  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     }  {
     }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
  }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   dateintmean=dateintsum/k2cpt;    free((FREE_ARG)(m+nrl-NR_END));
    }
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  /*************** function subdirf ***********/
   free_vector(pp,1,nlstate);  char *subdirf(char fileres[])
   {
   /* End of Freq */    /* Caution optionfilefiname is hidden */
 }    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
 /************ Prevalence ********************/    strcat(tmpout,fileres);
 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)    return tmpout;
 {  /* Some frequencies */  }
    
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  /*************** function subdirf2 ***********/
   double ***freq; /* Frequencies */  char *subdirf2(char fileres[], char *preop)
   double *pp;  {
   double pos, k2;    
     /* Caution optionfilefiname is hidden */
   pp=vector(1,nlstate);    strcpy(tmpout,optionfilefiname);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    strcat(tmpout,"/");
      strcat(tmpout,preop);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    strcat(tmpout,fileres);
   j1=0;    return tmpout;
    }
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  /*************** function subdirf3 ***********/
    char *subdirf3(char fileres[], char *preop, char *preop2)
  for(k1=1; k1<=j;k1++){  {
     for(i1=1; i1<=ncodemax[k1];i1++){    
       j1++;    /* Caution optionfilefiname is hidden */
      strcpy(tmpout,optionfilefiname);
       for (i=-1; i<=nlstate+ndeath; i++)      strcat(tmpout,"/");
         for (jk=-1; jk<=nlstate+ndeath; jk++)      strcat(tmpout,preop);
           for(m=agemin; m <= agemax+3; m++)    strcat(tmpout,preop2);
             freq[i][jk][m]=0;    strcat(tmpout,fileres);
          return tmpout;
       for (i=1; i<=imx; i++) {  }
         bool=1;  
         if  (cptcovn>0) {  char *asc_diff_time(long time_sec, char ascdiff[])
           for (z1=1; z1<=cptcoveff; z1++)  {
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    long sec_left, days, hours, minutes;
               bool=0;    days = (time_sec) / (60*60*24);
         }    sec_left = (time_sec) % (60*60*24);
         if (bool==1) {    hours = (sec_left) / (60*60) ;
           for(m=firstpass; m<=lastpass; m++){    sec_left = (sec_left) %(60*60);
             k2=anint[m][i]+(mint[m][i]/12.);    minutes = (sec_left) /60;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    sec_left = (sec_left) % (60);
               if(agev[m][i]==0) agev[m][i]=agemax+1;    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
               if(agev[m][i]==1) agev[m][i]=agemax+2;    return ascdiff;
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];  }
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */  
             }  /***************** f1dim *************************/
           }  extern int ncom; 
         }  extern double *pcom,*xicom;
       }  extern double (*nrfunc)(double []); 
         for(i=(int)agemin; i <= (int)agemax+3; i++){   
           for(jk=1; jk <=nlstate ; jk++){  double f1dim(double x) 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  { 
               pp[jk] += freq[jk][m][i];    int j; 
           }    double f;
           for(jk=1; jk <=nlstate ; jk++){    double *xt; 
             for(m=-1, pos=0; m <=0 ; m++)   
             pos += freq[jk][m][i];    xt=vector(1,ncom); 
         }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
            f=(*nrfunc)(xt); 
          for(jk=1; jk <=nlstate ; jk++){    free_vector(xt,1,ncom); 
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    return f; 
              pp[jk] += freq[jk][m][i];  } 
          }  
            /*****************brent *************************/
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   {
          for(jk=1; jk <=nlstate ; jk++){              /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
            if( i <= (int) agemax){     * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
              if(pos>=1.e-5){     * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
                probs[i][jk][j1]= pp[jk]/pos;     * the minimum is returned as xmin, and the minimum function value is returned as brent , the
              }     * returned function value. 
            }    */
          }    int iter; 
              double a,b,d,etemp;
         }    double fu=0,fv,fw,fx;
     }    double ftemp=0.;
   }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
      double e=0.0; 
     
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    a=(ax < cx ? ax : cx); 
   free_vector(pp,1,nlstate);    b=(ax > cx ? ax : cx); 
      x=w=v=bx; 
 }  /* End of Freq */    fw=fv=fx=(*f)(x); 
     for (iter=1;iter<=ITMAX;iter++) { 
 /************* Waves Concatenation ***************/      xm=0.5*(a+b); 
       tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 {      printf(".");fflush(stdout);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      fprintf(ficlog,".");fflush(ficlog);
      Death is a valid wave (if date is known).  #ifdef DEBUGBRENT
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      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);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      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);
      and mw[mi+1][i]. dh depends on stepm.      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
      */  #endif
       if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   int i, mi, m;        *xmin=x; 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        return fx; 
      double sum=0., jmean=0.;*/      } 
       ftemp=fu;
   int j, k=0,jk, ju, jl;      if (fabs(e) > tol1) { 
   double sum=0.;        r=(x-w)*(fx-fv); 
   jmin=1e+5;        q=(x-v)*(fx-fw); 
   jmax=-1;        p=(x-v)*q-(x-w)*r; 
   jmean=0.;        q=2.0*(q-r); 
   for(i=1; i<=imx; i++){        if (q > 0.0) p = -p; 
     mi=0;        q=fabs(q); 
     m=firstpass;        etemp=e; 
     while(s[m][i] <= nlstate){        e=d; 
       if(s[m][i]>=1)        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         mw[++mi][i]=m;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       if(m >=lastpass)        else { 
         break;          d=p/q; 
       else          u=x+d; 
         m++;          if (u-a < tol2 || b-u < tol2) 
     }/* end while */            d=SIGN(tol1,xm-x); 
     if (s[m][i] > nlstate){        } 
       mi++;     /* Death is another wave */      } else { 
       /* if(mi==0)  never been interviewed correctly before death */        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
          /* Only death is a correct wave */      } 
       mw[mi][i]=m;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     }      fu=(*f)(u); 
       if (fu <= fx) { 
     wav[i]=mi;        if (u >= x) a=x; else b=x; 
     if(mi==0)        SHFT(v,w,x,u) 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        SHFT(fv,fw,fx,fu) 
   }      } else { 
         if (u < x) a=u; else b=u; 
   for(i=1; i<=imx; i++){        if (fu <= fw || w == x) { 
     for(mi=1; mi<wav[i];mi++){          v=w; 
       if (stepm <=0)          w=u; 
         dh[mi][i]=1;          fv=fw; 
       else{          fw=fu; 
         if (s[mw[mi+1][i]][i] > nlstate) {        } else if (fu <= fv || v == x || v == w) { 
           if (agedc[i] < 2*AGESUP) {          v=u; 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          fv=fu; 
           if(j==0) j=1;  /* Survives at least one month after exam */        } 
           k=k+1;      } 
           if (j >= jmax) jmax=j;    } 
           if (j <= jmin) jmin=j;    nrerror("Too many iterations in brent"); 
           sum=sum+j;    *xmin=x; 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    return fx; 
           }  } 
         }  
         else{  /****************** mnbrak ***********************/
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  
           k=k+1;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
           if (j >= jmax) jmax=j;              double (*func)(double)) 
           else if (j <= jmin)jmin=j;  { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  the downhill direction (defined by the function as evaluated at the initial points) and returns
           sum=sum+j;  new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
         }  values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
         jk= j/stepm;     */
         jl= j -jk*stepm;    double ulim,u,r,q, dum;
         ju= j -(jk+1)*stepm;    double fu; 
         if(jl <= -ju)  
           dh[mi][i]=jk;    double scale=10.;
         else    int iterscale=0;
           dh[mi][i]=jk+1;  
         if(dh[mi][i]==0)    *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
           dh[mi][i]=1; /* At least one step */    *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
       }  
     }  
   }    /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
   jmean=sum/k;    /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    /*   *bx = *ax - (*ax - *bx)/scale; */
  }    /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
 /*********** Tricode ****************************/    /* } */
 void tricode(int *Tvar, int **nbcode, int imx)  
 {    if (*fb > *fa) { 
   int Ndum[20],ij=1, k, j, i;      SHFT(dum,*ax,*bx,dum) 
   int cptcode=0;      SHFT(dum,*fb,*fa,dum) 
   cptcoveff=0;    } 
      *cx=(*bx)+GOLD*(*bx-*ax); 
   for (k=0; k<19; k++) Ndum[k]=0;    *fc=(*func)(*cx); 
   for (k=1; k<=7; k++) ncodemax[k]=0;  #ifdef DEBUG
     printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
     for (i=1; i<=imx; i++) {  #endif
       ij=(int)(covar[Tvar[j]][i]);    while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
       Ndum[ij]++;      r=(*bx-*ax)*(*fb-*fc); 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      q=(*bx-*cx)*(*fb-*fa); 
       if (ij > cptcode) cptcode=ij;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
       ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
     for (i=0; i<=cptcode; i++) {      if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
       if(Ndum[i]!=0) ncodemax[j]++;        fu=(*func)(u); 
     }  #ifdef DEBUG
     ij=1;        /* f(x)=A(x-u)**2+f(u) */
         double A, fparabu; 
         A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
     for (i=1; i<=ncodemax[j]; i++) {        fparabu= *fa - A*(*ax-u)*(*ax-u);
       for (k=0; k<=19; k++) {        printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
         if (Ndum[k] != 0) {        fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
           nbcode[Tvar[j]][ij]=k;        /* And thus,it can be that fu > *fc even if fparabu < *fc */
           ij++;        /* 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) */
         if (ij > ncodemax[j]) break;        /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
       }    #endif 
     }  #ifdef MNBRAKORIGINAL
   }    #else
   /*       if (fu > *fc) { */
  for (k=0; k<19; k++) Ndum[k]=0;  /* #ifdef DEBUG */
   /*       printf("mnbrak4  fu > fc \n"); */
  for (i=1; i<=ncovmodel-2; i++) {  /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
       ij=Tvar[i];  /* #endif */
       Ndum[ij]++;  /*      /\* 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 *\\/  *\/ */
     }  /*      /\* 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 *\/ */
  ij=1;  /*      u = *cx; */
  for (i=1; i<=10; i++) {  /*      *cx = dum; */
    if((Ndum[i]!=0) && (i<=ncov)){  /*      dum = fu; */
      Tvaraff[ij]=i;  /*      fu = *fc; */
      ij++;  /*      *fc =dum; */
    }  /*       } else { /\* end *\/ */
  }  /* #ifdef DEBUG */
    /*       printf("mnbrak3  fu < fc \n"); */
     cptcoveff=ij-1;  /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
 }  /* #endif */
   /*      dum=u; /\* Shifting c and u *\/ */
 /*********** Health Expectancies ****************/  /*      u = *cx; */
   /*      *cx = dum; */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)  /*      dum = fu; */
 {  /*      fu = *fc; */
   /* Health expectancies */  /*      *fc =dum; */
   int i, j, nhstepm, hstepm, h, nstepm, k;  /*       } */
   double age, agelim,hf;  #ifdef DEBUG
   double ***p3mat;        printf("mnbrak34  fu < or >= fc \n");
          fprintf(ficlog, "mnbrak34 fu < fc\n");
   fprintf(ficreseij,"# Health expectancies\n");  #endif
   fprintf(ficreseij,"# Age");        dum=u; /* Shifting c and u */
   for(i=1; i<=nlstate;i++)        u = *cx;
     for(j=1; j<=nlstate;j++)        *cx = dum;
       fprintf(ficreseij," %1d-%1d",i,j);        dum = fu;
   fprintf(ficreseij,"\n");        fu = *fc;
         *fc =dum;
   k=1;             /* For example stepm=6 months */  #endif
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */  #ifdef DEBUG
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        printf("mnbrak2  u after c but before ulim\n");
      nhstepm is the number of hstepm from age to agelim        fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
      nstepm is the number of stepm from age to agelin.  #endif
      Look at hpijx to understand the reason of that which relies in memory size        fu=(*func)(u); 
      and note for a fixed period like k years */        if (fu < *fc) { 
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  #ifdef DEBUG
      survival function given by stepm (the optimization length). Unfortunately it        printf("mnbrak2  u after c but before ulim AND fu < fc\n");
      means that if the survival funtion is printed only each two years of age and if        fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  #endif
      results. So we changed our mind and took the option of the best precision.          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   */          SHFT(*fb,*fc,fu,(*func)(u)) 
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */        } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
   agelim=AGESUP;  #ifdef DEBUG
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
     /* nhstepm age range expressed in number of stepm */        fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
     nstepm=(int) rint((agelim-age)*YEARM/stepm);  #endif
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */        u=ulim; 
     if (stepm >= YEARM) hstepm=1;        fu=(*func)(u); 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      } else { /* u could be left to b (if r > q parabola has a maximum) */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  #ifdef DEBUG
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    #endif
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        u=(*cx)+GOLD*(*cx-*bx); 
     for(i=1; i<=nlstate;i++)        fu=(*func)(u); 
       for(j=1; j<=nlstate;j++)      } /* end tests */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){      SHFT(*ax,*bx,*cx,u) 
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      SHFT(*fa,*fb,*fc,fu) 
           /* 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]);*/  #ifdef DEBUG
         }        printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
     fprintf(ficreseij,"%3.0f",age );        fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
     for(i=1; i<=nlstate;i++)  #endif
       for(j=1; j<=nlstate;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) */
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);  } 
       }  
     fprintf(ficreseij,"\n");  /*************** linmin ************************/
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
   }  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
   the value of func at the returned location p . This is actually all accomplished by calling the
 /************ Variance ******************/  routines mnbrak and brent .*/
 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 ncom; 
 {  double *pcom,*xicom;
   /* Variance of health expectancies */  double (*nrfunc)(double []); 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/   
   double **newm;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   double **dnewm,**doldm;  { 
   int i, j, nhstepm, hstepm, h;    double brent(double ax, double bx, double cx, 
   int k, cptcode;                 double (*f)(double), double tol, double *xmin); 
   double *xp;    double f1dim(double x); 
   double **gp, **gm;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   double ***gradg, ***trgradg;                double *fc, double (*func)(double)); 
   double ***p3mat;    int j; 
   double age,agelim;    double xx,xmin,bx,ax; 
   int theta;    double fx,fb,fa;
   
    fprintf(ficresvij,"# Covariances of life expectancies\n");    double scale=10., axs, xxs, xxss; /* Scale added for infinity */
   fprintf(ficresvij,"# Age");   
   for(i=1; i<=nlstate;i++)    ncom=n; 
     for(j=1; j<=nlstate;j++)    pcom=vector(1,n); 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    xicom=vector(1,n); 
   fprintf(ficresvij,"\n");    nrfunc=func; 
     for (j=1;j<=n;j++) { 
   xp=vector(1,npar);      pcom[j]=p[j]; 
   dnewm=matrix(1,nlstate,1,npar);      xicom[j]=xi[j]; 
   doldm=matrix(1,nlstate,1,nlstate);    } 
    
   hstepm=1*YEARM; /* Every year of age */    /* axs=0.0; */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    /* xxss=1; /\* 1 and using scale *\/ */
   agelim = AGESUP;    xxs=1;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /* do{ */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      ax=0.;
     if (stepm >= YEARM) hstepm=1;      xx= xxs;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      /* 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))   */
     gp=matrix(0,nhstepm,1,nlstate);      /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
     gm=matrix(0,nhstepm,1,nlstate);      /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
       /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
     for(theta=1; theta <=npar; theta++){      /* 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]]*/
       for(i=1; i<=npar; i++){ /* Computes gradient */    /*   if (fx != fx){ */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    /*    xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */
       }    /*    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); */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      /*   } */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /* }while(fx != fx); */
   
       if (popbased==1) {  #ifdef DEBUGLINMIN
         for(i=1; i<=nlstate;i++)    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);
           prlim[i][i]=probs[(int)age][i][ij];  #endif
       }    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
      /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
       for(j=1; j<= nlstate; j++){    /* fmin = f(p[j] + xmin * xi[j]) */
         for(h=0; h<=nhstepm; h++){    /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  #ifdef DEBUG
         }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
      #endif
       for(i=1; i<=npar; i++) /* Computes gradient */  #ifdef DEBUGLINMIN
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    printf("linmin end ");
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    #endif
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for (j=1;j<=n;j++) { 
        /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
       if (popbased==1) {      xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
         for(i=1; i<=nlstate;i++)      /* if(xxs <1.0) */
           prlim[i][i]=probs[(int)age][i][ij];      /*   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 ); */
       }      p[j] += xi[j]; /* Parameters values are updated accordingly */
     } 
       for(j=1; j<= nlstate; j++){    /* printf("\n"); */
         for(h=0; h<=nhstepm; h++){  #ifdef DEBUGLINMIN
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    for (j=1;j<=n;j++) { 
         }      printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);
       }      if(j % ncovmodel == 0)
         printf("\n");
       for(j=1; j<= nlstate; j++)    }
         for(h=0; h<=nhstepm; h++){  #endif
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    free_vector(xicom,1,n); 
         }    free_vector(pcom,1,n); 
     } /* End theta */  } 
   
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  
   /*************** powell ************************/
     for(h=0; h<=nhstepm; h++)  /*
       for(j=1; j<=nlstate;j++)  Minimization of a function func of n variables. Input consists of an initial starting point
         for(theta=1; theta <=npar; theta++)  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
           trgradg[h][j][theta]=gradg[h][theta][j];  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
     for(i=1;i<=nlstate;i++)  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
       for(j=1;j<=nlstate;j++)  function value at p , and iter is the number of iterations taken. The routine linmin is used.
         vareij[i][j][(int)age] =0.;   */
     for(h=0;h<=nhstepm;h++){  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       for(k=0;k<=nhstepm;k++){              double (*func)(double [])) 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);  { 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    void linmin(double p[], double xi[], int n, double *fret, 
         for(i=1;i<=nlstate;i++)                double (*func)(double [])); 
           for(j=1;j<=nlstate;j++)    int i,ibig,j; 
             vareij[i][j][(int)age] += doldm[i][j];    double del,t,*pt,*ptt,*xit;
       }    double directest;
     }    double fp,fptt;
     h=1;    double *xits;
     if (stepm >= YEARM) h=stepm/YEARM;    int niterf, itmp;
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)    pt=vector(1,n); 
       for(j=1; j<=nlstate;j++){    ptt=vector(1,n); 
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    xit=vector(1,n); 
       }    xits=vector(1,n); 
     fprintf(ficresvij,"\n");    *fret=(*func)(p); 
     free_matrix(gp,0,nhstepm,1,nlstate);    for (j=1;j<=n;j++) pt[j]=p[j]; 
     free_matrix(gm,0,nhstepm,1,nlstate);      rcurr_time = time(NULL);  
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    for (*iter=1;;++(*iter)) { 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      fp=(*fret); /* From former iteration or initial value */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      ibig=0; 
   } /* End age */      del=0.0; 
        rlast_time=rcurr_time;
   free_vector(xp,1,npar);      /* (void) gettimeofday(&curr_time,&tzp); */
   free_matrix(doldm,1,nlstate,1,npar);      rcurr_time = time(NULL);  
   free_matrix(dnewm,1,nlstate,1,nlstate);      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(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
   /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
 /************ Variance of prevlim ******************/      for (i=1;i<=n;i++) {
 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)        printf(" %d %.12f",i, p[i]);
 {        fprintf(ficlog," %d %.12lf",i, p[i]);
   /* Variance of prevalence limit */        fprintf(ficrespow," %.12lf", p[i]);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      }
   double **newm;      printf("\n");
   double **dnewm,**doldm;      fprintf(ficlog,"\n");
   int i, j, nhstepm, hstepm;      fprintf(ficrespow,"\n");fflush(ficrespow);
   int k, cptcode;      if(*iter <=3){
   double *xp;        tml = *localtime(&rcurr_time);
   double *gp, *gm;        strcpy(strcurr,asctime(&tml));
   double **gradg, **trgradg;        rforecast_time=rcurr_time; 
   double age,agelim;        itmp = strlen(strcurr);
   int theta;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
              strcurr[itmp-1]='\0';
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
   fprintf(ficresvpl,"# Age");        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
   for(i=1; i<=nlstate;i++)        for(niterf=10;niterf<=30;niterf+=10){
       fprintf(ficresvpl," %1d-%1d",i,i);          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
   fprintf(ficresvpl,"\n");          forecast_time = *localtime(&rforecast_time);
           strcpy(strfor,asctime(&forecast_time));
   xp=vector(1,npar);          itmp = strlen(strfor);
   dnewm=matrix(1,nlstate,1,npar);          if(strfor[itmp-1]=='\n')
   doldm=matrix(1,nlstate,1,nlstate);          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);
   hstepm=1*YEARM; /* Every year of age */          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);
   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 */      for (i=1;i<=n;i++) { /* For each direction i */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
     if (stepm >= YEARM) hstepm=1;        fptt=(*fret); 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  #ifdef DEBUG
     gradg=matrix(1,npar,1,nlstate);            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
     gp=vector(1,nlstate);            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
     gm=vector(1,nlstate);  #endif
             printf("%d",i);fflush(stdout); /* print direction (parameter) i */
     for(theta=1; theta <=npar; theta++){        fprintf(ficlog,"%d",i);fflush(ficlog);
       for(i=1; i<=npar; i++){ /* Computes gradient */        linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                                      /* Outputs are fret(new point p) p is updated and xit rescaled */
       }        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          /* because that direction will be replaced unless the gain del is small */
       for(i=1;i<=nlstate;i++)          /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
         gp[i] = prlim[i][i];          /* Unless the n directions are conjugate some gain in the determinant may be obtained */
              /* with the new direction. */
       for(i=1; i<=npar; i++) /* Computes gradient */          del=fabs(fptt-(*fret)); 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          ibig=i; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        } 
       for(i=1;i<=nlstate;i++)  #ifdef DEBUG
         gm[i] = prlim[i][i];        printf("%d %.12e",i,(*fret));
         fprintf(ficlog,"%d %.12e",i,(*fret));
       for(i=1;i<=nlstate;i++)        for (j=1;j<=n;j++) {
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     } /* End theta */          printf(" x(%d)=%.12e",j,xit[j]);
           fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     trgradg =matrix(1,nlstate,1,npar);        }
         for(j=1;j<=n;j++) {
     for(j=1; j<=nlstate;j++)          printf(" p(%d)=%.12e",j,p[j]);
       for(theta=1; theta <=npar; theta++)          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
         trgradg[j][theta]=gradg[theta][j];        }
         printf("\n");
     for(i=1;i<=nlstate;i++)        fprintf(ficlog,"\n");
       varpl[i][(int)age] =0.;  #endif
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      } /* end loop on each direction i */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 
     for(i=1;i<=nlstate;i++)      /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      /* New value of last point Pn is not computed, P(n-1) */
       if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
     fprintf(ficresvpl,"%.0f ",age );        /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
     for(i=1; i<=nlstate;i++)        /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
     fprintf(ficresvpl,"\n");        /* decreased of more than 3.84  */
     free_vector(gp,1,nlstate);        /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
     free_vector(gm,1,nlstate);        /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
     free_matrix(gradg,1,npar,1,nlstate);        /* By adding 10 parameters more the gain should be 18.31 */
     free_matrix(trgradg,1,nlstate,1,npar);  
   } /* End age */        /* Starting the program with initial values given by a former maximization will simply change */
         /* the scales of the directions and the directions, because the are reset to canonical directions */
   free_vector(xp,1,npar);        /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
   free_matrix(doldm,1,nlstate,1,npar);        /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
   free_matrix(dnewm,1,nlstate,1,nlstate);  #ifdef DEBUG
         int k[2],l;
 }        k[0]=1;
         k[1]=-1;
 /************ Variance of one-step probabilities  ******************/        printf("Max: %.12e",(*func)(p));
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        fprintf(ficlog,"Max: %.12e",(*func)(p));
 {        for (j=1;j<=n;j++) {
   int i, j;          printf(" %.12e",p[j]);
   int k=0, cptcode;          fprintf(ficlog," %.12e",p[j]);
   double **dnewm,**doldm;        }
   double *xp;        printf("\n");
   double *gp, *gm;        fprintf(ficlog,"\n");
   double **gradg, **trgradg;        for(l=0;l<=1;l++) {
   double age,agelim, cov[NCOVMAX];          for (j=1;j<=n;j++) {
   int theta;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   char fileresprob[FILENAMELENGTH];            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]);
   strcpy(fileresprob,"prob");          }
   strcat(fileresprob,fileres);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     printf("Problem with resultfile: %s\n", fileresprob);        }
   }  #endif
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);  
    
         free_vector(xit,1,n); 
   xp=vector(1,npar);        free_vector(xits,1,n); 
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        free_vector(ptt,1,n); 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));        free_vector(pt,1,n); 
          return; 
   cov[1]=1;      } /* enough precision */ 
   for (age=bage; age<=fage; age ++){      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     cov[2]=age;      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
     gradg=matrix(1,npar,1,9);        ptt[j]=2.0*p[j]-pt[j]; 
     trgradg=matrix(1,9,1,npar);        xit[j]=p[j]-pt[j]; 
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        pt[j]=p[j]; 
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      } 
          fptt=(*func)(ptt); /* f_3 */
     for(theta=1; theta <=npar; theta++){  #ifdef POWELLF1F3
       for(i=1; i<=npar; i++)  #else
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
        #endif
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
            /* From x1 (P0) distance of x2 is at h and x3 is 2h */
       k=0;        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
       for(i=1; i<= (nlstate+ndeath); i++){        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
         for(j=1; j<=(nlstate+ndeath);j++){        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
            k=k+1;        /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
           gp[k]=pmmij[i][j];        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
         }  #ifdef NRCORIGINAL
       }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
   #else
       for(i=1; i<=npar; i++)        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        t= t- del*SQR(fp-fptt);
      #endif
         directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  #ifdef DEBUG
       k=0;        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);
       for(i=1; i<=(nlstate+ndeath); i++){        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);
         for(j=1; j<=(nlstate+ndeath);j++){        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
           k=k+1;               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
           gm[k]=pmmij[i][j];        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));
       }        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);
              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);
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  #endif
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    #ifdef POWELLORIGINAL
     }        if (t < 0.0) { /* Then we use it for new direction */
   #else
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)        if (directest*t < 0.0) { /* Contradiction between both tests */
       for(theta=1; theta <=npar; theta++)          printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
       trgradg[j][theta]=gradg[theta][j];          printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
            fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);        } 
         if (directest < 0.0) { /* Then we use it for new direction */
      pmij(pmmij,cov,ncovmodel,x,nlstate);  #endif
   #ifdef DEBUGLINMIN
      k=0;          printf("Before linmin in direction P%d-P0\n",n);
      for(i=1; i<=(nlstate+ndeath); i++){          for (j=1;j<=n;j++) { 
        for(j=1; j<=(nlstate+ndeath);j++){            printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
          k=k+1;            if(j % ncovmodel == 0)
          gm[k]=pmmij[i][j];              printf("\n");
         }          }
      }  #endif
                linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
      /*printf("\n%d ",(int)age);  #ifdef DEBUGLINMIN
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          for (j=1;j<=n;j++) { 
                    printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
             if(j % ncovmodel == 0)
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));              printf("\n");
      }*/          }
   #endif
   fprintf(ficresprob,"\n%d ",(int)age);          for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          }
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          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);
   
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  #ifdef DEBUG
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          for(j=1;j<=n;j++){
 }            printf(" %.12e",xit[j]);
  free_vector(xp,1,npar);            fprintf(ficlog," %.12e",xit[j]);
 fclose(ficresprob);          }
           printf("\n");
 }          fprintf(ficlog,"\n");
   #endif
 /******************* Printing html file ***********/        } /* end of t or directest negative */
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){  #ifdef POWELLF1F3
   int jj1, k1, i1, cpt;  #else
   FILE *fichtm;      } /* end if (fptt < fp)  */
   /*char optionfilehtm[FILENAMELENGTH];*/  #endif
     } /* loop iteration */ 
   strcpy(optionfilehtm,optionfile);  } 
   strcat(optionfilehtm,".htm");  
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  /**** Prevalence limit (stable or period prevalence)  ****************/
     printf("Problem with %s \n",optionfilehtm), exit(0);  
   }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   {
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71c </font> <hr size=\"2\" color=\"#EC5E5E\">    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>       matrix by transitions matrix until convergence is reached */
     
 Total number of observations=%d <br>    int i, ii,j,k;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>    double min, max, maxmin, maxmax,sumnew=0.;
 <hr  size=\"2\" color=\"#EC5E5E\">    /* double **matprod2(); */ /* test */
 <li>Outputs files<br><br>\n    double **out, cov[NCOVMAX+1], **pmij();
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    double **newm;
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    double agefin, delaymax=50 ; /* Max number of years to converge */
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    for (ii=1;ii<=nlstate+ndeath;ii++)
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>      for (j=1;j<=nlstate+ndeath;j++){
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>      }
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>    cov[1]=1.;
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>    
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
        newm=savm;
 fprintf(fichtm," <li>Graphs</li><p>");      /* Covariates have to be included here again */
       cov[2]=agefin;
  m=cptcoveff;      if(nagesqr==1)
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        cov[3]= agefin*agefin;;
       for (k=1; k<=cptcovn;k++) {
  jj1=0;        /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
  for(k1=1; k1<=m;k1++){        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
    for(i1=1; i1<=ncodemax[k1];i1++){        /* 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])]); */
        jj1++;      }
        if (cptcovn > 0) {      /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
          for (cpt=1; cpt<=cptcoveff;cpt++)      for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      for (k=1; k<=cptcovprod;k++) /* Useless */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        /* 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)];
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
        for(cpt=1; cpt<nlstate;cpt++){      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
        }      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
     for(cpt=1; cpt<=nlstate;cpt++) {      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      
 interval) in state (%d): v%s%d%d.gif <br>      savm=oldm;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        oldm=newm;
      }      maxmax=0.;
      for(cpt=1; cpt<=nlstate;cpt++) {      for(j=1;j<=nlstate;j++){
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        min=1.;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        max=0.;
      }        for(i=1; i<=nlstate; i++) {
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          sumnew=0;
 health expectancies in states (1) and (2): e%s%d.gif<br>          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          prlim[i][j]= newm[i][j]/(1-sumnew);
 fprintf(fichtm,"\n</body>");          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
    }          max=FMAX(max,prlim[i][j]);
    }          min=FMIN(min,prlim[i][j]);
 fclose(fichtm);        }
 }        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
 /******************* Gnuplot file **************/      } /* j loop */
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){      if(maxmax < ftolpl){
         return prlim;
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      }
     } /* age loop */
   strcpy(optionfilegnuplot,optionfilefiname);    return prlim; /* should not reach here */
   strcat(optionfilegnuplot,".plt");  }
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  
     printf("Problem with file %s",optionfilegnuplot);  /*************** transition probabilities ***************/ 
   }  
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 #ifdef windows  {
     fprintf(ficgp,"cd \"%s\" \n",pathc);    /* According to parameters values stored in x and the covariate's values stored in cov,
 #endif       computes the probability to be observed in state j being in state i by appying the
 m=pow(2,cptcoveff);       model to the ncovmodel covariates (including constant and age).
         lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
  /* 1eme*/       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
   for (cpt=1; cpt<= nlstate ; cpt ++) {       ncth covariate in the global vector x is given by the formula:
    for (k1=1; k1<= m ; k1 ++) {       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
        j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
 #ifdef windows       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
 #endif       Outputs ps[i][j] the probability to be observed in j being in j according to
 #ifdef unix       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    */
 #endif    double s1, lnpijopii;
     /*double t34;*/
 for (i=1; i<= nlstate ; i ++) {    int i,j, nc, ii, jj;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(i=1; i<= nlstate; i++){
 }        for(j=1; j<i;j++){
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     for (i=1; i<= nlstate ; i ++) {            /*lnpijopii += param[i][j][nc]*cov[nc];*/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
   else fprintf(ficgp," \%%*lf (\%%*lf)");  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
 }          }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
      for (i=1; i<= nlstate ; i ++) {  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=i+1; j<=nlstate+ndeath;j++){
 }            for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
 #ifdef unix            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
 fprintf(ficgp,"\nset ter gif small size 400,300");  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
 #endif          }
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
    }        }
   }      }
   /*2 eme*/      
       for(i=1; i<= nlstate; i++){
   for (k1=1; k1<= m ; k1 ++) {        s1=0;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);        for(j=1; j<i; j++){
              s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     for (i=1; i<= nlstate+1 ; i ++) {          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       k=2*i;        }
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        for(j=i+1; j<=nlstate+ndeath; j++){
       for (j=1; j<= nlstate+1 ; j ++) {          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }          /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        ps[i][i]=1./(s1+1.);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        /* Computing other pijs */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        for(j=1; j<i; j++)
       for (j=1; j<= nlstate+1 ; j ++) {          ps[i][j]= exp(ps[i][j])*ps[i][i];
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(j=i+1; j<=nlstate+ndeath; j++)
         else fprintf(ficgp," \%%*lf (\%%*lf)");          ps[i][j]= exp(ps[i][j])*ps[i][i];
 }          /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       fprintf(ficgp,"\" t\"\" w l 0,");      } /* end i */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      
       for (j=1; j<= nlstate+1 ; j ++) {      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(jj=1; jj<= nlstate+ndeath; jj++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");          ps[ii][jj]=0;
 }            ps[ii][ii]=1;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        }
       else fprintf(ficgp,"\" t\"\" w l 0,");      }
     }      
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      
   }      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
        /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
   /*3eme*/      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
       /*   } */
   for (k1=1; k1<= m ; k1 ++) {      /*   printf("\n "); */
     for (cpt=1; cpt<= nlstate ; cpt ++) {      /* } */
       k=2+nlstate*(cpt-1);      /* printf("\n ");printf("%lf ",cov[2]);*/
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);      /*
       for (i=1; i< nlstate ; i ++) {        for(i=1; i<= npar; i++) printf("%f ",x[i]);
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);        goto end;*/
       }      return ps;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  }
     }  
     }  /**************** Product of 2 matrices ******************/
    
   /* CV preval stat */  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
     for (k1=1; k1<= m ; k1 ++) {  {
     for (cpt=1; cpt<nlstate ; cpt ++) {    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       k=3;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);    /* in, b, out are matrice of pointers which should have been initialized 
        before: only the contents of out is modified. The function returns
       for (i=1; i< nlstate ; i ++)       a pointer to pointers identical to out */
         fprintf(ficgp,"+$%d",k+i+1);    int i, j, k;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    for(i=nrl; i<= nrh; i++)
            for(k=ncolol; k<=ncoloh; k++){
       l=3+(nlstate+ndeath)*cpt;        out[i][k]=0.;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        for(j=ncl; j<=nch; j++)
       for (i=1; i< nlstate ; i ++) {          out[i][k] +=in[i][j]*b[j][k];
         l=3+(nlstate+ndeath)*cpt;      }
         fprintf(ficgp,"+$%d",l+i+1);    return out;
       }  }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }  /************* Higher Matrix Product ***************/
   }    
    double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   /* proba elementaires */  {
    for(i=1,jk=1; i <=nlstate; i++){    /* Computes the transition matrix starting at age 'age' over 
     for(k=1; k <=(nlstate+ndeath); k++){       'nhstepm*hstepm*stepm' months (i.e. until
       if (k != i) {       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         for(j=1; j <=ncovmodel; j++){       nhstepm*hstepm matrices. 
               Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);       (typically every 2 years instead of every month which is too big 
           jk++;       for the memory).
           fprintf(ficgp,"\n");       Model is determined by parameters x and covariates have to be 
         }       included manually here. 
       }  
     }       */
     }  
     int i, j, d, h, k;
     for(jk=1; jk <=m; jk++) {    double **out, cov[NCOVMAX+1];
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);    double **newm;
    i=1;    double agexact;
    for(k2=1; k2<=nlstate; k2++) {  
      k3=i;    /* Hstepm could be zero and should return the unit matrix */
      for(k=1; k<=(nlstate+ndeath); k++) {    for (i=1;i<=nlstate+ndeath;i++)
        if (k != k2){      for (j=1;j<=nlstate+ndeath;j++){
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        oldm[i][j]=(i==j ? 1.0 : 0.0);
 ij=1;        po[i][j][0]=(i==j ? 1.0 : 0.0);
         for(j=3; j <=ncovmodel; j++) {      }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    for(h=1; h <=nhstepm; h++){
             ij++;      for(d=1; d <=hstepm; d++){
           }        newm=savm;
           else        /* Covariates have to be included here again */
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        cov[1]=1.;
         }        agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
           fprintf(ficgp,")/(1");        cov[2]=agexact;
                if(nagesqr==1)
         for(k1=1; k1 <=nlstate; k1++){            cov[3]= agexact*agexact;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        for (k=1; k<=cptcovn;k++) 
 ij=1;          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
           for(j=3; j <=ncovmodel; j++){          /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
             ij++;          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
           }          /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
           else        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
           }          /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
           fprintf(ficgp,")");  
         }  
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         i=i+ncovmodel;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
        }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
      }        savm=oldm;
    }        oldm=newm;
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      }
    }      for(i=1; i<=nlstate+ndeath; i++)
            for(j=1;j<=nlstate+ndeath;j++) {
   fclose(ficgp);          po[i][j][h]=newm[i][j];
 }  /* end gnuplot */          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         }
       /*printf("h=%d ",h);*/
 /*************** Moving average **************/    } /* end h */
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){  /*     printf("\n H=%d \n",h); */
     return po;
   int i, cpt, cptcod;  }
     for (agedeb=agemin; agedeb<=fage; agedeb++)  
       for (i=1; i<=nlstate;i++)  #ifdef NLOPT
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
           mobaverage[(int)agedeb][i][cptcod]=0.;    double fret;
        double *xt;
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){    int j;
       for (i=1; i<=nlstate;i++){    myfunc_data *d2 = (myfunc_data *) pd;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  /* xt = (p1-1); */
           for (cpt=0;cpt<=4;cpt++){    xt=vector(1,n); 
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
           }  
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
         }    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
       }    printf("Function = %.12lf ",fret);
     }    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
        printf("\n");
 }   free_vector(xt,1,n);
     return fret;
   }
 /************** Forecasting ******************/  #endif
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){  
    /*************** log-likelihood *************/
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  double func( double *x)
   int *popage;  {
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    int i, ii, j, k, mi, d, kk;
   double *popeffectif,*popcount;    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double ***p3mat;    double **out;
   char fileresf[FILENAMELENGTH];    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
  agelim=AGESUP;    int s1, s2;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    double bbh, survp;
     long ipmx;
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    double agexact;
      /*extern weight */
      /* We are differentiating ll according to initial status */
   strcpy(fileresf,"f");    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   strcat(fileresf,fileres);    /*for(i=1;i<imx;i++) 
   if((ficresf=fopen(fileresf,"w"))==NULL) {      printf(" %d\n",s[4][i]);
     printf("Problem with forecast resultfile: %s\n", fileresf);    */
   }  
   printf("Computing forecasting: result on file '%s' \n", fileresf);    ++countcallfunc;
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    cov[1]=1.;
   
   if (mobilav==1) {    for(k=1; k<=nlstate; k++) ll[k]=0.;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     movingaverage(agedeb, fage, agemin, mobaverage);    if(mle==1){
   }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         /* Computes the values of the ncovmodel covariates of the model
   stepsize=(int) (stepm+YEARM-1)/YEARM;           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
   if (stepm<=12) stepsize=1;           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
             to be observed in j being in i according to the model.
   agelim=AGESUP;         */
          for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
   hstepm=1;            cov[2+nagesqr+k]=covar[Tvar[k]][i];
   hstepm=hstepm/stepm;        }
   yp1=modf(dateintmean,&yp);        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
   anprojmean=yp;           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
   yp2=modf((yp1*12),&yp);           has been calculated etc */
   mprojmean=yp;        for(mi=1; mi<= wav[i]-1; mi++){
   yp1=modf((yp2*30.5),&yp);          for (ii=1;ii<=nlstate+ndeath;ii++)
   jprojmean=yp;            for (j=1;j<=nlstate+ndeath;j++){
   if(jprojmean==0) jprojmean=1;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   if(mprojmean==0) jprojmean=1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
   for(cptcov=1;cptcov<=i2;cptcov++){            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            cov[2]=agexact;
       k=k+1;            if(nagesqr==1)
       fprintf(ficresf,"\n#******");              cov[3]= agexact*agexact;
       for(j=1;j<=cptcoveff;j++) {            for (kk=1; kk<=cptcovage;kk++) {
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
       }            }
       fprintf(ficresf,"******\n");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       fprintf(ficresf,"# StartingAge FinalAge");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);            savm=oldm;
                  oldm=newm;
                } /* end mult */
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {        
         fprintf(ficresf,"\n");          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            /* But now since version 0.9 we anticipate for bias at large stepm.
            * If stepm is larger than one month (smallest stepm) and if the exact delay 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){           * (in months) between two waves is not a multiple of stepm, we rounded to 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);           * the nearest (and in case of equal distance, to the lowest) interval but now
           nhstepm = nhstepm/hstepm;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
                     * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           * probability in order to take into account the bias as a fraction of the way
           oldm=oldms;savm=savms;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);             * -stepm/2 to stepm/2 .
                   * For stepm=1 the results are the same as for previous versions of Imach.
           for (h=0; h<=nhstepm; h++){           * For stepm > 1 the results are less biased than in previous versions. 
             if (h==(int) (calagedate+YEARM*cpt)) {           */
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);          s1=s[mw[mi][i]][i];
             }          s2=s[mw[mi+1][i]][i];
             for(j=1; j<=nlstate+ndeath;j++) {          bbh=(double)bh[mi][i]/(double)stepm; 
               kk1=0.;kk2=0;          /* bias bh is positive if real duration
               for(i=1; i<=nlstate;i++) {                         * is higher than the multiple of stepm and negative otherwise.
                 if (mobilav==1)           */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][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]));*/
                 else {          if( s2 > nlstate){ 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            /* i.e. if s2 is a death state and if the date of death is known 
                 }               then the contribution to the likelihood is the probability to 
                               die between last step unit time and current  step unit time, 
               }               which is also equal to probability to die before dh 
               if (h==(int)(calagedate+12*cpt)){               minus probability to die before dh-stepm . 
                 fprintf(ficresf," %.3f", kk1);               In version up to 0.92 likelihood was computed
                                  as if date of death was unknown. Death was treated as any other
               }          health state: the date of the interview describes the actual state
             }          and not the date of a change in health state. The former idea was
           }          to consider that at each interview the state was recorded
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          (healthy, disable or death) and IMaCh was corrected; but when we
         }          introduced the exact date of death then we should have modified
       }          the contribution of an exact death to the likelihood. This new
     }          contribution is smaller and very dependent of the step unit
   }          stepm. It is no more the probability to die between last interview
                  and month of death but the probability to survive from last
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          interview up to one month before death multiplied by the
           probability to die within a month. Thanks to Chris
   fclose(ficresf);          Jackson for correcting this bug.  Former versions increased
 }          mortality artificially. The bad side is that we add another loop
 /************** Forecasting ******************/          which slows down the processing. The difference can be up to 10%
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){          lower mortality.
              */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          /* If, at the beginning of the maximization mostly, the
   int *popage;             cumulative probability or probability to be dead is
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;             constant (ie = 1) over time d, the difference is equal to
   double *popeffectif,*popcount;             0.  out[s1][3] = savm[s1][3]: probability, being at state
   double ***p3mat,***tabpop,***tabpopprev;             s1 at precedent wave, to be dead a month before current
   char filerespop[FILENAMELENGTH];             wave is equal to probability, being at state s1 at
              precedent wave, to be dead at mont of the current
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);             wave. Then the observed probability (that this person died)
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);             is null according to current estimated parameter. In fact,
   agelim=AGESUP;             it should be very low but not zero otherwise the log go to
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;             infinity.
            */
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  /* #ifdef INFINITYORIGINAL */
    /*          lli=log(out[s1][s2] - savm[s1][s2]); */
    /* #else */
   strcpy(filerespop,"pop");  /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
   strcat(filerespop,fileres);  /*          lli=log(mytinydouble); */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {  /*        else */
     printf("Problem with forecast resultfile: %s\n", filerespop);  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
   }  /* #endif */
   printf("Computing forecasting: result on file '%s' \n", filerespop);              lli=log(out[s1][s2] - savm[s1][s2]);
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          } else if  (s2==-2) {
             for (j=1,survp=0. ; j<=nlstate; j++) 
   if (mobilav==1) {              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            /*survp += out[s1][j]; */
     movingaverage(agedeb, fage, agemin, mobaverage);            lli= log(survp);
   }          }
           
   stepsize=(int) (stepm+YEARM-1)/YEARM;          else if  (s2==-4) { 
   if (stepm<=12) stepsize=1;            for (j=3,survp=0. ; j<=nlstate; j++)  
                survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   agelim=AGESUP;            lli= log(survp); 
            } 
   hstepm=1;  
   hstepm=hstepm/stepm;          else if  (s2==-5) { 
              for (j=1,survp=0. ; j<=2; j++)  
   if (popforecast==1) {              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     if((ficpop=fopen(popfile,"r"))==NULL) {            lli= log(survp); 
       printf("Problem with population file : %s\n",popfile);exit(0);          } 
     }          
     popage=ivector(0,AGESUP);          else{
     popeffectif=vector(0,AGESUP);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     popcount=vector(0,AGESUP);            /*  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 */
              } 
     i=1;            /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;          /*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); */
     imx=i;          ipmx +=1;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          sw += weight[i];
   }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           /* if (lli < log(mytinydouble)){ */
   for(cptcov=1;cptcov<=i2;cptcov++){          /*   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); */
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          /*   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]); */
       k=k+1;          /* } */
       fprintf(ficrespop,"\n#******");        } /* end of wave */
       for(j=1;j<=cptcoveff;j++) {      } /* end of individual */
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    }  else if(mle==2){
       }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       fprintf(ficrespop,"******\n");        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       fprintf(ficrespop,"# Age");        for(mi=1; mi<= wav[i]-1; mi++){
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);          for (ii=1;ii<=nlstate+ndeath;ii++)
       if (popforecast==1)  fprintf(ficrespop," [Population]");            for (j=1;j<=nlstate+ndeath;j++){
                    oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (cpt=0; cpt<=0;cpt++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);              }
                  for(d=0; d<=dh[mi][i]; d++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){            newm=savm;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
           nhstepm = nhstepm/hstepm;            cov[2]=agexact;
                      if(nagesqr==1)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              cov[3]= agexact*agexact;
           oldm=oldms;savm=savms;            for (kk=1; kk<=cptcovage;kk++) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                    }
           for (h=0; h<=nhstepm; h++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             if (h==(int) (calagedate+YEARM*cpt)) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);            savm=oldm;
             }            oldm=newm;
             for(j=1; j<=nlstate+ndeath;j++) {          } /* end mult */
               kk1=0.;kk2=0;        
               for(i=1; i<=nlstate;i++) {                        s1=s[mw[mi][i]][i];
                 if (mobilav==1)          s2=s[mw[mi+1][i]][i];
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          bbh=(double)bh[mi][i]/(double)stepm; 
                 else {          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 */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          ipmx +=1;
                 }          sw += weight[i];
               }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
               if (h==(int)(calagedate+12*cpt)){        } /* end of wave */
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      } /* end of individual */
                   /*fprintf(ficrespop," %.3f", kk1);    }  else if(mle==3){  /* exponential inter-extrapolation */
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      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(i=1; i<=nlstate;i++){          for (ii=1;ii<=nlstate+ndeath;ii++)
               kk1=0.;            for (j=1;j<=nlstate+ndeath;j++){
                 for(j=1; j<=nlstate;j++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                 }            }
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];          for(d=0; d<dh[mi][i]; d++){
             }            newm=savm;
             agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)            cov[2]=agexact;
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);            if(nagesqr==1)
           }              cov[3]= agexact*agexact;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            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;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {            oldm=newm;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            } /* end mult */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){        
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          s1=s[mw[mi][i]][i];
           nhstepm = nhstepm/hstepm;          s2=s[mw[mi+1][i]][i];
                    bbh=(double)bh[mi][i]/(double)stepm; 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          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 */
           oldm=oldms;savm=savms;          ipmx +=1;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            sw += weight[i];
           for (h=0; h<=nhstepm; h++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             if (h==(int) (calagedate+YEARM*cpt)) {        } /* end of wave */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      } /* end of individual */
             }    }else if (mle==4){  /* ml=4 no inter-extrapolation */
             for(j=1; j<=nlstate+ndeath;j++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
               kk1=0.;kk2=0;        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
               for(i=1; i<=nlstate;i++) {                      for(mi=1; mi<= wav[i]-1; mi++){
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              for (ii=1;ii<=nlstate+ndeath;ii++)
               }            for (j=1;j<=nlstate+ndeath;j++){
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }            }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          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;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
   if (popforecast==1) {            }
     free_ivector(popage,0,AGESUP);          
     free_vector(popeffectif,0,AGESUP);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     free_vector(popcount,0,AGESUP);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            oldm=newm;
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          } /* end mult */
   fclose(ficrespop);        
 }          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
 /***********************************************/          if( s2 > nlstate){ 
 /**************** Main Program *****************/            lli=log(out[s1][s2] - savm[s1][s2]);
 /***********************************************/          }else{
             lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 int main(int argc, char *argv[])          }
 {          ipmx +=1;
           sw += weight[i];
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double agedeb, agefin,hf;  /*      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]); */
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;        } /* end of wave */
       } /* end of individual */
   double fret;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   double **xi,tmp,delta;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
   double dum; /* Dummy variable */        for(mi=1; mi<= wav[i]-1; mi++){
   double ***p3mat;          for (ii=1;ii<=nlstate+ndeath;ii++)
   int *indx;            for (j=1;j<=nlstate+ndeath;j++){
   char line[MAXLINE], linepar[MAXLINE];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   char title[MAXLINE];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];            }
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
             cov[2]=agexact;
   char filerest[FILENAMELENGTH];            if(nagesqr==1)
   char fileregp[FILENAMELENGTH];              cov[3]= agexact*agexact;
   char popfile[FILENAMELENGTH];            for (kk=1; kk<=cptcovage;kk++) {
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
   int firstobs=1, lastobs=10;            }
   int sdeb, sfin; /* Status at beginning and end */          
   int c,  h , cpt,l;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int ju,jl, mi;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            savm=oldm;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            oldm=newm;
   int mobilav=0,popforecast=0;          } /* end mult */
   int hstepm, nhstepm;        
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   double bage, fage, age, agelim, agebase;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   double ftolpl=FTOL;          ipmx +=1;
   double **prlim;          sw += weight[i];
   double *severity;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double ***param; /* Matrix of parameters */          /*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]);*/
   double  *p;        } /* end of wave */
   double **matcov; /* Matrix of covariance */      } /* end of individual */
   double ***delti3; /* Scale */    } /* End of if */
   double *delti; /* Scale */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   double ***eij, ***vareij;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   double **varpl; /* Variances of prevalence limits by age */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   double *epj, vepp;    return -l;
   double kk1, kk2;  }
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;  
    /*************** log-likelihood *************/
   double funcone( double *x)
   char version[80]="Imach version 0.71c, March 2002, INED-EUROREVES ";  {
   char *alph[]={"a","a","b","c","d","e"}, str[4];    /* Same as likeli but slower because of a lot of printf and if */
     int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   char z[1]="c", occ;    double **out;
 #include <sys/time.h>    double lli; /* Individual log likelihood */
 #include <time.h>    double llt;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    int s1, s2;
      double bbh, survp;
   /* long total_usecs;    double agexact;
   struct timeval start_time, end_time;    /*extern weight */
      /* We are differentiating ll according to initial status */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
   printf("\n%s",version);    */
   if(argc <=1){    cov[1]=1.;
     printf("\nEnter the parameter file name: ");  
     scanf("%s",pathtot);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   }  
   else{    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     strcpy(pathtot,argv[1]);      for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
   }      for(mi=1; mi<= wav[i]-1; mi++){
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        for (ii=1;ii<=nlstate+ndeath;ii++)
   /*cygwin_split_path(pathtot,path,optionfile);          for (j=1;j<=nlstate+ndeath;j++){
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* cutv(path,optionfile,pathtot,'\\');*/            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        for(d=0; d<dh[mi][i]; d++){
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);          newm=savm;
   chdir(path);          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
   replace(pathc,path);          cov[2]=agexact;
           if(nagesqr==1)
 /*-------- arguments in the command line --------*/            cov[3]= agexact*agexact;
           for (kk=1; kk<=cptcovage;kk++) {
   strcpy(fileres,"r");            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
   strcat(fileres, optionfilefiname);          }
   strcat(fileres,".txt");    /* Other files have txt extension */  
           /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   /*---------arguments file --------*/          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
     printf("Problem with optionfile %s\n",optionfile);          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
     goto end;          savm=oldm;
   }          oldm=newm;
         } /* end mult */
   strcpy(filereso,"o");        
   strcat(filereso,fileres);        s1=s[mw[mi][i]][i];
   if((ficparo=fopen(filereso,"w"))==NULL) {        s2=s[mw[mi+1][i]][i];
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        bbh=(double)bh[mi][i]/(double)stepm; 
   }        /* bias is positive if real duration
          * is higher than the multiple of stepm and negative otherwise.
   /* Reads comments: lines beginning with '#' */         */
   while((c=getc(ficpar))=='#' && c!= EOF){        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     ungetc(c,ficpar);          lli=log(out[s1][s2] - savm[s1][s2]);
     fgets(line, MAXLINE, ficpar);        } else if  (s2==-2) {
     puts(line);          for (j=1,survp=0. ; j<=nlstate; j++) 
     fputs(line,ficparo);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   }          lli= log(survp);
   ungetc(c,ficpar);        }else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);        } else if(mle==2){
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);          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 */
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);        } else if(mle==3){  /* exponential inter-extrapolation */
 while((c=getc(ficpar))=='#' && c!= EOF){          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 */
     ungetc(c,ficpar);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     fgets(line, MAXLINE, ficpar);          lli=log(out[s1][s2]); /* Original formula */
     puts(line);        } else{  /* mle=0 back to 1 */
     fputs(line,ficparo);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   }          /*lli=log(out[s1][s2]); */ /* Original formula */
   ungetc(c,ficpar);        } /* End of if */
          ipmx +=1;
            sw += weight[i];
   covar=matrix(0,NCOVMAX,1,n);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   cptcovn=0;        /*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 (strlen(model)>1) cptcovn=nbocc(model,'+')+1;        if(globpr){
           fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   ncovmodel=2+cptcovn;   %11.6f %11.6f %11.6f ", \
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                    2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   /* Read guess parameters */          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   /* Reads comments: lines beginning with '#' */            llt +=ll[k]*gipmx/gsw;
   while((c=getc(ficpar))=='#' && c!= EOF){            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);          fprintf(ficresilk," %10.6f\n", -llt);
     puts(line);        }
     fputs(line,ficparo);      } /* end of wave */
   }    } /* end of individual */
   ungetc(c,ficpar);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
      /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     for(i=1; i <=nlstate; i++)    if(globpr==0){ /* First time we count the contributions and weights */
     for(j=1; j <=nlstate+ndeath-1; j++){      gipmx=ipmx;
       fscanf(ficpar,"%1d%1d",&i1,&j1);      gsw=sw;
       fprintf(ficparo,"%1d%1d",i1,j1);    }
       printf("%1d%1d",i,j);    return -l;
       for(k=1; k<=ncovmodel;k++){  }
         fscanf(ficpar," %lf",&param[i][j][k]);  
         printf(" %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);  /*************** function likelione ***********/
       }  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
       fscanf(ficpar,"\n");  {
       printf("\n");    /* This routine should help understanding what is done with 
       fprintf(ficparo,"\n");       the selection of individuals/waves and
     }       to check the exact contribution to the likelihood.
         Plotting could be done.
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;     */
     int k;
   p=param[1][1];  
      if(*globpri !=0){ /* Just counts and sums, no printings */
   /* Reads comments: lines beginning with '#' */      strcpy(fileresilk,"ILK_"); 
   while((c=getc(ficpar))=='#' && c!= EOF){      strcat(fileresilk,fileres);
     ungetc(c,ficpar);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     fgets(line, MAXLINE, ficpar);        printf("Problem with resultfile: %s\n", fileresilk);
     puts(line);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     fputs(line,ficparo);      }
   }      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
   ungetc(c,ficpar);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli 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]); */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      for(k=1; k<=nlstate; k++) 
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   for(i=1; i <=nlstate; i++){      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     for(j=1; j <=nlstate+ndeath-1; j++){    }
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);    *fretone=(*funcone)(p);
       fprintf(ficparo,"%1d%1d",i1,j1);    if(*globpri !=0){
       for(k=1; k<=ncovmodel;k++){      fclose(ficresilk);
         fscanf(ficpar,"%le",&delti3[i][j][k]);      fprintf(fichtm,"\n<br>File of contributions to the likelihood (if mle=1): <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
         printf(" %le",delti3[i][j][k]);      fflush(fichtm); 
         fprintf(ficparo," %le",delti3[i][j][k]);    } 
       }    return;
       fscanf(ficpar,"\n");  }
       printf("\n");  
       fprintf(ficparo,"\n");  
     }  /*********** Maximum Likelihood Estimation ***************/
   }  
   delti=delti3[1][1];  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
    {
   /* Reads comments: lines beginning with '#' */    int i,j, iter=0;
   while((c=getc(ficpar))=='#' && c!= EOF){    double **xi;
     ungetc(c,ficpar);    double fret;
     fgets(line, MAXLINE, ficpar);    double fretone; /* Only one call to likelihood */
     puts(line);    /*  char filerespow[FILENAMELENGTH];*/
     fputs(line,ficparo);  
   }  #ifdef NLOPT
   ungetc(c,ficpar);    int creturn;
      nlopt_opt opt;
   matcov=matrix(1,npar,1,npar);    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
   for(i=1; i <=npar; i++){    double *lb;
     fscanf(ficpar,"%s",&str);    double minf; /* the minimum objective value, upon return */
     printf("%s",str);    double * p1; /* Shifted parameters from 0 instead of 1 */
     fprintf(ficparo,"%s",str);    myfunc_data dinst, *d = &dinst;
     for(j=1; j <=i; j++){  #endif
       fscanf(ficpar," %le",&matcov[i][j]);  
       printf(" %.5le",matcov[i][j]);  
       fprintf(ficparo," %.5le",matcov[i][j]);    xi=matrix(1,npar,1,npar);
     }    for (i=1;i<=npar;i++)
     fscanf(ficpar,"\n");      for (j=1;j<=npar;j++)
     printf("\n");        xi[i][j]=(i==j ? 1.0 : 0.0);
     fprintf(ficparo,"\n");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   }    strcpy(filerespow,"POW_"); 
   for(i=1; i <=npar; i++)    strcat(filerespow,fileres);
     for(j=i+1;j<=npar;j++)    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       matcov[i][j]=matcov[j][i];      printf("Problem with resultfile: %s\n", filerespow);
          fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   printf("\n");    }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (i=1;i<=nlstate;i++)
     /*-------- Rewriting paramater file ----------*/      for(j=1;j<=nlstate+ndeath;j++)
      strcpy(rfileres,"r");    /* "Rparameterfile */        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    fprintf(ficrespow,"\n");
      strcat(rfileres,".");    /* */  #ifdef POWELL
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    powell(p,xi,npar,ftol,&iter,&fret,func);
     if((ficres =fopen(rfileres,"w"))==NULL) {  #endif
       printf("Problem writing new parameter file: %s\n", fileres);goto end;  
     }  #ifdef NLOPT
     fprintf(ficres,"#%s\n",version);  #ifdef NEWUOA
        opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
     /*-------- data file ----------*/  #else
     if((fic=fopen(datafile,"r"))==NULL)    {    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
       printf("Problem with datafile: %s\n", datafile);goto end;  #endif
     }    lb=vector(0,npar-1);
     for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
     n= lastobs;    nlopt_set_lower_bounds(opt, lb);
     severity = vector(1,maxwav);    nlopt_set_initial_step1(opt, 0.1);
     outcome=imatrix(1,maxwav+1,1,n);    
     num=ivector(1,n);    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
     moisnais=vector(1,n);    d->function = func;
     annais=vector(1,n);    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
     moisdc=vector(1,n);    nlopt_set_min_objective(opt, myfunc, d);
     andc=vector(1,n);    nlopt_set_xtol_rel(opt, ftol);
     agedc=vector(1,n);    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
     cod=ivector(1,n);      printf("nlopt failed! %d\n",creturn); 
     weight=vector(1,n);    }
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    else {
     mint=matrix(1,maxwav,1,n);      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
     anint=matrix(1,maxwav,1,n);      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
     s=imatrix(1,maxwav+1,1,n);      iter=1; /* not equal */
     adl=imatrix(1,maxwav+1,1,n);        }
     tab=ivector(1,NCOVMAX);    nlopt_destroy(opt);
     ncodemax=ivector(1,8);  #endif
     free_matrix(xi,1,npar,1,npar);
     i=1;    fclose(ficrespow);
     while (fgets(line, MAXLINE, fic) != NULL)    {    printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
       if ((i >= firstobs) && (i <=lastobs)) {    fprintf(ficlog,"#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));
         for (j=maxwav;j>=1;j--){  
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  }
           strcpy(line,stra);  
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  /**** Computes Hessian and covariance matrix ***/
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
         }  {
            double  **a,**y,*x,pd;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    double **hess;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    int i, j;
     int *indx;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    void lubksb(double **a, int npar, int *indx, double b[]) ;
         for (j=ncov;j>=1;j--){    void ludcmp(double **a, int npar, int *indx, double *d) ;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double gompertz(double p[]);
         }    hess=matrix(1,npar,1,npar);
         num[i]=atol(stra);  
            printf("\nCalculation of the hessian matrix. Wait...\n");
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
           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;}*/    for (i=1;i<=npar;i++){
       printf("%d",i);fflush(stdout);
         i=i+1;      fprintf(ficlog,"%d",i);fflush(ficlog);
       }     
     }       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     /* printf("ii=%d", ij);      
        scanf("%d",i);*/      /*  printf(" %f ",p[i]);
   imx=i-1; /* Number of individuals */          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }
   /* for (i=1; i<=imx; i++){    
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    for (i=1;i<=npar;i++) {
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      for (j=1;j<=npar;j++)  {
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;        if (j>i) { 
     }          printf(".%d%d",i,j);fflush(stdout);
           fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     for (i=1; i<=imx; i++)          hess[i][j]=hessij(p,delti,i,j,func,npar);
     if (covar[1][i]==0) 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]));*/          
           hess[j][i]=hess[i][j];    
   /* Calculation of the number of parameter from char model*/          /*printf(" %lf ",hess[i][j]);*/
   Tvar=ivector(1,15);        }
   Tprod=ivector(1,15);      }
   Tvaraff=ivector(1,15);    }
   Tvard=imatrix(1,15,1,2);    printf("\n");
   Tage=ivector(1,15);          fprintf(ficlog,"\n");
      
   if (strlen(model) >1){    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     j=0, j1=0, k1=1, k2=1;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     j=nbocc(model,'+');    
     j1=nbocc(model,'*');    a=matrix(1,npar,1,npar);
     cptcovn=j+1;    y=matrix(1,npar,1,npar);
     cptcovprod=j1;    x=vector(1,npar);
        indx=ivector(1,npar);
        for (i=1;i<=npar;i++)
     strcpy(modelsav,model);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    ludcmp(a,npar,indx,&pd);
       printf("Error. Non available option model=%s ",model);  
       goto end;    for (j=1;j<=npar;j++) {
     }      for (i=1;i<=npar;i++) x[i]=0;
          x[j]=1;
     for(i=(j+1); i>=1;i--){      lubksb(a,npar,indx,x);
       cutv(stra,strb,modelsav,'+');      for (i=1;i<=npar;i++){ 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        matcov[i][j]=x[i];
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      }
       /*scanf("%d",i);*/    }
       if (strchr(strb,'*')) {  
         cutv(strd,strc,strb,'*');    printf("\n#Hessian matrix#\n");
         if (strcmp(strc,"age")==0) {    fprintf(ficlog,"\n#Hessian matrix#\n");
           cptcovprod--;    for (i=1;i<=npar;i++) { 
           cutv(strb,stre,strd,'V');      for (j=1;j<=npar;j++) { 
           Tvar[i]=atoi(stre);        printf("%.3e ",hess[i][j]);
           cptcovage++;        fprintf(ficlog,"%.3e ",hess[i][j]);
             Tage[cptcovage]=i;      }
             /*printf("stre=%s ", stre);*/      printf("\n");
         }      fprintf(ficlog,"\n");
         else if (strcmp(strd,"age")==0) {    }
           cptcovprod--;  
           cutv(strb,stre,strc,'V');    /* Recompute Inverse */
           Tvar[i]=atoi(stre);    for (i=1;i<=npar;i++)
           cptcovage++;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
           Tage[cptcovage]=i;    ludcmp(a,npar,indx,&pd);
         }  
         else {    /*  printf("\n#Hessian matrix recomputed#\n");
           cutv(strb,stre,strc,'V');  
           Tvar[i]=ncov+k1;    for (j=1;j<=npar;j++) {
           cutv(strb,strc,strd,'V');      for (i=1;i<=npar;i++) x[i]=0;
           Tprod[k1]=i;      x[j]=1;
           Tvard[k1][1]=atoi(strc);      lubksb(a,npar,indx,x);
           Tvard[k1][2]=atoi(stre);      for (i=1;i<=npar;i++){ 
           Tvar[cptcovn+k2]=Tvard[k1][1];        y[i][j]=x[i];
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        printf("%.3e ",y[i][j]);
           for (k=1; k<=lastobs;k++)        fprintf(ficlog,"%.3e ",y[i][j]);
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      }
           k1++;      printf("\n");
           k2=k2+2;      fprintf(ficlog,"\n");
         }    }
       }    */
       else {  
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    free_matrix(a,1,npar,1,npar);
        /*  scanf("%d",i);*/    free_matrix(y,1,npar,1,npar);
       cutv(strd,strc,strb,'V');    free_vector(x,1,npar);
       Tvar[i]=atoi(strc);    free_ivector(indx,1,npar);
       }    free_matrix(hess,1,npar,1,npar);
       strcpy(modelsav,stra);    
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  
         scanf("%d",i);*/  }
     }  
 }  /*************** hessian matrix ****************/
    double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);  {
   printf("cptcovprod=%d ", cptcovprod);    int i;
   scanf("%d ",i);*/    int l=1, lmax=20;
     fclose(fic);    double k1,k2;
     double p2[MAXPARM+1]; /* identical to x */
     /*  if(mle==1){*/    double res;
     if (weightopt != 1) { /* Maximisation without weights*/    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       for(i=1;i<=n;i++) weight[i]=1.0;    double fx;
     }    int k=0,kmax=10;
     /*-calculation of age at interview from date of interview and age at death -*/    double l1;
     agev=matrix(1,maxwav,1,imx);  
     fx=func(x);
    for (i=1; i<=imx; i++)    for (i=1;i<=npar;i++) p2[i]=x[i];
      for(m=2; (m<= maxwav); m++)    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      l1=pow(10,l);
          anint[m][i]=9999;      delts=delt;
          s[m][i]=-1;      for(k=1 ; k <kmax; k=k+1){
        }        delt = delta*(l1*k);
            p2[theta]=x[theta] +delt;
     for (i=1; i<=imx; i++)  {        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        p2[theta]=x[theta]-delt;
       for(m=1; (m<= maxwav); m++){        k2=func(p2)-fx;
         if(s[m][i] >0){        /*res= (k1-2.0*fx+k2)/delt/delt; */
           if (s[m][i] == nlstate+1) {        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
             if(agedc[i]>0)        
               if(moisdc[i]!=99 && andc[i]!=9999)  #ifdef DEBUGHESS
               agev[m][i]=agedc[i];        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);
             else {        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);
               if (andc[i]!=9999){  #endif
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
               agev[m][i]=-1;        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. */
           else if(s[m][i] !=9){ /* Should no more exist */          k=kmax; l=lmax*10;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        }
             if(mint[m][i]==99 || anint[m][i]==9999)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
               agev[m][i]=1;          delts=delt;
             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);*/    }
             }    delti[theta]=delts;
             else if(agev[m][i] >agemax){    return res; 
               agemax=agev[m][i];    
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  }
             }  
             /*agev[m][i]=anint[m][i]-annais[i];*/  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
             /*   agev[m][i] = age[i]+2*m;*/  {
           }    int i;
           else { /* =9 */    int l=1, lmax=20;
             agev[m][i]=1;    double k1,k2,k3,k4,res,fx;
             s[m][i]=-1;    double p2[MAXPARM+1];
           }    int k;
         }  
         else /*= 0 Unknown */    fx=func(x);
           agev[m][i]=1;    for (k=1; k<=2; 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;
     for (i=1; i<=imx; i++)  {      k1=func(p2)-fx;
       for(m=1; (m<= maxwav); m++){    
         if (s[m][i] > (nlstate+ndeath)) {      p2[thetai]=x[thetai]+delti[thetai]/k;
           printf("Error: Wrong value in nlstate or ndeath\n");        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           goto end;      k2=func(p2)-fx;
         }    
       }      p2[thetai]=x[thetai]-delti[thetai]/k;
     }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    
       p2[thetai]=x[thetai]-delti[thetai]/k;
     free_vector(severity,1,maxwav);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     free_imatrix(outcome,1,maxwav+1,1,n);      k4=func(p2)-fx;
     free_vector(moisnais,1,n);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     free_vector(annais,1,n);  #ifdef DEBUG
     /* free_matrix(mint,1,maxwav,1,n);      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);
        free_matrix(anint,1,maxwav,1,n);*/      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);
     free_vector(moisdc,1,n);  #endif
     free_vector(andc,1,n);    }
     return res;
      }
     wav=ivector(1,imx);  
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  /************** Inverse of matrix **************/
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  void ludcmp(double **a, int n, int *indx, double *d) 
      { 
     /* Concatenates waves */    int i,imax,j,k; 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    double big,dum,sum,temp; 
     double *vv; 
    
       Tcode=ivector(1,100);    vv=vector(1,n); 
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    *d=1.0; 
       ncodemax[1]=1;    for (i=1;i<=n;i++) { 
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      big=0.0; 
            for (j=1;j<=n;j++) 
    codtab=imatrix(1,100,1,10);        if ((temp=fabs(a[i][j])) > big) big=temp; 
    h=0;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
    m=pow(2,cptcoveff);      vv[i]=1.0/big; 
      } 
    for(k=1;k<=cptcoveff; k++){    for (j=1;j<=n;j++) { 
      for(i=1; i <=(m/pow(2,k));i++){      for (i=1;i<j;i++) { 
        for(j=1; j <= ncodemax[k]; j++){        sum=a[i][j]; 
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
            h++;        a[i][j]=sum; 
            if (h>m) h=1;codtab[h][k]=j;      } 
          }      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; 
    /*for(i=1; i <=m ;i++){        if ( (dum=vv[i]*fabs(sum)) >= big) { 
      for(k=1; k <=cptcovn; k++){          big=dum; 
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);          imax=i; 
      }        } 
      printf("\n");      } 
    }      if (j != imax) { 
    scanf("%d",i);*/        for (k=1;k<=n;k++) { 
              dum=a[imax][k]; 
    /* Calculates basic frequencies. Computes observed prevalence at single age          a[imax][k]=a[j][k]; 
        and prints on file fileres'p'. */          a[j][k]=dum; 
         } 
            *d = -(*d); 
            vv[imax]=vv[j]; 
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      } 
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      indx[j]=imax; 
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      if (a[j][j] == 0.0) a[j][j]=TINY; 
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      if (j != n) { 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        dum=1.0/(a[j][j]); 
              for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     /* 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) */    free_vector(vv,1,n);  /* Doesn't work */
   ;
     if(mle==1){  } 
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }  void lubksb(double **a, int n, int *indx, double b[]) 
      { 
     /*--------- results files --------------*/    int i,ii=0,ip,j; 
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);    double sum; 
     
     for (i=1;i<=n;i++) { 
    jk=1;      ip=indx[i]; 
    fprintf(ficres,"# Parameters\n");      sum=b[ip]; 
    printf("# Parameters\n");      b[ip]=b[i]; 
    for(i=1,jk=1; i <=nlstate; i++){      if (ii) 
      for(k=1; k <=(nlstate+ndeath); k++){        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
        if (k != i)      else if (sum) ii=i; 
          {      b[i]=sum; 
            printf("%d%d ",i,k);    } 
            fprintf(ficres,"%1d%1d ",i,k);    for (i=n;i>=1;i--) { 
            for(j=1; j <=ncovmodel; j++){      sum=b[i]; 
              printf("%f ",p[jk]);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
              fprintf(ficres,"%f ",p[jk]);      b[i]=sum/a[i][i]; 
              jk++;    } 
            }  } 
            printf("\n");  
            fprintf(ficres,"\n");  void pstamp(FILE *fichier)
          }  {
      }    fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
    }  }
  if(mle==1){  
     /* Computing hessian and covariance matrix */  /************ Frequencies ********************/
     ftolhess=ftol; /* Usually correct */  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
     hesscov(matcov, p, npar, delti, ftolhess, func);  {  /* Some frequencies */
  }    
     fprintf(ficres,"# Scales\n");    int i, m, jk, j1, bool, z1,j;
     printf("# Scales\n");    int first;
      for(i=1,jk=1; i <=nlstate; i++){    double ***freq; /* Frequencies */
       for(j=1; j <=nlstate+ndeath; j++){    double *pp, **prop;
         if (j!=i) {    double pos,posprop, k2, dateintsum=0,k2cpt=0;
           fprintf(ficres,"%1d%1d",i,j);    char fileresp[FILENAMELENGTH];
           printf("%1d%1d",i,j);    
           for(k=1; k<=ncovmodel;k++){    pp=vector(1,nlstate);
             printf(" %.5e",delti[jk]);    prop=matrix(1,nlstate,iagemin,iagemax+3);
             fprintf(ficres," %.5e",delti[jk]);    strcpy(fileresp,"P_");
             jk++;    strcat(fileresp,fileresu);
           }    if((ficresp=fopen(fileresp,"w"))==NULL) {
           printf("\n");      printf("Problem with prevalence resultfile: %s\n", fileresp);
           fprintf(ficres,"\n");      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
         }      exit(0);
       }    }
      }    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
        j1=0;
     k=1;    
     fprintf(ficres,"# Covariance\n");    j=cptcoveff;
     printf("# Covariance\n");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     for(i=1;i<=npar;i++){  
       /*  if (k>nlstate) k=1;    first=1;
       i1=(i-1)/(ncovmodel*nlstate)+1;  
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
       printf("%s%d%d",alph[k],i1,tab[i]);*/    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
       fprintf(ficres,"%3d",i);    /*    j1++; */
       printf("%3d",i);    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
       for(j=1; j<=i;j++){        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         fprintf(ficres," %.5e",matcov[i][j]);          scanf("%d", i);*/
         printf(" %.5e",matcov[i][j]);        for (i=-5; i<=nlstate+ndeath; i++)  
       }          for (jk=-5; jk<=nlstate+ndeath; jk++)  
       fprintf(ficres,"\n");            for(m=iagemin; m <= iagemax+3; m++)
       printf("\n");              freq[i][jk][m]=0;
       k++;        
     }        for (i=1; i<=nlstate; i++)  
              for(m=iagemin; m <= iagemax+3; m++)
     while((c=getc(ficpar))=='#' && c!= EOF){            prop[i][m]=0;
       ungetc(c,ficpar);        
       fgets(line, MAXLINE, ficpar);        dateintsum=0;
       puts(line);        k2cpt=0;
       fputs(line,ficparo);        for (i=1; i<=imx; i++) {
     }          bool=1;
     ungetc(c,ficpar);          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
              for (z1=1; z1<=cptcoveff; z1++)       
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
                      /* Tests if the value of each of the covariates of i is equal to filter j1 */
     if (fage <= 2) {                bool=0;
       bage = agemin;                /* 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", 
       fage = agemaxpar;                  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*/
     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\n",agemin,agemaxpar,bage,fage);          }
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);   
            if (bool==1){
     while((c=getc(ficpar))=='#' && c!= EOF){            for(m=firstpass; m<=lastpass; m++){
     ungetc(c,ficpar);              k2=anint[m][i]+(mint[m][i]/12.);
     fgets(line, MAXLINE, ficpar);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     puts(line);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     fputs(line,ficparo);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   }                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   ungetc(c,ficpar);                if (m<lastpass) {
                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                }
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                
                      if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   while((c=getc(ficpar))=='#' && c!= EOF){                  dateintsum=dateintsum+k2;
     ungetc(c,ficpar);                  k2cpt++;
     fgets(line, MAXLINE, ficpar);                }
     puts(line);                /*}*/
     fputs(line,ficparo);            }
   }          }
   ungetc(c,ficpar);        } /* end i */
           
         /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        pstamp(ficresp);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
   fscanf(ficpar,"pop_based=%d\n",&popbased);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
   fprintf(ficparo,"pop_based=%d\n",popbased);            fprintf(ficresp, "**********\n#");
   fprintf(ficres,"pop_based=%d\n",popbased);            fprintf(ficlog, "\n#********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficlog, "**********\n#");
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);        for(i=1; i<=nlstate;i++) 
     puts(line);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     fputs(line,ficparo);        fprintf(ficresp, "\n");
   }        
   ungetc(c,ficpar);        for(i=iagemin; i <= iagemax+3; i++){
           if(i==iagemax+3){
   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);            fprintf(ficlog,"Total");
 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);          }else{
 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);            if(first==1){
               first=0;
               printf("See log file for details...\n");
 while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);            fprintf(ficlog,"Age %d", i);
     fgets(line, MAXLINE, ficpar);          }
     puts(line);          for(jk=1; jk <=nlstate ; jk++){
     fputs(line,ficparo);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   }              pp[jk] += freq[jk][m][i]; 
   ungetc(c,ficpar);          }
           for(jk=1; jk <=nlstate ; jk++){
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);            for(m=-1, pos=0; m <=0 ; m++)
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);              pos += freq[jk][m][i];
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);            if(pp[jk]>=1.e-10){
               if(first==1){
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               }
 /*------------ gnuplot -------------*/              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);            }else{
                if(first==1)
 /*------------ free_vector  -------------*/                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
  chdir(path);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
              }
  free_ivector(wav,1,imx);          }
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            for(jk=1; jk <=nlstate ; jk++){
  free_ivector(num,1,n);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
  free_vector(agedc,1,n);              pp[jk] += freq[jk][m][i];
  /*free_matrix(covar,1,NCOVMAX,1,n);*/          }       
  fclose(ficparo);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
  fclose(ficres);            pos += pp[jk];
             posprop += prop[jk][i];
 /*--------- index.htm --------*/          }
           for(jk=1; jk <=nlstate ; jk++){
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);            if(pos>=1.e-5){
               if(first==1)
                  printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   /*--------------- Prevalence limit --------------*/              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
              }else{
   strcpy(filerespl,"pl");              if(first==1)
   strcat(filerespl,fileres);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;            }
   }            if( i <= iagemax){
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);              if(pos>=1.e-5){
   fprintf(ficrespl,"#Prevalence limit\n");                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   fprintf(ficrespl,"#Age ");                /*probs[i][jk][j1]= pp[jk]/pos;*/
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   fprintf(ficrespl,"\n");              }
                else
   prlim=matrix(1,nlstate,1,nlstate);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   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 */          for(jk=-1; jk <=nlstate+ndeath; jk++)
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            for(m=-1; m <=nlstate+ndeath; m++)
   k=0;              if(freq[jk][m][i] !=0 ) {
   agebase=agemin;              if(first==1)
   agelim=agemaxpar;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   ftolpl=1.e-10;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   i1=cptcoveff;              }
   if (cptcovn < 1){i1=1;}          if(i <= iagemax)
             fprintf(ficresp,"\n");
   for(cptcov=1;cptcov<=i1;cptcov++){          if(first==1)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            printf("Others in log...\n");
         k=k+1;          fprintf(ficlog,"\n");
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        }
         fprintf(ficrespl,"\n#******");        /*}*/
         for(j=1;j<=cptcoveff;j++)    }
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    dateintmean=dateintsum/k2cpt; 
         fprintf(ficrespl,"******\n");   
            fclose(ficresp);
         for (age=agebase; age<=agelim; age++){    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    free_vector(pp,1,nlstate);
           fprintf(ficrespl,"%.0f",age );    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
           for(i=1; i<=nlstate;i++)    /* End of Freq */
           fprintf(ficrespl," %.5f", prlim[i][i]);  }
           fprintf(ficrespl,"\n");  
         }  /************ 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)
     }  {  
   fclose(ficrespl);    /* 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).
   /*------------- h Pij x at various ages ------------*/       We still use firstpass and lastpass as another selection.
      */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);   
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    int i, m, jk, j1, bool, z1,j;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  
   }    double **prop;
   printf("Computing pij: result on file '%s' \n", filerespij);    double posprop; 
      double  y2; /* in fractional years */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    int iagemin, iagemax;
   /*if (stepm<=24) stepsize=2;*/    int first; /** to stop verbosity which is redirected to log file */
   
   agelim=AGESUP;    iagemin= (int) agemin;
   hstepm=stepsize*YEARM; /* Every year of age */    iagemax= (int) agemax;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    /*pp=vector(1,nlstate);*/
      prop=matrix(1,nlstate,iagemin,iagemax+3); 
   k=0;    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   for(cptcov=1;cptcov<=i1;cptcov++){    j1=0;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    
       k=k+1;    /*j=cptcoveff;*/
         fprintf(ficrespij,"\n#****** ");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         for(j=1;j<=cptcoveff;j++)    
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    first=1;
         fprintf(ficrespij,"******\n");    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
              /*for(i1=1; i1<=ncodemax[k1];i1++){
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        j1++;*/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        for (i=1; i<=nlstate; i++)  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(m=iagemin; m <= iagemax+3; m++)
           oldm=oldms;savm=savms;            prop[i][m]=0.0;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         
           fprintf(ficrespij,"# Age");        for (i=1; i<=imx; i++) { /* Each individual */
           for(i=1; i<=nlstate;i++)          bool=1;
             for(j=1; j<=nlstate+ndeath;j++)          if  (cptcovn>0) {
               fprintf(ficrespij," %1d-%1d",i,j);            for (z1=1; z1<=cptcoveff; z1++) 
           fprintf(ficrespij,"\n");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) 
           for (h=0; h<=nhstepm; h++){                bool=0;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          } 
             for(i=1; i<=nlstate;i++)          if (bool==1) { 
               for(j=1; j<=nlstate+ndeath;j++)            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
             fprintf(ficrespij,"\n");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
           }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           fprintf(ficrespij,"\n");                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
         }                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];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/                } 
               }
   fclose(ficrespij);            } /* end selection of waves */
           }
         }
   /*---------- Forecasting ------------------*/        for(i=iagemin; i <= iagemax+3; i++){  
   if((stepm == 1) && (strcmp(model,".")==0)){          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);            posprop += prop[jk][i]; 
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);          } 
     free_matrix(mint,1,maxwav,1,n);          
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);          for(jk=1; jk <=nlstate ; jk++){     
     free_vector(weight,1,n);}            if( i <=  iagemax){ 
   else{              if(posprop>=1.e-5){ 
     erreur=108;                probs[i][jk][j1]= prop[jk][i]/posprop;
     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);              } else{
   }                if(first==1){
                    first=0;
                   printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
   /*---------- Health expectancies and variances ------------*/                }
               }
   strcpy(filerest,"t");            } 
   strcat(filerest,fileres);          }/* end jk */ 
   if((ficrest=fopen(filerest,"w"))==NULL) {        }/* end i */ 
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      /*} *//* end i1 */
   }    } /* end j1 */
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    
     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     /*free_vector(pp,1,nlstate);*/
   strcpy(filerese,"e");    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   strcat(filerese,fileres);  }  /* End of prevalence */
   if((ficreseij=fopen(filerese,"w"))==NULL) {  
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  /************* Waves Concatenation ***************/
   }  
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  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)
   {
  strcpy(fileresv,"v");    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   strcat(fileresv,fileres);       Death is a valid wave (if date is known).
   if((ficresvij=fopen(fileresv,"w"))==NULL) {       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);       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.
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);       */
   
   k=0;    int i, mi, m;
   for(cptcov=1;cptcov<=i1;cptcov++){    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       double sum=0., jmean=0.;*/
       k=k+1;    int first;
       fprintf(ficrest,"\n#****** ");    int j, k=0,jk, ju, jl;
       for(j=1;j<=cptcoveff;j++)    double sum=0.;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    first=0;
       fprintf(ficrest,"******\n");    jmin=100000;
     jmax=-1;
       fprintf(ficreseij,"\n#****** ");    jmean=0.;
       for(j=1;j<=cptcoveff;j++)    for(i=1; i<=imx; i++){
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      mi=0;
       fprintf(ficreseij,"******\n");      m=firstpass;
       while(s[m][i] <= nlstate){
       fprintf(ficresvij,"\n#****** ");        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
       for(j=1;j<=cptcoveff;j++)          mw[++mi][i]=m;
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);        if(m >=lastpass)
       fprintf(ficresvij,"******\n");          break;
         else
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          m++;
       oldm=oldms;savm=savms;      }/* end while */
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);        if (s[m][i] > nlstate){
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        mi++;     /* Death is another wave */
       oldm=oldms;savm=savms;        /* if(mi==0)  never been interviewed correctly before death */
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);           /* Only death is a correct wave */
            mw[mi][i]=m;
       }
    
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      wav[i]=mi;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      if(mi==0){
       fprintf(ficrest,"\n");        nbwarn++;
         if(first==0){
       hf=1;          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       if (stepm >= YEARM) hf=stepm/YEARM;          first=1;
       epj=vector(1,nlstate+1);        }
       for(age=bage; age <=fage ;age++){        if(first==1){
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         if (popbased==1) {        }
           for(i=1; i<=nlstate;i++)      } /* end mi==0 */
             prlim[i][i]=probs[(int)age][i][k];    } /* End individuals */
         }  
            for(i=1; i<=imx; i++){
         fprintf(ficrest," %.0f",age);      for(mi=1; mi<wav[i];mi++){
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){        if (stepm <=0)
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          dh[mi][i]=1;
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];        else{
           }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           epj[nlstate+1] +=epj[j];            if (agedc[i] < 2*AGESUP) {
         }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
         for(i=1, vepp=0.;i <=nlstate;i++)              if(j==0) j=1;  /* Survives at least one month after exam */
           for(j=1;j <=nlstate;j++)              else if(j<0){
             vepp += vareij[i][j][(int)age];                nberr++;
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));                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]);
         for(j=1;j <=nlstate;j++){                j=1; /* Temporary Dangerous patch */
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));                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(ficrest,"\n");                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;
   fclose(ficreseij);                ijmax=i;
   fclose(ficresvij);              }
   fclose(ficrest);              if (j <= jmin){
   fclose(ficpar);                jmin=j;
   free_vector(epj,1,nlstate+1);                ijmin=i;
                }
   /*------- Variance limit prevalence------*/                sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   strcpy(fileresvpl,"vpl");              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   strcat(fileresvpl,fileres);            }
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          }
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);          else{
     exit(0);            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]); */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  
             k=k+1;
   k=0;            if (j >= jmax) {
   for(cptcov=1;cptcov<=i1;cptcov++){              jmax=j;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              ijmax=i;
       k=k+1;            }
       fprintf(ficresvpl,"\n#****** ");            else if (j <= jmin){
       for(j=1;j<=cptcoveff;j++)              jmin=j;
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              ijmin=i;
       fprintf(ficresvpl,"******\n");            }
                  /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       varpl=matrix(1,nlstate,(int) bage, (int) fage);            /*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]);*/
       oldm=oldms;savm=savms;            if(j<0){
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);              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]);
             }
   fclose(ficresvpl);            sum=sum+j;
           }
   /*---------- End : free ----------------*/          jk= j/stepm;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          jl= j -jk*stepm;
            ju= j -(jk+1)*stepm;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);            if(jl==0){
                dh[mi][i]=jk;
                bh[mi][i]=0;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);            }else{ /* We want a negative bias in order to only have interpolation ie
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);                    * to avoid the price of an extra matrix product in likelihood */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);              dh[mi][i]=jk+1;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);              bh[mi][i]=ju;
              }
   free_matrix(matcov,1,npar,1,npar);          }else{
   free_vector(delti,1,npar);            if(jl <= -ju){
   free_matrix(agev,1,maxwav,1,imx);              dh[mi][i]=jk;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);              bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
   if(erreur >0)                                   */
     printf("End of Imach with error %d\n",erreur);            }
   else   printf("End of Imach\n");            else{
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */              dh[mi][i]=jk+1;
                bh[mi][i]=ju;
   /* 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);*/            }
   /*printf("Total time was %d uSec.\n", total_usecs);*/            if(dh[mi][i]==0){
   /*------ End -----------*/              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:            }
 #ifdef windows          } /* end if mle */
   /* chdir(pathcd);*/        }
 #endif      } /* end wave */
  /*system("wgnuplot graph.plt");*/    }
  /*system("../gp37mgw/wgnuplot graph.plt");*/    jmean=sum/k;
  /*system("cd ../gp37mgw");*/    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);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    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);
  strcpy(plotcmd,GNUPLOTPROGRAM);   }
  strcat(plotcmd," ");  
  strcat(plotcmd,optionfilegnuplot);  /*********** Tricode ****************************/
  system(plotcmd);  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   {
 #ifdef windows    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   while (z[0] != 'q') {    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
     chdir(path);     * Boring subroutine which should only output nbcode[Tvar[j]][k]
     printf("\nType e to edit output files, c to start again, and q for exiting: ");     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
     scanf("%s",z);     * nbcode[Tvar[j]][1]= 
     if (z[0] == 'c') system("./imach");    */
     else if (z[0] == 'e') {  
       chdir(path);    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
       system(optionfilehtm);    int modmaxcovj=0; /* Modality max of covariates j */
     }    int cptcode=0; /* Modality max of covariates j */
     else if (z[0] == 'q') exit(0);    int modmincovj=0; /* Modality min of covariates j */
   }  
 #endif  
 }    cptcoveff=0; 
    
     for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   
     /* Loop on covariates without age and products */
     for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
       for (k=-1; k < maxncov; k++) Ndum[k]=0;
       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[j]][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 is 1, then modmaxcovj=1.*/
       } /* end for loop on individuals i */
       printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
       fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], 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 (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
         printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
         fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
         if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
           if( k != -1){
             ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th
                                covariate for which somebody answered excluding 
                                undefined. Usually 2: 0 and 1. */
           }
           ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
                                covariate for which somebody answered including 
                                undefined. Usually 3: -1, 0 and 1. */
         }
         /* In fact  ncodemax[j]=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[j]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
           cptcode = ij; /* New max modality for covar j */
       } /* end of loop on modality i=-1 to 1 or more */
         
       /*   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; 
     
     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 might be -1 if status was unknown */ 
      Ndum[ij]++; /* Might be supersed V1 + V1*age */
    } 
   
    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) */
      /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
      if((Ndum[i]!=0) && (i<=ncovcol)){
        ij++;
        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
        Tvaraff[ij]=i; /*For printing (unclear) */
      }else{
          /* Tvaraff[ij]=0; */
      }
    }
    /* ij--; */
    cptcoveff=ij; /*Number of total covariates*/
   
   }
   
   
   /*********** 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[] )
   
   {
     /* 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 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 */ 
   
     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);  
       
       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[] )
   
   {
     /* 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);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
         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);  
       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]);*/
   
           }
   
       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");
   
       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 ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* 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,fileres);
     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,"# 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 agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
     /* 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);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         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];
           }
         }
     
         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];
           }
         }
         /* 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,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         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];
           }
         }
   
         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 probability of death */
   
         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];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       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];
     
   
       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.;
   
       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 */
       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 */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       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.
       */
       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 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, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=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);
       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);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* 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];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       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++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       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(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(dnewm,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,fileres);
     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,fileres);
     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.</li>\n",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(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
         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#");    
         }
         
         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 */
                     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<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(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }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(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(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 covariates */
     }
     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 estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      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><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,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,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . 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_"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      /* 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++){ 
            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);
          }
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* aij, bij */
        fprintf(fichtm,"<br>- Logit model, for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
   <img src=\"%s_%d-1.svg\">",subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
        /* Pij */
        fprintf(fichtm,"<br>\n- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \
   <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>\n- Iij 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 hPij \
   divided by h: hPij/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
   <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); 
        /* 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.svg\">%s%d_%d.svg</a><br> \
   <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
        }
        /* State specific survival functions (period) */
        for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Survival functions from state %d in any different live states and total.\
    Or probability to survive in various states (1 to %d) being in state %d at different ages.\
    <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
        }
        /* 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 to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
   <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
        }
        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.svg\">%s%d%d.svg</a> <br> \
   <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
        }
      /* } /\* 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.<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(k1=1; k1<=m;k1++){
      /* 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++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.svg <br>\
   <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);  
        }
        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: %s_%d.svg<br>\
   <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
      /* } /\* end i1 *\/ */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
     int vpopbased;
   /*   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);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
        fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter svg size 640, 480\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
   
        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+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
        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:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
        fprintf(ficgp,"\nset out \n");
       } /* k1 */
     } /* cpt */
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
         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_"),k1-1,k1-1, 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_"),k1-1,k1-1,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_"),k1-1,k1-1,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.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
     } /* k1 */
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
         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_"),k1-1,k1-1,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_"),k1-1,k1-1,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_"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* Survival functions (period) from state i in state j by initial state i */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'lij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
   set ter svg size 640, 480\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         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\n");
       } /* end cpt state*/ 
     } /* end covariate */  
   
     /* Survival functions (period) from state i in state j by final state j */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
         k=3;
         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);
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
   set ter svg size 640, 480\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         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\n");
       } /* end cpt state*/ 
     } /* end covariate */  
   
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter svg size 640, 480\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         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/($%d",k1,k+l+(cpt-1),k+l);
           for (j=2; j<= nlstate ; j ++)
             fprintf(ficgp,"+$%d",k+l+j-1);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\nset out\n");
       } /* end cpt state*/ 
     } /* end covariate */  
   
     /* proba elementaires */
     fprintf(ficgp,"\n##############\n#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;*/
     fprintf(ficgp,"\n##############\n#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,"# ng=%d\n",ng);
        fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"#    jk=%d\n",jk);
          fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
          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 */
                for(j=3; j <=ncovmodel-nagesqr; j++) {
                  /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
                  if(ij <=cptcovage) { /* Bug valgrind */
                    if((j-2)==Tage[ij]) { /* Bug valgrind */
                      fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                      /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                      ij++;
                    }
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                }
                if(ng != 1){
                  fprintf(ficgp,")/(1");
                
                  for(k1=1; k1 <=nlstate; k1++){ 
                    if(nagesqr==0)
                      fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                    else /* nagesqr =1 */
                      fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
                    
                    ij=1;
                    for(j=3; j <=ncovmodel-nagesqr; j++){
                      if(ij <=cptcovage) { /* Bug valgrind */
                        if((j-2)==Tage[ij]) { /* Bug valgrind */
                          fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                          /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                          ij++;
                        }
                      }
                      else
                        fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                    }
                    fprintf(ficgp,")");
                  }
                  fprintf(ficgp,")");
                  if(ng ==2)
                    fprintf(ficgp," t \"p%d%d\" ", k2,k);
                  else /* ng= 3 */
                    fprintf(ficgp," t \"i%d%d\" ", k2,k);
                }else{ /* end ng <> 1 */
                  fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
                }
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
          fprintf(ficgp,"\n set out\n");
        } /* end jk */
      } /* end ng */
    /* avoid: */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;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 (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               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;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     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 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;
     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;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     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("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     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;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     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=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(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%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--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 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]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   void 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){
     
     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=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]);*/
   
     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;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);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);
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           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;
         
         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 Waves */
       
       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);
       
       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);
       
       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 (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           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 removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ == *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode 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;
     int  j1, k1, k2;
     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 =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=> 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]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
          *  Tvar[k] # of the kth covariate:  Tvar[1]=2  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 */
           Tvar[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 */
               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);
               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+k1; /* 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+V3*V2
                                      Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
               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  */
               Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
               Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
               k2=k2+2;
               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) */
               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 */
             cptcovn++;
             Tvar[k]=atoi(strd);
           }
           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);*/
   
   
     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 )
   {
     int i, m;
   
     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;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr = *nberr + 1;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           (*nberr)++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* 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]==-2 || s[m][i]==-4 || s[m][i]==-5){
           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 */
           }
           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;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     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){
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     int i, j, k, i1 ;
     double ftolpl = 1.e-10;
     double age, agebase, agelim;
   
       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("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       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,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       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++) {
             fprintf(ficrespl," 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)]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
   
           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,"\n");
           
           for (age=agebase; age<=agelim; age++){
           /* for (age=agebase; age<=agebase; age++){ */
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           } /* Age */
           /* was end of cptcod */
       } /* cptcov */
           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;
   
     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 (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         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);  
           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;
   }
   
   
   /***********************************************/
   /**************** 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 jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int num_filled;
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     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 fret;
     double dum=0.; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
   
     char model[MAXLINE], modeltemp[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 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 ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     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: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      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{
       strcpy(pathtot,argv[1]);
     }
     /*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;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
   
       /* First 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,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,ficlog);
         continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
                           &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
       if (num_filled != 8) {
         printf("Not 8\n");
       }
       printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);
     }
   
     /* 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,ficlog);
         continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
       if (num_filled == 0)
               model[0]='\0';
       else 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); */
     }
     /* 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); */
     if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
       model[strlen(model)-1]='\0';
     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=1+age%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"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);
     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 with '.' \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 file.\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 */
     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 */
       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==-3) { /* 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);
     }
     else{
       /* 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);
       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 scales values */
       p=param[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);
       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%1d",&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%1d",i1,j1,jk);
         fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
         fprintf(ficparo,"%1d%1d%1d",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);
       
       /*-------- 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;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* 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);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) 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. */
     /*  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 position of a product */
     /* 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)
     */
     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
                         */  
   
   /* Main decodemodel */
   
   
     if(decodemodel(model, lastobs) == 1)
       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);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* 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);  
     if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
     /* Nbcode gives the value of the lth modality of jth covariate, in
        V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
     /* 1 to ncodemax[j] 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).*/
     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 2**k
              * codtabm(h,k)=  1 & (h-1) >> (k-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
              */
     for(h=1; h <=100 ;h++){ 
       /* printf("h=%2d ", h); */
        /* for(k=1; k <=10; k++){ */
          /* printf("k=%d %d ",k,codtabm(h,k)); */
        /*   codtab[h][k]=codtabm(h,k); */
        /* } */
        /* printf("\n"); */
     }
     /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
     /*   for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 *\/  */
     /*     for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
     /*    for(cpt=1; cpt <=pow(2,k-1); cpt++){  /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/  */
     /*      h++; */
     /*      if (h>m)  */
     /*        h=1; */
     /*      codtab[h][k]=j; */
     /*      /\* codtab[12][3]=1; *\/ */
     /*      /\*codtab[h][Tvar[k]]=j;*\/ */
     /*      /\* printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); *\/ */
     /*    }  */
     /*     } */
     /*   } */
     /* }  */
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* 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); */
     /*    } */
     /*    printf("\n"); */
     /* } */
     /*   scanf("%d",i);*/
   
    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# %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=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %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=%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 prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<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); 
       /*     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, 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 ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\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 / */
       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
         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);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 mortality only */
     /* Standard maximisation */
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       /* Computes likelihood for initial parameters */
       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");
       globpr=1; /* again, to print the contributions */
       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");
       if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       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=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, 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 */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, 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");
           }
         }
       }
   
       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)
         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(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",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((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\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\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
   
       /* Other stuffs, more or less useful */    
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"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);
       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(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((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"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);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"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(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.*/
       
       
       
        /* 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, pathc,p);
       
       printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,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);
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
       /*#include "hpijx.h"*/
       hPijx(p, bage, fage);
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        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); */
         /*        fprintf(ficlog,"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); */
         /*      } */
       }
    
       /* ------ Other prevalence ratios------------ */
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       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);
         }
       }
   
   
       /*---------- 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' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           }
           fprintf(ficreseij,"******\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);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health 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); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"STDE_");
       strcat(fileresstde,fileresu);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health 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. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health 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 DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficrest,"******\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)]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           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 */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* 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"); */
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); /*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);
               /* 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");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       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);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       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' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    /* endfree:*/
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       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);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,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(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(ncodemaxwundef,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,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\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\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 -----------*/
   
   
      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);
     }
   }

Removed from v.1.32  
changed lines
  Added in v.1.201


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