Diff for /imach/src/imach.c between versions 1.36 and 1.198

version 1.36, 2002/03/29 15:27:27 version 1.198, 2015/09/03 07:14:39
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.198  2015/09/03 07:14:39  brouard
      Summary: 0.98q5 Flavia
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.197  2015/09/01 18:24:39  brouard
   first survey ("cross") where individuals from different ages are    *** empty log message ***
   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 1.196  2015/08/18 23:17:52  brouard
   second wave of interviews ("longitudinal") which measure each change    Summary: 0.98q5
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.195  2015/08/18 16:28:39  brouard
   model. More health states you consider, more time is necessary to reach the    Summary: Adding a hack for testing purpose
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    After reading the title, ftol and model lines, if the comment line has
   probabibility to be observed in state j at the second wave    a q, starting with #q, the answer at the end of the run is quit. It
   conditional to be observed in state i at the first wave. Therefore    permits to run test files in batch with ctest. The former workaround was
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    $ echo q | imach foo.imach
   '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 1.194  2015/08/18 13:32:00  brouard
   where the markup *Covariates have to be included here again* invites    Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.193  2015/08/04 07:17:42  brouard
     Summary: 0.98q4
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.192  2015/07/16 16:49:02  brouard
   identical for each individual. Also, if a individual missed an    Summary: Fixing some outputs
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.191  2015/07/14 10:00:33  brouard
     Summary: Some fixes
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    Revision 1.190  2015/05/05 08:51:13  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    Summary: Adding digits in output parameters (7 digits instead of 6)
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Fix 1+age+.
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.189  2015/04/30 14:45:16  brouard
   hPijx.    Summary: 0.98q2
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.188  2015/04/30 08:27:53  brouard
   of the life expectancies. It also computes the prevalence limits.    *** empty log message ***
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.187  2015/04/29 09:11:15  brouard
            Institut national d'études démographiques, Paris.    *** empty log message ***
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.186  2015/04/23 12:01:52  brouard
   It is copyrighted identically to a GNU software product, ie programme and    Summary: V1*age is working now, version 0.98q1
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Some codes had been disabled in order to simplify and Vn*age was
   **********************************************************************/    working in the optimization phase, ie, giving correct MLE parameters,
      but, as usual, outputs were not correct and program core dumped.
 #include <math.h>  
 #include <stdio.h>    Revision 1.185  2015/03/11 13:26:42  brouard
 #include <stdlib.h>    Summary: Inclusion of compile and links command line for Intel Compiler
 #include <unistd.h>  
     Revision 1.184  2015/03/11 11:52:39  brouard
 #define MAXLINE 256    Summary: Back from Windows 8. Intel Compiler
 #define GNUPLOTPROGRAM "wgnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.183  2015/03/10 20:34:32  brouard
 #define FILENAMELENGTH 80    Summary: 0.98q0, trying with directest, mnbrak fixed
 /*#define DEBUG*/  
 #define windows    We use directest instead of original Powell test; probably no
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    incidence on the results, but better justifications;
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    We fixed Numerical Recipes mnbrak routine which was wrong and gave
     wrong results.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.182  2015/02/12 08:19:57  brouard
     Summary: Trying to keep directest which seems simpler and more general
 #define NINTERVMAX 8    Author: Nicolas Brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.181  2015/02/11 23:22:24  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    Summary: Comments on Powell added
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Author:
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.180  2015/02/11 17:33:45  brouard
     Summary: Finishing move from main to function (hpijx and prevalence_limit)
   
 int erreur; /* Error number */    Revision 1.179  2015/01/04 09:57:06  brouard
 int nvar;    Summary: back to OS/X
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.178  2015/01/04 09:35:48  brouard
 int nlstate=2; /* Number of live states */    *** empty log message ***
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.177  2015/01/03 18:40:56  brouard
 int popbased=0;    Summary: Still testing ilc32 on OSX
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.176  2015/01/03 16:45:04  brouard
 int maxwav; /* Maxim number of waves */    *** empty log message ***
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.175  2015/01/03 16:33:42  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    *** empty log message ***
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Revision 1.174  2015/01/03 16:15:49  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Summary: Still in cross-compilation
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Revision 1.173  2015/01/03 12:06:26  brouard
 FILE *ficgp,*ficresprob,*ficpop;    Summary: trying to detect cross-compilation
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.172  2014/12/27 12:07:47  brouard
  FILE  *ficresvij;    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.171  2014/12/23 13:26:59  brouard
   char fileresvpl[FILENAMELENGTH];    Summary: Back from Visual C
   
 #define NR_END 1    Still problem with utsname.h on Windows
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.170  2014/12/23 11:17:12  brouard
     Summary: Cleaning some \%% back to %%
 #define NRANSI  
 #define ITMAX 200    The escape was mandatory for a specific compiler (which one?), but too many warnings.
   
 #define TOL 2.0e-4    Revision 1.169  2014/12/22 23:08:31  brouard
     Summary: 0.98p
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Outputs some informations on compiler used, OS etc. Testing on different platforms.
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.168  2014/12/22 15:17:42  brouard
 #define GOLD 1.618034    Summary: update
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.167  2014/12/22 13:50:56  brouard
     Summary: Testing uname and compiler version and if compiled 32 or 64
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Testing on Linux 64
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.166  2014/12/22 11:40:47  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    *** empty log message ***
 #define rint(a) floor(a+0.5)  
     Revision 1.165  2014/12/16 11:20:36  brouard
 static double sqrarg;    Summary: After compiling on Visual C
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    * imach.c (Module): Merging 1.61 to 1.162
   
 int imx;    Revision 1.164  2014/12/16 10:52:11  brouard
 int stepm;    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 /* Stepm, step in month: minimum step interpolation*/  
     * imach.c (Module): Merging 1.61 to 1.162
 int estepm;  
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    Revision 1.163  2014/12/16 10:30:11  brouard
     * imach.c (Module): Merging 1.61 to 1.162
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.162  2014/09/25 11:43:39  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Summary: temporary backup 0.99!
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;    Revision 1.1  2014/09/16 11:06:58  brouard
     Summary: With some code (wrong) for nlopt
 double *weight;  
 int **s; /* Status */    Author:
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.161  2014/09/15 20:41:41  brouard
     Summary: Problem with macro SQR on Intel compiler
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.160  2014/09/02 09:24:05  brouard
     *** empty log message ***
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Revision 1.159  2014/09/01 10:34:10  brouard
 {    Summary: WIN32
    char *s;                             /* pointer */    Author: Brouard
    int  l1, l2;                         /* length counters */  
     Revision 1.158  2014/08/27 17:11:51  brouard
    l1 = strlen( path );                 /* length of path */    *** empty log message ***
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows    Revision 1.157  2014/08/27 16:26:55  brouard
    s = strrchr( path, '\\' );           /* find last / */    Summary: Preparing windows Visual studio version
 #else    Author: Brouard
    s = strrchr( path, '/' );            /* find last / */  
 #endif    In order to compile on Visual studio, time.h is now correct and time_t
    if ( s == NULL ) {                   /* no directory, so use current */    and tm struct should be used. difftime should be used but sometimes I
 #if     defined(__bsd__)                /* get current working directory */    just make the differences in raw time format (time(&now).
       extern char       *getwd( );    Trying to suppress #ifdef LINUX
     Add xdg-open for __linux in order to open default browser.
       if ( getwd( dirc ) == NULL ) {  
 #else    Revision 1.156  2014/08/25 20:10:10  brouard
       extern char       *getcwd( );    *** empty log message ***
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.155  2014/08/25 18:32:34  brouard
 #endif    Summary: New compile, minor changes
          return( GLOCK_ERROR_GETCWD );    Author: Brouard
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.154  2014/06/20 17:32:08  brouard
    } else {                             /* strip direcotry from path */    Summary: Outputs now all graphs of convergence to period prevalence
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    Revision 1.153  2014/06/20 16:45:46  brouard
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Summary: If 3 live state, convergence to period prevalence on same graph
       strcpy( name, s );                /* save file name */    Author: Brouard
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    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
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows    Revision 1.151  2014/06/18 16:43:30  brouard
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    *** empty log message ***
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    Revision 1.150  2014/06/18 16:42:35  brouard
 #endif    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
    s = strrchr( name, '.' );            /* find last / */    Author: brouard
    s++;  
    strcpy(ext,s);                       /* save extension */    Revision 1.149  2014/06/18 15:51:14  brouard
    l1= strlen( name);    Summary: Some fixes in parameter files errors
    l2= strlen( s)+1;    Author: Nicolas Brouard
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    Revision 1.148  2014/06/17 17:38:48  brouard
    return( 0 );                         /* we're done */    Summary: Nothing new
 }    Author: Brouard
   
     Just a new packaging for OS/X version 0.98nS
 /******************************************/  
     Revision 1.147  2014/06/16 10:33:11  brouard
 void replace(char *s, char*t)    *** empty log message ***
 {  
   int i;    Revision 1.146  2014/06/16 10:20:28  brouard
   int lg=20;    Summary: Merge
   i=0;    Author: Brouard
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Merge, before building revised version.
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Revision 1.145  2014/06/10 21:23:15  brouard
   }    Summary: Debugging with valgrind
 }    Author: Nicolas Brouard
   
 int nbocc(char *s, char occ)    Lot of changes in order to output the results with some covariates
 {    After the Edimburgh REVES conference 2014, it seems mandatory to
   int i,j=0;    improve the code.
   int lg=20;    No more memory valgrind error but a lot has to be done in order to
   i=0;    continue the work of splitting the code into subroutines.
   lg=strlen(s);    Also, decodemodel has been improved. Tricode is still not
   for(i=0; i<= lg; i++) {    optimal. nbcode should be improved. Documentation has been added in
   if  (s[i] == occ ) j++;    the source code.
   }  
   return 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
   
 void cutv(char *u,char *v, char*t, char occ)    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 {    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   int i,lg,j,p=0;  
   i=0;    Revision 1.142  2014/01/26 03:57:36  brouard
   for(j=0; j<=strlen(t)-1; j++) {    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   
   lg=strlen(t);    Revision 1.141  2014/01/26 02:42:01  brouard
   for(j=0; j<p; j++) {    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
     (u[j] = t[j]);  
   }    Revision 1.140  2011/09/02 10:37:54  brouard
      u[p]='\0';    Summary: times.h is ok with mingw32 now.
   
    for(j=0; j<= lg; j++) {    Revision 1.139  2010/06/14 07:50:17  brouard
     if (j>=(p+1))(v[j-p-1] = t[j]);    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.
 }  
     Revision 1.138  2010/04/30 18:19:40  brouard
 /********************** nrerror ********************/    *** empty log message ***
   
 void nrerror(char error_text[])    Revision 1.137  2010/04/29 18:11:38  brouard
 {    (Module): Checking covariates for more complex models
   fprintf(stderr,"ERREUR ...\n");    than V1+V2. A lot of change to be done. Unstable.
   fprintf(stderr,"%s\n",error_text);  
   exit(1);    Revision 1.136  2010/04/26 20:30:53  brouard
 }    (Module): merging some libgsl code. Fixing computation
 /*********************** vector *******************/    of likelione (using inter/intrapolation if mle = 0) in order to
 double *vector(int nl, int nh)    get same likelihood as if mle=1.
 {    Some cleaning of code and comments added.
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Revision 1.135  2009/10/29 15:33:14  brouard
   if (!v) nrerror("allocation failure in vector");    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   return v-nl+NR_END;  
 }    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 vector ******************/  
 void free_vector(double*v, int nl, int nh)    Revision 1.133  2009/07/06 10:21:25  brouard
 {    just nforces
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.132  2009/07/06 08:22:05  brouard
     Many tings
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    Revision 1.131  2009/06/20 16:22:47  brouard
 {    Some dimensions resccaled
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    Revision 1.130  2009/05/26 06:44:34  brouard
   if (!v) nrerror("allocation failure in ivector");    (Module): Max Covariate is now set to 20 instead of 8. A
   return v-nl+NR_END;    lot of cleaning with variables initialized to 0. Trying to make
 }    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   
 /******************free ivector **************************/    Revision 1.129  2007/08/31 13:49:27  lievre
 void free_ivector(int *v, long nl, long nh)    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 {  
   free((FREE_ARG)(v+nl-NR_END));    Revision 1.128  2006/06/30 13:02:05  brouard
 }    (Module): Clarifications on computing e.j
   
 /******************* imatrix *******************************/    Revision 1.127  2006/04/28 18:11:50  brouard
 int **imatrix(long nrl, long nrh, long ncl, long nch)    (Module): Yes the sum of survivors was wrong since
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    imach-114 because nhstepm was no more computed in the age
 {    loop. Now we define nhstepma in the age loop.
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    (Module): In order to speed up (in case of numerous covariates) we
   int **m;    compute health expectancies (without variances) in a first step
      and then all the health expectancies with variances or standard
   /* allocate pointers to rows */    deviation (needs data from the Hessian matrices) which slows the
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    computation.
   if (!m) nrerror("allocation failure 1 in matrix()");    In the future we should be able to stop the program is only health
   m += NR_END;    expectancies and graph are needed without standard deviations.
   m -= nrl;  
      Revision 1.126  2006/04/28 17:23:28  brouard
      (Module): Yes the sum of survivors was wrong since
   /* allocate rows and set pointers to them */    imach-114 because nhstepm was no more computed in the age
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    loop. Now we define nhstepma in the age loop.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Version 0.98h
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.125  2006/04/04 15:20:31  lievre
      Errors in calculation of health expectancies. Age was not initialized.
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    Forecasting file added.
    
   /* return pointer to array of pointers to rows */    Revision 1.124  2006/03/22 17:13:53  lievre
   return m;    Parameters are printed with %lf instead of %f (more numbers after the comma).
 }    The log-likelihood is printed in the log file
   
 /****************** free_imatrix *************************/    Revision 1.123  2006/03/20 10:52:43  brouard
 void free_imatrix(m,nrl,nrh,ncl,nch)    * imach.c (Module): <title> changed, corresponds to .htm file
       int **m;    name. <head> headers where missing.
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */    * imach.c (Module): Weights can have a decimal point as for
 {    English (a comma might work with a correct LC_NUMERIC environment,
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    otherwise the weight is truncated).
   free((FREE_ARG) (m+nrl-NR_END));    Modification of warning when the covariates values are not 0 or
 }    1.
     Version 0.98g
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    Revision 1.122  2006/03/20 09:45:41  brouard
 {    (Module): Weights can have a decimal point as for
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    English (a comma might work with a correct LC_NUMERIC environment,
   double **m;    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    1.
   if (!m) nrerror("allocation failure 1 in matrix()");    Version 0.98g
   m += NR_END;  
   m -= nrl;    Revision 1.121  2006/03/16 17:45:01  lievre
     * imach.c (Module): Comments concerning covariates added
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    * imach.c (Module): refinements in the computation of lli if
   m[nrl] += NR_END;    status=-2 in order to have more reliable computation if stepm is
   m[nrl] -= ncl;    not 1 month. Version 0.98f
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Revision 1.120  2006/03/16 15:10:38  lievre
   return m;    (Module): refinements in the computation of lli if
 }    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    Revision 1.119  2006/03/15 17:42:26  brouard
 {    (Module): Bug if status = -2, the loglikelihood was
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    computed as likelihood omitting the logarithm. Version O.98e
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Revision 1.118  2006/03/14 18:20:07  brouard
     (Module): varevsij Comments added explaining the second
 /******************* ma3x *******************************/    table of variances if popbased=1 .
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 {    (Module): Function pstamp added
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    (Module): Version 0.98d
   double ***m;  
     Revision 1.117  2006/03/14 17:16:22  brouard
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    (Module): varevsij Comments added explaining the second
   if (!m) nrerror("allocation failure 1 in matrix()");    table of variances if popbased=1 .
   m += NR_END;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   m -= nrl;    (Module): Function pstamp added
     (Module): Version 0.98d
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.116  2006/03/06 10:29:27  brouard
   m[nrl] += NR_END;    (Module): Variance-covariance wrong links and
   m[nrl] -= ncl;    varian-covariance of ej. is needed (Saito).
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Revision 1.115  2006/02/27 12:17:45  brouard
     (Module): One freematrix added in mlikeli! 0.98c
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    Revision 1.114  2006/02/26 12:57:58  brouard
   m[nrl][ncl] += NR_END;    (Module): Some improvements in processing parameter
   m[nrl][ncl] -= nll;    filename with strsep.
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;    Revision 1.113  2006/02/24 14:20:24  brouard
      (Module): Memory leaks checks with valgrind and:
   for (i=nrl+1; i<=nrh; i++) {    datafile was not closed, some imatrix were not freed and on matrix
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    allocation too.
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;    Revision 1.112  2006/01/30 09:55:26  brouard
   }    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   return m;  
 }    Revision 1.111  2006/01/25 20:38:18  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 /*************************free ma3x ************************/    (Module): Comments can be added in data file. Missing date values
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    can be a simple dot '.'.
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    Revision 1.110  2006/01/25 00:51:50  brouard
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    (Module): Lots of cleaning and bugs added (Gompertz)
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Revision 1.109  2006/01/24 19:37:15  brouard
     (Module): Comments (lines starting with a #) are allowed in data.
 /***************** f1dim *************************/  
 extern int ncom;    Revision 1.108  2006/01/19 18:05:42  lievre
 extern double *pcom,*xicom;    Gnuplot problem appeared...
 extern double (*nrfunc)(double []);    To be fixed
    
 double f1dim(double x)    Revision 1.107  2006/01/19 16:20:37  brouard
 {    Test existence of gnuplot in imach path
   int j;  
   double f;    Revision 1.106  2006/01/19 13:24:36  brouard
   double *xt;    Some cleaning and links added in html output
    
   xt=vector(1,ncom);    Revision 1.105  2006/01/05 20:23:19  lievre
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    *** empty log message ***
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);    Revision 1.104  2005/09/30 16:11:43  lievre
   return f;    (Module): sump fixed, loop imx fixed, and simplifications.
 }    (Module): If the status is missing at the last wave but we know
     that the person is alive, then we can code his/her status as -2
 /*****************brent *************************/    (instead of missing=-1 in earlier versions) and his/her
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    contributions to the likelihood is 1 - Prob of dying from last
 {    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   int iter;    the healthy state at last known wave). Version is 0.98
   double a,b,d,etemp;  
   double fu,fv,fw,fx;    Revision 1.103  2005/09/30 15:54:49  lievre
   double ftemp;    (Module): sump fixed, loop imx fixed, and simplifications.
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;    Revision 1.102  2004/09/15 17:31:30  brouard
      Add the possibility to read data file including tab characters.
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);    Revision 1.101  2004/09/15 10:38:38  brouard
   x=w=v=bx;    Fix on curr_time
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {    Revision 1.100  2004/07/12 18:29:06  brouard
     xm=0.5*(a+b);    Add version for Mac OS X. Just define UNIX in Makefile
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    Revision 1.99  2004/06/05 08:57:40  brouard
     printf(".");fflush(stdout);    *** empty log message ***
 #ifdef DEBUG  
     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);    Revision 1.98  2004/05/16 15:05:56  brouard
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    New version 0.97 . First attempt to estimate force of mortality
 #endif    directly from the data i.e. without the need of knowing the health
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    state at each age, but using a Gompertz model: log u =a + b*age .
       *xmin=x;    This is the basic analysis of mortality and should be done before any
       return fx;    other analysis, in order to test if the mortality estimated from the
     }    cross-longitudinal survey is different from the mortality estimated
     ftemp=fu;    from other sources like vital statistic data.
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);    The same imach parameter file can be used but the option for mle should be -3.
       q=(x-v)*(fx-fw);  
       p=(x-v)*q-(x-w)*r;    Agnès, who wrote this part of the code, tried to keep most of the
       q=2.0*(q-r);    former routines in order to include the new code within the former code.
       if (q > 0.0) p = -p;  
       q=fabs(q);    The output is very simple: only an estimate of the intercept and of
       etemp=e;    the slope with 95% confident intervals.
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    Current limitations:
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    A) Even if you enter covariates, i.e. with the
       else {    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
         d=p/q;    B) There is no computation of Life Expectancy nor Life Table.
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)    Revision 1.97  2004/02/20 13:25:42  lievre
           d=SIGN(tol1,xm-x);    Version 0.96d. Population forecasting command line is (temporarily)
       }    suppressed.
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    Revision 1.96  2003/07/15 15:38:55  brouard
     }    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    rewritten within the same printf. Workaround: many printfs.
     fu=(*f)(u);  
     if (fu <= fx) {    Revision 1.95  2003/07/08 07:54:34  brouard
       if (u >= x) a=x; else b=x;    * imach.c (Repository):
       SHFT(v,w,x,u)    (Repository): Using imachwizard code to output a more meaningful covariance
         SHFT(fv,fw,fx,fu)    matrix (cov(a12,c31) instead of numbers.
         } else {  
           if (u < x) a=u; else b=u;    Revision 1.94  2003/06/27 13:00:02  brouard
           if (fu <= fw || w == x) {    Just cleaning
             v=w;  
             w=u;    Revision 1.93  2003/06/25 16:33:55  brouard
             fv=fw;    (Module): On windows (cygwin) function asctime_r doesn't
             fw=fu;    exist so I changed back to asctime which exists.
           } else if (fu <= fv || v == x || v == w) {    (Module): Version 0.96b
             v=u;  
             fv=fu;    Revision 1.92  2003/06/25 16:30:45  brouard
           }    (Module): On windows (cygwin) function asctime_r doesn't
         }    exist so I changed back to asctime which exists.
   }  
   nrerror("Too many iterations in brent");    Revision 1.91  2003/06/25 15:30:29  brouard
   *xmin=x;    * imach.c (Repository): Duplicated warning errors corrected.
   return fx;    (Repository): Elapsed time after each iteration is now output. It
 }    helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
 /****************** mnbrak ***********************/    concerning matrix of covariance. It has extension -cov.htm.
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    Revision 1.90  2003/06/24 12:34:15  brouard
             double (*func)(double))    (Module): Some bugs corrected for windows. Also, when
 {    mle=-1 a template is output in file "or"mypar.txt with the design
   double ulim,u,r,q, dum;    of the covariance matrix to be input.
   double fu;  
      Revision 1.89  2003/06/24 12:30:52  brouard
   *fa=(*func)(*ax);    (Module): Some bugs corrected for windows. Also, when
   *fb=(*func)(*bx);    mle=-1 a template is output in file "or"mypar.txt with the design
   if (*fb > *fa) {    of the covariance matrix to be input.
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)    Revision 1.88  2003/06/23 17:54:56  brouard
       }    * 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.
   *cx=(*bx)+GOLD*(*bx-*ax);  
   *fc=(*func)(*cx);    Revision 1.87  2003/06/18 12:26:01  brouard
   while (*fb > *fc) {    Version 0.96
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);    Revision 1.86  2003/06/17 20:04:08  brouard
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    (Module): Change position of html and gnuplot routines and added
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    routine fileappend.
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {    Revision 1.85  2003/06/17 13:12:43  brouard
       fu=(*func)(u);    * imach.c (Repository): Check when date of death was earlier that
     } else if ((*cx-u)*(u-ulim) > 0.0) {    current date of interview. It may happen when the death was just
       fu=(*func)(u);    prior to the death. In this case, dh was negative and likelihood
       if (fu < *fc) {    was wrong (infinity). We still send an "Error" but patch by
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    assuming that the date of death was just one stepm after the
           SHFT(*fb,*fc,fu,(*func)(u))    interview.
           }    (Repository): Because some people have very long ID (first column)
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    we changed int to long in num[] and we added a new lvector for
       u=ulim;    memory allocation. But we also truncated to 8 characters (left
       fu=(*func)(u);    truncation)
     } else {    (Repository): No more line truncation errors.
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);    Revision 1.84  2003/06/13 21:44:43  brouard
     }    * imach.c (Repository): Replace "freqsummary" at a correct
     SHFT(*ax,*bx,*cx,u)    place. It differs from routine "prevalence" which may be called
       SHFT(*fa,*fb,*fc,fu)    many times. Probs is memory consuming and must be used with
       }    parcimony.
 }    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 /*************** linmin ************************/    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
 int ncom;  
 double *pcom,*xicom;    Revision 1.82  2003/06/05 15:57:20  brouard
 double (*nrfunc)(double []);    Add log in  imach.c and  fullversion number is now printed.
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  */
 {  /*
   double brent(double ax, double bx, double cx,     Interpolated Markov Chain
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);    Short summary of the programme:
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    
               double *fc, double (*func)(double));    This program computes Healthy Life Expectancies from
   int j;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   double xx,xmin,bx,ax;    first survey ("cross") where individuals from different ages are
   double fx,fb,fa;    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
   ncom=n;    second wave of interviews ("longitudinal") which measure each change
   pcom=vector(1,n);    (if any) in individual health status.  Health expectancies are
   xicom=vector(1,n);    computed from the time spent in each health state according to a
   nrfunc=func;    model. More health states you consider, more time is necessary to reach the
   for (j=1;j<=n;j++) {    Maximum Likelihood of the parameters involved in the model.  The
     pcom[j]=p[j];    simplest model is the multinomial logistic model where pij is the
     xicom[j]=xi[j];    probability to be observed in state j at the second wave
   }    conditional to be observed in state i at the first wave. Therefore
   ax=0.0;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   xx=1.0;    'age' is age and 'sex' is a covariate. If you want to have a more
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    complex model than "constant and age", you should modify the program
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    where the markup *Covariates have to be included here again* invites
 #ifdef DEBUG    you to do it.  More covariates you add, slower the
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    convergence.
 #endif  
   for (j=1;j<=n;j++) {    The advantage of this computer programme, compared to a simple
     xi[j] *= xmin;    multinomial logistic model, is clear when the delay between waves is not
     p[j] += xi[j];    identical for each individual. Also, if a individual missed an
   }    intermediate interview, the information is lost, but taken into
   free_vector(xicom,1,n);    account using an interpolation or extrapolation.  
   free_vector(pcom,1,n);  
 }    hPijx is the probability to be observed in state i at age x+h
     conditional to the observed state i at age x. The delay 'h' can be
 /*************** powell ************************/    split into an exact number (nh*stepm) of unobserved intermediate
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    states. This elementary transition (by month, quarter,
             double (*func)(double []))    semester or year) is modelled as a multinomial logistic.  The hPx
 {    matrix is simply the matrix product of nh*stepm elementary matrices
   void linmin(double p[], double xi[], int n, double *fret,    and the contribution of each individual to the likelihood is simply
               double (*func)(double []));    hPijx.
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;    Also this programme outputs the covariance matrix of the parameters but also
   double fp,fptt;    of the life expectancies. It also computes the period (stable) prevalence. 
   double *xits;    
   pt=vector(1,n);    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   ptt=vector(1,n);             Institut national d'études démographiques, Paris.
   xit=vector(1,n);    This software have been partly granted by Euro-REVES, a concerted action
   xits=vector(1,n);    from the European Union.
   *fret=(*func)(p);    It is copyrighted identically to a GNU software product, ie programme and
   for (j=1;j<=n;j++) pt[j]=p[j];    software can be distributed freely for non commercial use. Latest version
   for (*iter=1;;++(*iter)) {    can be accessed at http://euroreves.ined.fr/imach .
     fp=(*fret);  
     ibig=0;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     del=0.0;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    
     for (i=1;i<=n;i++)    **********************************************************************/
       printf(" %d %.12f",i, p[i]);  /*
     printf("\n");    main
     for (i=1;i<=n;i++) {    read parameterfile
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    read datafile
       fptt=(*fret);    concatwav
 #ifdef DEBUG    freqsummary
       printf("fret=%lf \n",*fret);    if (mle >= 1)
 #endif      mlikeli
       printf("%d",i);fflush(stdout);    print results files
       linmin(p,xit,n,fret,func);    if mle==1 
       if (fabs(fptt-(*fret)) > del) {       computes hessian
         del=fabs(fptt-(*fret));    read end of parameter file: agemin, agemax, bage, fage, estepm
         ibig=i;        begin-prev-date,...
       }    open gnuplot file
 #ifdef DEBUG    open html file
       printf("%d %.12e",i,(*fret));    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
       for (j=1;j<=n;j++) {     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
         printf(" x(%d)=%.12e",j,xit[j]);      freexexit2 possible for memory heap.
       }  
       for(j=1;j<=n;j++)    h Pij x                         | pij_nom  ficrestpij
         printf(" p=%.12e",p[j]);     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
       printf("\n");         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
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
 #ifdef DEBUG         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
       int k[2],l;    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
       k[0]=1;     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
       k[1]=-1;     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
       printf("Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++)    forecasting if prevfcast==1 prevforecast call prevalence()
         printf(" %.12e",p[j]);    health expectancies
       printf("\n");    Variance-covariance of DFLE
       for(l=0;l<=1;l++) {    prevalence()
         for (j=1;j<=n;j++) {     movingaverage()
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    varevsij() 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    if popbased==1 varevsij(,popbased)
         }    total life expectancies
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    Variance of period (stable) prevalence
       }   end
 #endif  */
   
   /* #define DEBUG */
       free_vector(xit,1,n);  /* #define DEBUGBRENT */
       free_vector(xits,1,n);  #define POWELL /* Instead of NLOPT */
       free_vector(ptt,1,n);  #define POWELLF1F3 /* Skip test */
       free_vector(pt,1,n);  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
       return;  /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  #include <math.h>
     for (j=1;j<=n;j++) {  #include <stdio.h>
       ptt[j]=2.0*p[j]-pt[j];  #include <stdlib.h>
       xit[j]=p[j]-pt[j];  #include <string.h>
       pt[j]=p[j];  
     }  #ifdef _WIN32
     fptt=(*func)(ptt);  #include <io.h>
     if (fptt < fp) {  #include <windows.h>
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  #include <tchar.h>
       if (t < 0.0) {  #else
         linmin(p,xit,n,fret,func);  #include <unistd.h>
         for (j=1;j<=n;j++) {  #endif
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];  #include <limits.h>
         }  #include <sys/types.h>
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #if defined(__GNUC__)
         for(j=1;j<=n;j++)  #include <sys/utsname.h> /* Doesn't work on Windows */
           printf(" %.12e",xit[j]);  #endif
         printf("\n");  
 #endif  #include <sys/stat.h>
       }  #include <errno.h>
     }  /* extern int errno; */
   }  
 }  /* #ifdef LINUX */
   /* #include <time.h> */
 /**** Prevalence limit ****************/  /* #include "timeval.h" */
   /* #else */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  /* #include <sys/time.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 <time.h>
   
   int i, ii,j,k;  #ifdef GSL
   double min, max, maxmin, maxmax,sumnew=0.;  #include <gsl/gsl_errno.h>
   double **matprod2();  #include <gsl/gsl_multimin.h>
   double **out, cov[NCOVMAX], **pmij();  #endif
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */  
   #ifdef NLOPT
   for (ii=1;ii<=nlstate+ndeath;ii++)  #include <nlopt.h>
     for (j=1;j<=nlstate+ndeath;j++){  typedef struct {
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    double (* function)(double [] );
     }  } myfunc_data ;
   #endif
    cov[1]=1.;  
    /* #include <libintl.h> */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /* #define _(String) gettext (String) */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  
     newm=savm;  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
     /* Covariates have to be included here again */  
      cov[2]=agefin;  #define GNUPLOTPROGRAM "gnuplot"
    /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       for (k=1; k<=cptcovn;k++) {  #define FILENAMELENGTH 132
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       }  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  #define NINTERVMAX 8
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
   #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
     savm=oldm;  #define MAXN 20000
     oldm=newm;  #define YEARM 12. /**< Number of months per year */
     maxmax=0.;  #define AGESUP 130
     for(j=1;j<=nlstate;j++){  #define AGEBASE 40
       min=1.;  #define AGEOVERFLOW 1.e20
       max=0.;  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
       for(i=1; i<=nlstate; i++) {  #ifdef _WIN32
         sumnew=0;  #define DIRSEPARATOR '\\'
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  #define CHARSEPARATOR "\\"
         prlim[i][j]= newm[i][j]/(1-sumnew);  #define ODIRSEPARATOR '/'
         max=FMAX(max,prlim[i][j]);  #else
         min=FMIN(min,prlim[i][j]);  #define DIRSEPARATOR '/'
       }  #define CHARSEPARATOR "/"
       maxmin=max-min;  #define ODIRSEPARATOR '\\'
       maxmax=FMAX(maxmax,maxmin);  #endif
     }  
     if(maxmax < ftolpl){  /* $Id$ */
       return prlim;  /* $State$ */
     }  #include "version.h"
   }  char version[]=__IMACH_VERSION__;
 }  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";
   char fullversion[]="$Revision$ $Date$"; 
 /*************** transition probabilities ***************/  char strstart[80];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 {  int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
   double s1, s2;  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   /*double t34;*/  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
   int i,j,j1, nc, ii, jj;  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 */
     for(i=1; i<= nlstate; i++){  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
     for(j=1; j<i;j++){  int cptcovprodnoage=0; /**< Number of covariate products without age */   
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  int cptcoveff=0; /* Total number of covariates to vary for printing results */
         /*s2 += param[i][j][nc]*cov[nc];*/  int cptcov=0; /* Working variable */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  int npar=NPARMAX;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  int nlstate=2; /* Number of live states */
       }  int ndeath=1; /* Number of dead states */
       ps[i][j]=s2;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  int popbased=0;
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){  int *wav; /* Number of waves for this individuual 0 is possible */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  int maxwav=0; /* Maxim number of waves */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
       }  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
       ps[i][j]=s2;                     to the likelihood and the sum of weights (done by funcone)*/
     }  int mle=1, weightopt=0;
   }  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
     /*ps[3][2]=1;*/  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   for(i=1; i<= nlstate; i++){             * wave mi and wave mi+1 is not an exact multiple of stepm. */
      s1=0;  int countcallfunc=0;  /* Count the number of calls to func */
     for(j=1; j<i; j++)  double jmean=1; /* Mean space between 2 waves */
       s1+=exp(ps[i][j]);  double **matprod2(); /* test */
     for(j=i+1; j<=nlstate+ndeath; j++)  double **oldm, **newm, **savm; /* Working pointers to matrices */
       s1+=exp(ps[i][j]);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     ps[i][i]=1./(s1+1.);  /*FILE *fic ; */ /* Used in readdata only */
     for(j=1; j<i; j++)  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  FILE *ficlog, *ficrespow;
     for(j=i+1; j<=nlstate+ndeath; j++)  int globpr=0; /* Global variable for printing or not */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  double fretone; /* Only one call to likelihood */
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  long ipmx=0; /* Number of contributions */
   } /* end i */  double sw; /* Sum of weights */
   char filerespow[FILENAMELENGTH];
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
     for(jj=1; jj<= nlstate+ndeath; jj++){  FILE *ficresilk;
       ps[ii][jj]=0;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       ps[ii][ii]=1;  FILE *ficresprobmorprev;
     }  FILE *fichtm, *fichtmcov; /* Html File */
   }  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
   FILE *ficresstdeij;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  char fileresstde[FILENAMELENGTH];
     for(jj=1; jj<= nlstate+ndeath; jj++){  FILE *ficrescveij;
      printf("%lf ",ps[ii][jj]);  char filerescve[FILENAMELENGTH];
    }  FILE  *ficresvij;
     printf("\n ");  char fileresv[FILENAMELENGTH];
     }  FILE  *ficresvpl;
     printf("\n ");printf("%lf ",cov[2]);*/  char fileresvpl[FILENAMELENGTH];
 /*  char title[MAXLINE];
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   goto end;*/  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     return ps;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 }  char command[FILENAMELENGTH];
   int  outcmd=0;
 /**************** Product of 2 matrices ******************/  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  
 {  char filelog[FILENAMELENGTH]; /* Log file */
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  char filerest[FILENAMELENGTH];
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  char fileregp[FILENAMELENGTH];
   /* in, b, out are matrice of pointers which should have been initialized  char popfile[FILENAMELENGTH];
      before: only the contents of out is modified. The function returns  
      a pointer to pointers identical to out */  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
     for(k=ncolol; k<=ncoloh; k++)  /* struct timezone tzp; */
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  /* extern int gettimeofday(); */
         out[i][k] +=in[i][j]*b[j][k];  struct tm tml, *gmtime(), *localtime();
   
   return out;  extern time_t time();
 }  
   struct tm start_time, end_time, curr_time, last_time, forecast_time;
   time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
 /************* Higher Matrix Product ***************/  struct tm tm;
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  char strcurr[80], strfor[80];
 {  
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  char *endptr;
      duration (i.e. until  long lval;
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  double dval;
      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).  #define NR_END 1
      Model is determined by parameters x and covariates have to be  #define FREE_ARG char*
      included manually here.  #define FTOL 1.0e-10
   
      */  #define NRANSI 
   #define ITMAX 200 
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];  #define TOL 2.0e-4 
   double **newm;  
   #define CGOLD 0.3819660 
   /* Hstepm could be zero and should return the unit matrix */  #define ZEPS 1.0e-10 
   for (i=1;i<=nlstate+ndeath;i++)  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);  #define GOLD 1.618034 
       po[i][j][0]=(i==j ? 1.0 : 0.0);  #define GLIMIT 100.0 
     }  #define TINY 1.0e-20 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(h=1; h <=nhstepm; h++){  static double maxarg1,maxarg2;
     for(d=1; d <=hstepm; d++){  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       newm=savm;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       /* Covariates have to be included here again */    
       cov[1]=1.;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  #define rint(a) floor(a+0.5)
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
       for (k=1; k<=cptcovage;k++)  #define mytinydouble 1.0e-16
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
       for (k=1; k<=cptcovprod;k++)  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  /* static double dsqrarg; */
   /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
   static double sqrarg;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  int agegomp= AGEGOMP;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;  int imx; 
       oldm=newm;  int stepm=1;
     }  /* Stepm, step in month: minimum step interpolation*/
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {  int estepm;
         po[i][j][h]=newm[i][j];  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  
          */  int m,nb;
       }  long *num;
   } /* end h */  int firstpass=0, lastpass=4,*cod, *cens;
   return po;  int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
 }                     covariate for which somebody answered excluding 
                      undefined. Usually 2: 0 and 1. */
   int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
 /*************** log-likelihood *************/                               covariate for which somebody answered including 
 double func( double *x)                               undefined. Usually 3: -1, 0 and 1. */
 {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   int i, ii, j, k, mi, d, kk;  double **pmmij, ***probs;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  double *ageexmed,*agecens;
   double **out;  double dateintmean=0;
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */  double *weight;
   long ipmx;  int **s; /* Status */
   /*extern weight */  double *agedc;
   /* We are differentiating ll according to initial status */  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/                    * covar=matrix(0,NCOVMAX,1,n); 
   /*for(i=1;i<imx;i++)                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
     printf(" %d\n",s[4][i]);  double  idx; 
   */  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   cov[1]=1.;  int *Tage;
   int *Ndum; /** Freq of modality (tricode */
   for(k=1; k<=nlstate; k++) ll[k]=0.;  int **codtab; /**< codtab=imatrix(1,100,1,10); */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  double *lsurv, *lpop, *tpop;
     for(mi=1; mi<= wav[i]-1; mi++){  
       for (ii=1;ii<=nlstate+ndeath;ii++)  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  double ftolhess; /**< Tolerance for computing hessian */
       for(d=0; d<dh[mi][i]; d++){  
         newm=savm;  /**************** split *************************/
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
         for (kk=1; kk<=cptcovage;kk++) {  {
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    /* 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)
            */ 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    char  *ss;                            /* pointer */
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    int   l1=0, l2=0;                             /* length counters */
         savm=oldm;  
         oldm=newm;    l1 = strlen(path );                   /* length of path */
            if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
            ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       } /* end mult */    if ( ss == NULL ) {                   /* no directory, so determine current directory */
            strcpy( name, path );               /* we got the fullname name because no directory */
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       ipmx +=1;      /* get current working directory */
       sw += weight[i];      /*    extern  char* getcwd ( char *buf , int len);*/
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  #ifdef WIN32
     } /* end of wave */      if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
   } /* end of individual */  #else
           if (getcwd(dirc, FILENAME_MAX) == NULL) {
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  #endif
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        return( GLOCK_ERROR_GETCWD );
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      }
   return -l;      /* got dirc from getcwd*/
 }      printf(" DIRC = %s \n",dirc);
     } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
 /*********** Maximum Likelihood Estimation ***************/      l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      strcpy( name, ss );         /* save file name */
 {      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   int i,j, iter;      dirc[l1-l2] = '\0';                 /* add zero */
   double **xi,*delti;      printf(" DIRC2 = %s \n",dirc);
   double fret;    }
   xi=matrix(1,npar,1,npar);    /* We add a separator at the end of dirc if not exists */
   for (i=1;i<=npar;i++)    l1 = strlen( dirc );                  /* length of directory */
     for (j=1;j<=npar;j++)    if( dirc[l1-1] != DIRSEPARATOR ){
       xi[i][j]=(i==j ? 1.0 : 0.0);      dirc[l1] =  DIRSEPARATOR;
   printf("Powell\n");      dirc[l1+1] = 0; 
   powell(p,xi,npar,ftol,&iter,&fret,func);      printf(" DIRC3 = %s \n",dirc);
     }
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    ss = strrchr( name, '.' );            /* find last / */
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    if (ss >0){
       ss++;
 }      strcpy(ext,ss);                     /* save extension */
       l1= strlen( name);
 /**** Computes Hessian and covariance matrix ***/      l2= strlen(ss)+1;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      strncpy( finame, name, l1-l2);
 {      finame[l1-l2]= 0;
   double  **a,**y,*x,pd;    }
   double **hess;  
   int i, j,jk;    return( 0 );                          /* we're done */
   int *indx;  }
   
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);  /******************************************/
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;  void replace_back_to_slash(char *s, char*t)
   {
   hess=matrix(1,npar,1,npar);    int i;
     int lg=0;
   printf("\nCalculation of the hessian matrix. Wait...\n");    i=0;
   for (i=1;i<=npar;i++){    lg=strlen(t);
     printf("%d",i);fflush(stdout);    for(i=0; i<= lg; i++) {
     hess[i][i]=hessii(p,ftolhess,i,delti);      (s[i] = t[i]);
     /*printf(" %f ",p[i]);*/      if (t[i]== '\\') s[i]='/';
     /*printf(" %lf ",hess[i][i]);*/    }
   }  }
    
   for (i=1;i<=npar;i++) {  char *trimbb(char *out, char *in)
     for (j=1;j<=npar;j++)  {  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
       if (j>i) {    char *s;
         printf(".%d%d",i,j);fflush(stdout);    s=out;
         hess[i][j]=hessij(p,delti,i,j);    while (*in != '\0'){
         hess[j][i]=hess[i][j];          while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
         /*printf(" %lf ",hess[i][j]);*/        in++;
       }      }
     }      *out++ = *in++;
   }    }
   printf("\n");    *out='\0';
     return s;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  }
    
   a=matrix(1,npar,1,npar);  /* char *substrchaine(char *out, char *in, char *chain) */
   y=matrix(1,npar,1,npar);  /* { */
   x=vector(1,npar);  /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
   indx=ivector(1,npar);  /*   char *s, *t; */
   for (i=1;i<=npar;i++)  /*   t=in;s=out; */
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  /*   while ((*in != *chain) && (*in != '\0')){ */
   ludcmp(a,npar,indx,&pd);  /*     *out++ = *in++; */
   /*   } */
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  /*   /\* *in matches *chain *\/ */
     x[j]=1;  /*   while ((*in++ == *chain++) && (*in != '\0')){ */
     lubksb(a,npar,indx,x);  /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
     for (i=1;i<=npar;i++){  /*   } */
       matcov[i][j]=x[i];  /*   in--; chain--; */
     }  /*   while ( (*in != '\0')){ */
   }  /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   /*     *out++ = *in++; */
   printf("\n#Hessian matrix#\n");  /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   for (i=1;i<=npar;i++) {  /*   } */
     for (j=1;j<=npar;j++) {  /*   *out='\0'; */
       printf("%.3e ",hess[i][j]);  /*   out=s; */
     }  /*   return out; */
     printf("\n");  /* } */
   }  char *substrchaine(char *out, char *in, char *chain)
   {
   /* Recompute Inverse */    /* Substract chain 'chain' from 'in', return and output 'out' */
   for (i=1;i<=npar;i++)    /* in="V1+V1*age+age*age+V2", chain="age*age" */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  
   ludcmp(a,npar,indx,&pd);    char *strloc;
   
   /*  printf("\n#Hessian matrix recomputed#\n");    strcpy (out, in); 
     strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
   for (j=1;j<=npar;j++) {    printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
     for (i=1;i<=npar;i++) x[i]=0;    if(strloc != NULL){ 
     x[j]=1;      /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
     lubksb(a,npar,indx,x);      memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
     for (i=1;i<=npar;i++){      /* strcpy (strloc, strloc +strlen(chain));*/
       y[i][j]=x[i];    }
       printf("%.3e ",y[i][j]);    printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
     }    return out;
     printf("\n");  }
   }  
   */  
   char *cutl(char *blocc, char *alocc, char *in, char occ)
   free_matrix(a,1,npar,1,npar);  {
   free_matrix(y,1,npar,1,npar);    /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' 
   free_vector(x,1,npar);       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   free_ivector(indx,1,npar);       gives blocc="abcdef" and alocc="ghi2j".
   free_matrix(hess,1,npar,1,npar);       If occ is not found blocc is null and alocc is equal to in. Returns blocc
     */
     char *s, *t;
 }    t=in;s=in;
     while ((*in != occ) && (*in != '\0')){
 /*************** hessian matrix ****************/      *alocc++ = *in++;
 double hessii( double x[], double delta, int theta, double delti[])    }
 {    if( *in == occ){
   int i;      *(alocc)='\0';
   int l=1, lmax=20;      s=++in;
   double k1,k2;    }
   double p2[NPARMAX+1];   
   double res;    if (s == t) {/* occ not found */
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      *(alocc-(in-s))='\0';
   double fx;      in=s;
   int k=0,kmax=10;    }
   double l1;    while ( *in != '\0'){
       *blocc++ = *in++;
   fx=func(x);    }
   for (i=1;i<=npar;i++) p2[i]=x[i];  
   for(l=0 ; l <=lmax; l++){    *blocc='\0';
     l1=pow(10,l);    return t;
     delts=delt;  }
     for(k=1 ; k <kmax; k=k+1){  char *cutv(char *blocc, char *alocc, char *in, char occ)
       delt = delta*(l1*k);  {
       p2[theta]=x[theta] +delt;    /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' 
       k1=func(p2)-fx;       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       p2[theta]=x[theta]-delt;       gives blocc="abcdef2ghi" and alocc="j".
       k2=func(p2)-fx;       If occ is not found blocc is null and alocc is equal to in. Returns alocc
       /*res= (k1-2.0*fx+k2)/delt/delt; */    */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    char *s, *t;
          t=in;s=in;
 #ifdef DEBUG    while (*in != '\0'){
       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 == occ){
 #endif        *blocc++ = *in++;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        s=in;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      }
         k=kmax;      *blocc++ = *in++;
       }    }
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    if (s == t) /* occ not found */
         k=kmax; l=lmax*10.;      *(blocc-(in-s))='\0';
       }    else
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      *(blocc-(in-s)-1)='\0';
         delts=delt;    in=s;
       }    while ( *in != '\0'){
     }      *alocc++ = *in++;
   }    }
   delti[theta]=delts;  
   return res;    *alocc='\0';
      return s;
 }  }
   
 double hessij( double x[], double delti[], int thetai,int thetaj)  int nbocc(char *s, char occ)
 {  {
   int i;    int i,j=0;
   int l=1, l1, lmax=20;    int lg=20;
   double k1,k2,k3,k4,res,fx;    i=0;
   double p2[NPARMAX+1];    lg=strlen(s);
   int k;    for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
   fx=func(x);    }
   for (k=1; k<=2; k++) {    return j;
     for (i=1;i<=npar;i++) p2[i]=x[i];  }
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  /* void cutv(char *u,char *v, char*t, char occ) */
     k1=func(p2)-fx;  /* { */
    /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
     p2[thetai]=x[thetai]+delti[thetai]/k;  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  /*      gives u="abcdef2ghi" and v="j" *\/ */
     k2=func(p2)-fx;  /*   int i,lg,j,p=0; */
    /*   i=0; */
     p2[thetai]=x[thetai]-delti[thetai]/k;  /*   lg=strlen(t); */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  /*   for(j=0; j<=lg-1; j++) { */
     k3=func(p2)-fx;  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
    /*   } */
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  /*   for(j=0; j<p; j++) { */
     k4=func(p2)-fx;  /*     (u[j] = t[j]); */
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  /*   } */
 #ifdef DEBUG  /*      u[p]='\0'; */
     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  /*    for(j=0; j<= lg; j++) { */
   }  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   return res;  /*   } */
 }  /* } */
   
 /************** Inverse of matrix **************/  #ifdef _WIN32
 void ludcmp(double **a, int n, int *indx, double *d)  char * strsep(char **pp, const char *delim)
 {  {
   int i,imax,j,k;    char *p, *q;
   double big,dum,sum,temp;           
   double *vv;    if ((p = *pp) == NULL)
        return 0;
   vv=vector(1,n);    if ((q = strpbrk (p, delim)) != NULL)
   *d=1.0;    {
   for (i=1;i<=n;i++) {      *pp = q + 1;
     big=0.0;      *q = '\0';
     for (j=1;j<=n;j++)    }
       if ((temp=fabs(a[i][j])) > big) big=temp;    else
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      *pp = 0;
     vv[i]=1.0/big;    return p;
   }  }
   for (j=1;j<=n;j++) {  #endif
     for (i=1;i<j;i++) {  
       sum=a[i][j];  /********************** nrerror ********************/
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;  void nrerror(char error_text[])
     }  {
     big=0.0;    fprintf(stderr,"ERREUR ...\n");
     for (i=j;i<=n;i++) {    fprintf(stderr,"%s\n",error_text);
       sum=a[i][j];    exit(EXIT_FAILURE);
       for (k=1;k<j;k++)  }
         sum -= a[i][k]*a[k][j];  /*********************** vector *******************/
       a[i][j]=sum;  double *vector(int nl, int nh)
       if ( (dum=vv[i]*fabs(sum)) >= big) {  {
         big=dum;    double *v;
         imax=i;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       }    if (!v) nrerror("allocation failure in vector");
     }    return v-nl+NR_END;
     if (j != imax) {  }
       for (k=1;k<=n;k++) {  
         dum=a[imax][k];  /************************ free vector ******************/
         a[imax][k]=a[j][k];  void free_vector(double*v, int nl, int nh)
         a[j][k]=dum;  {
       }    free((FREE_ARG)(v+nl-NR_END));
       *d = -(*d);  }
       vv[imax]=vv[j];  
     }  /************************ivector *******************************/
     indx[j]=imax;  int *ivector(long nl,long nh)
     if (a[j][j] == 0.0) a[j][j]=TINY;  {
     if (j != n) {    int *v;
       dum=1.0/(a[j][j]);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    if (!v) nrerror("allocation failure in ivector");
     }    return v-nl+NR_END;
   }  }
   free_vector(vv,1,n);  /* Doesn't work */  
 ;  /******************free ivector **************************/
 }  void free_ivector(int *v, long nl, long nh)
   {
 void lubksb(double **a, int n, int *indx, double b[])    free((FREE_ARG)(v+nl-NR_END));
 {  }
   int i,ii=0,ip,j;  
   double sum;  /************************lvector *******************************/
    long *lvector(long nl,long nh)
   for (i=1;i<=n;i++) {  {
     ip=indx[i];    long *v;
     sum=b[ip];    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     b[ip]=b[i];    if (!v) nrerror("allocation failure in ivector");
     if (ii)    return v-nl+NR_END;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  }
     else if (sum) ii=i;  
     b[i]=sum;  /******************free lvector **************************/
   }  void free_lvector(long *v, long nl, long nh)
   for (i=n;i>=1;i--) {  {
     sum=b[i];    free((FREE_ARG)(v+nl-NR_END));
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  }
     b[i]=sum/a[i][i];  
   }  /******************* imatrix *******************************/
 }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
        /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 /************ Frequencies ********************/  { 
 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)    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 {  /* Some frequencies */    int **m; 
      
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    /* allocate pointers to rows */ 
   double ***freq; /* Frequencies */    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   double *pp;    if (!m) nrerror("allocation failure 1 in matrix()"); 
   double pos, k2, dateintsum=0,k2cpt=0;    m += NR_END; 
   FILE *ficresp;    m -= nrl; 
   char fileresp[FILENAMELENGTH];    
      
   pp=vector(1,nlstate);    /* allocate rows and set pointers to them */ 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   strcpy(fileresp,"p");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   strcat(fileresp,fileres);    m[nrl] += NR_END; 
   if((ficresp=fopen(fileresp,"w"))==NULL) {    m[nrl] -= ncl; 
     printf("Problem with prevalence resultfile: %s\n", fileresp);    
     exit(0);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   }    
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    /* return pointer to array of pointers to rows */ 
   j1=0;    return m; 
    } 
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  /****************** free_imatrix *************************/
    void free_imatrix(m,nrl,nrh,ncl,nch)
   for(k1=1; k1<=j;k1++){        int **m;
     for(i1=1; i1<=ncodemax[k1];i1++){        long nch,ncl,nrh,nrl; 
       j1++;       /* free an int matrix allocated by imatrix() */ 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  { 
         scanf("%d", i);*/    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       for (i=-1; i<=nlstate+ndeath; i++)      free((FREE_ARG) (m+nrl-NR_END)); 
         for (jk=-1; jk<=nlstate+ndeath; jk++)    } 
           for(m=agemin; m <= agemax+3; m++)  
             freq[i][jk][m]=0;  /******************* matrix *******************************/
        double **matrix(long nrl, long nrh, long ncl, long nch)
       dateintsum=0;  {
       k2cpt=0;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       for (i=1; i<=imx; i++) {    double **m;
         bool=1;  
         if  (cptcovn>0) {    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
           for (z1=1; z1<=cptcoveff; z1++)    if (!m) nrerror("allocation failure 1 in matrix()");
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    m += NR_END;
               bool=0;    m -= nrl;
         }  
         if (bool==1) {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
           for(m=firstpass; m<=lastpass; m++){    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
             k2=anint[m][i]+(mint[m][i]/12.);    m[nrl] += NR_END;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    m[nrl] -= ncl;
               if(agev[m][i]==0) agev[m][i]=agemax+1;  
               if(agev[m][i]==1) agev[m][i]=agemax+2;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
               if (m<lastpass) {    return m;
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
               }  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
                   */
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  }
                 dateintsum=dateintsum+k2;  
                 k2cpt++;  /*************************free matrix ************************/
               }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
             }  {
           }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         }    free((FREE_ARG)(m+nrl-NR_END));
       }  }
          
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  /******************* ma3x *******************************/
   double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       if  (cptcovn>0) {  {
         fprintf(ficresp, "\n#********** Variable ");    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double ***m;
         fprintf(ficresp, "**********\n#");  
       }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       for(i=1; i<=nlstate;i++)    if (!m) nrerror("allocation failure 1 in matrix()");
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    m += NR_END;
       fprintf(ficresp, "\n");    m -= nrl;
        
       for(i=(int)agemin; i <= (int)agemax+3; i++){    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         if(i==(int)agemax+3)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
           printf("Total");    m[nrl] += NR_END;
         else    m[nrl] -= ncl;
           printf("Age %d", i);  
         for(jk=1; jk <=nlstate ; jk++){    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  
             pp[jk] += freq[jk][m][i];    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         }    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
         for(jk=1; jk <=nlstate ; jk++){    m[nrl][ncl] += NR_END;
           for(m=-1, pos=0; m <=0 ; m++)    m[nrl][ncl] -= nll;
             pos += freq[jk][m][i];    for (j=ncl+1; j<=nch; j++) 
           if(pp[jk]>=1.e-10)      m[nrl][j]=m[nrl][j-1]+nlay;
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    
           else    for (i=nrl+1; i<=nrh; i++) {
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         }      for (j=ncl+1; j<=nch; j++) 
         m[i][j]=m[i][j-1]+nlay;
         for(jk=1; jk <=nlstate ; jk++){    }
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    return m; 
             pp[jk] += freq[jk][m][i];    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
         }             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     */
         for(jk=1,pos=0; jk <=nlstate ; jk++)  }
           pos += pp[jk];  
         for(jk=1; jk <=nlstate ; jk++){  /*************************free ma3x ************************/
           if(pos>=1.e-5)  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  {
           else    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
           if( i <= (int) agemax){    free((FREE_ARG)(m+nrl-NR_END));
             if(pos>=1.e-5){  }
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  
               probs[i][jk][j1]= pp[jk]/pos;  /*************** function subdirf ***********/
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  char *subdirf(char fileres[])
             }  {
             else    /* Caution optionfilefiname is hidden */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    strcpy(tmpout,optionfilefiname);
           }    strcat(tmpout,"/"); /* Add to the right */
         }    strcat(tmpout,fileres);
            return tmpout;
         for(jk=-1; jk <=nlstate+ndeath; jk++)  }
           for(m=-1; m <=nlstate+ndeath; m++)  
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  /*************** function subdirf2 ***********/
         if(i <= (int) agemax)  char *subdirf2(char fileres[], char *preop)
           fprintf(ficresp,"\n");  {
         printf("\n");    
       }    /* Caution optionfilefiname is hidden */
     }    strcpy(tmpout,optionfilefiname);
   }    strcat(tmpout,"/");
   dateintmean=dateintsum/k2cpt;    strcat(tmpout,preop);
      strcat(tmpout,fileres);
   fclose(ficresp);    return tmpout;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  }
   free_vector(pp,1,nlstate);  
    /*************** function subdirf3 ***********/
   /* End of Freq */  char *subdirf3(char fileres[], char *preop, char *preop2)
 }  {
     
 /************ Prevalence ********************/    /* Caution optionfilefiname is hidden */
 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)    strcpy(tmpout,optionfilefiname);
 {  /* Some frequencies */    strcat(tmpout,"/");
      strcat(tmpout,preop);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    strcat(tmpout,preop2);
   double ***freq; /* Frequencies */    strcat(tmpout,fileres);
   double *pp;    return tmpout;
   double pos, k2;  }
   
   pp=vector(1,nlstate);  char *asc_diff_time(long time_sec, char ascdiff[])
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  {
      long sec_left, days, hours, minutes;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    days = (time_sec) / (60*60*24);
   j1=0;    sec_left = (time_sec) % (60*60*24);
      hours = (sec_left) / (60*60) ;
   j=cptcoveff;    sec_left = (sec_left) %(60*60);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    minutes = (sec_left) /60;
      sec_left = (sec_left) % (60);
  for(k1=1; k1<=j;k1++){    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
     for(i1=1; i1<=ncodemax[k1];i1++){    return ascdiff;
       j1++;  }
    
       for (i=-1; i<=nlstate+ndeath; i++)    /***************** f1dim *************************/
         for (jk=-1; jk<=nlstate+ndeath; jk++)    extern int ncom; 
           for(m=agemin; m <= agemax+3; m++)  extern double *pcom,*xicom;
             freq[i][jk][m]=0;  extern double (*nrfunc)(double []); 
         
       for (i=1; i<=imx; i++) {  double f1dim(double x) 
         bool=1;  { 
         if  (cptcovn>0) {    int j; 
           for (z1=1; z1<=cptcoveff; z1++)    double f;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    double *xt; 
               bool=0;   
         }    xt=vector(1,ncom); 
         if (bool==1) {    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
           for(m=firstpass; m<=lastpass; m++){    f=(*nrfunc)(xt); 
             k2=anint[m][i]+(mint[m][i]/12.);    free_vector(xt,1,ncom); 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    return f; 
               if(agev[m][i]==0) agev[m][i]=agemax+1;  } 
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];  /*****************brent *************************/
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
             }  {
           }    /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
         }     * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
       }     * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
         for(i=(int)agemin; i <= (int)agemax+3; i++){     * the minimum is returned as xmin, and the minimum function value is returned as brent , the
           for(jk=1; jk <=nlstate ; jk++){     * returned function value. 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    */
               pp[jk] += freq[jk][m][i];    int iter; 
           }    double a,b,d,etemp;
           for(jk=1; jk <=nlstate ; jk++){    double fu=0,fv,fw,fx;
             for(m=-1, pos=0; m <=0 ; m++)    double ftemp=0.;
             pos += freq[jk][m][i];    double p,q,r,tol1,tol2,u,v,w,x,xm; 
         }    double e=0.0; 
           
          for(jk=1; jk <=nlstate ; jk++){    a=(ax < cx ? ax : cx); 
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    b=(ax > cx ? ax : cx); 
              pp[jk] += freq[jk][m][i];    x=w=v=bx; 
          }    fw=fv=fx=(*f)(x); 
              for (iter=1;iter<=ITMAX;iter++) { 
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      xm=0.5*(a+b); 
       tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
          for(jk=1; jk <=nlstate ; jk++){                /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
            if( i <= (int) agemax){      printf(".");fflush(stdout);
              if(pos>=1.e-5){      fprintf(ficlog,".");fflush(ficlog);
                probs[i][jk][j1]= pp[jk]/pos;  #ifdef DEBUGBRENT
              }      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);
            }      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);
          }      /*          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))){ 
     }        *xmin=x; 
   }        return fx; 
        } 
        ftemp=fu;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      if (fabs(e) > tol1) { 
   free_vector(pp,1,nlstate);        r=(x-w)*(fx-fv); 
          q=(x-v)*(fx-fw); 
 }  /* End of Freq */        p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
 /************* Waves Concatenation ***************/        if (q > 0.0) p = -p; 
         q=fabs(q); 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        etemp=e; 
 {        e=d; 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
      Death is a valid wave (if date is known).          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        else { 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          d=p/q; 
      and mw[mi+1][i]. dh depends on stepm.          u=x+d; 
      */          if (u-a < tol2 || b-u < tol2) 
             d=SIGN(tol1,xm-x); 
   int i, mi, m;        } 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      } else { 
      double sum=0., jmean=0.;*/        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
   int j, k=0,jk, ju, jl;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   double sum=0.;      fu=(*f)(u); 
   jmin=1e+5;      if (fu <= fx) { 
   jmax=-1;        if (u >= x) a=x; else b=x; 
   jmean=0.;        SHFT(v,w,x,u) 
   for(i=1; i<=imx; i++){        SHFT(fv,fw,fx,fu) 
     mi=0;      } else { 
     m=firstpass;        if (u < x) a=u; else b=u; 
     while(s[m][i] <= nlstate){        if (fu <= fw || w == x) { 
       if(s[m][i]>=1)          v=w; 
         mw[++mi][i]=m;          w=u; 
       if(m >=lastpass)          fv=fw; 
         break;          fw=fu; 
       else        } else if (fu <= fv || v == x || v == w) { 
         m++;          v=u; 
     }/* end while */          fv=fu; 
     if (s[m][i] > nlstate){        } 
       mi++;     /* Death is another wave */      } 
       /* if(mi==0)  never been interviewed correctly before death */    } 
          /* Only death is a correct wave */    nrerror("Too many iterations in brent"); 
       mw[mi][i]=m;    *xmin=x; 
     }    return fx; 
   } 
     wav[i]=mi;  
     if(mi==0)  /****************** mnbrak ***********************/
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  
   }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               double (*func)(double)) 
   for(i=1; i<=imx; i++){  { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
     for(mi=1; mi<wav[i];mi++){  the downhill direction (defined by the function as evaluated at the initial points) and returns
       if (stepm <=0)  new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
         dh[mi][i]=1;  values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
       else{     */
         if (s[mw[mi+1][i]][i] > nlstate) {    double ulim,u,r,q, dum;
           if (agedc[i] < 2*AGESUP) {    double fu; 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  
           if(j==0) j=1;  /* Survives at least one month after exam */    double scale=10.;
           k=k+1;    int iterscale=0;
           if (j >= jmax) jmax=j;  
           if (j <= jmin) jmin=j;    *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
           sum=sum+j;    *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
           /*if (j<0) printf("j=%d num=%d \n",j,i); */  
           }  
         }    /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
         else{    /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    /*   *bx = *ax - (*ax - *bx)/scale; */
           k=k+1;    /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
           if (j >= jmax) jmax=j;    /* } */
           else if (j <= jmin)jmin=j;  
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    if (*fb > *fa) { 
           sum=sum+j;      SHFT(dum,*ax,*bx,dum) 
         }      SHFT(dum,*fb,*fa,dum) 
         jk= j/stepm;    } 
         jl= j -jk*stepm;    *cx=(*bx)+GOLD*(*bx-*ax); 
         ju= j -(jk+1)*stepm;    *fc=(*func)(*cx); 
         if(jl <= -ju)  #ifdef DEBUG
           dh[mi][i]=jk;    printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
         else    fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
           dh[mi][i]=jk+1;  #endif
         if(dh[mi][i]==0)    while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
           dh[mi][i]=1; /* At least one step */      r=(*bx-*ax)*(*fb-*fc); 
       }      q=(*bx-*cx)*(*fb-*fa); 
     }      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). */
   jmean=sum/k;      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
  }        fu=(*func)(u); 
 /*********** Tricode ****************************/  #ifdef DEBUG
 void tricode(int *Tvar, int **nbcode, int imx)        /* f(x)=A(x-u)**2+f(u) */
 {        double A, fparabu; 
   int Ndum[20],ij=1, k, j, i;        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
   int cptcode=0;        fparabu= *fa - A*(*ax-u)*(*ax-u);
   cptcoveff=0;        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);
          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);
   for (k=0; k<19; k++) Ndum[k]=0;        /* And thus,it can be that fu > *fc even if fparabu < *fc */
   for (k=1; k<=7; k++) ncodemax[k]=0;        /* 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) */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
     for (i=1; i<=imx; i++) {  #endif 
       ij=(int)(covar[Tvar[j]][i]);  #ifdef MNBRAKORIGINAL
       Ndum[ij]++;  #else
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  /*       if (fu > *fc) { */
       if (ij > cptcode) cptcode=ij;  /* #ifdef DEBUG */
     }  /*       printf("mnbrak4  fu > fc \n"); */
   /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
     for (i=0; i<=cptcode; i++) {  /* #endif */
       if(Ndum[i]!=0) ncodemax[j]++;  /*      /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/  *\/ */
     }  /*      /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\\/ *\/ */
     ij=1;  /*      dum=u; /\* Shifting c and u *\/ */
   /*      u = *cx; */
   /*      *cx = dum; */
     for (i=1; i<=ncodemax[j]; i++) {  /*      dum = fu; */
       for (k=0; k<=19; k++) {  /*      fu = *fc; */
         if (Ndum[k] != 0) {  /*      *fc =dum; */
           nbcode[Tvar[j]][ij]=k;  /*       } else { /\* end *\/ */
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/  /* #ifdef DEBUG */
           ij++;  /*       printf("mnbrak3  fu < fc \n"); */
         }  /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
         if (ij > ncodemax[j]) break;  /* #endif */
       }    /*      dum=u; /\* Shifting c and u *\/ */
     }  /*      u = *cx; */
   }    /*      *cx = dum; */
   /*      dum = fu; */
  for (k=0; k<19; k++) Ndum[k]=0;  /*      fu = *fc; */
   /*      *fc =dum; */
  for (i=1; i<=ncovmodel-2; i++) {  /*       } */
       ij=Tvar[i];  #ifdef DEBUG
       Ndum[ij]++;        printf("mnbrak34  fu < or >= fc \n");
     }        fprintf(ficlog, "mnbrak34 fu < fc\n");
   #endif
  ij=1;        dum=u; /* Shifting c and u */
  for (i=1; i<=10; i++) {        u = *cx;
    if((Ndum[i]!=0) && (i<=ncovcol)){        *cx = dum;
      Tvaraff[ij]=i;        dum = fu;
      ij++;        fu = *fc;
    }        *fc =dum;
  }  #endif
        } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
     cptcoveff=ij-1;  #ifdef DEBUG
 }        printf("mnbrak2  u after c but before ulim\n");
         fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
 /*********** Health Expectancies ****************/  #endif
         fu=(*func)(u); 
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)        if (fu < *fc) { 
 {  #ifdef DEBUG
   /* Health expectancies */        printf("mnbrak2  u after c but before ulim AND fu < fc\n");
   int i, j, nhstepm, hstepm, h, nstepm;        fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
   double age, agelim, hf;  #endif
   double ***p3mat;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
            SHFT(*fb,*fc,fu,(*func)(u)) 
   fprintf(ficreseij,"# Health expectancies\n");        } 
   fprintf(ficreseij,"# Age");      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
   for(i=1; i<=nlstate;i++)  #ifdef DEBUG
     for(j=1; j<=nlstate;j++)        printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
       fprintf(ficreseij," %1d-%1d",i,j);        fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
   fprintf(ficreseij,"\n");  #endif
         u=ulim; 
   if(estepm < stepm){        fu=(*func)(u); 
     printf ("Problem %d lower than %d\n",estepm, stepm);      } else { /* u could be left to b (if r > q parabola has a maximum) */
   }  #ifdef DEBUG
   else  hstepm=estepm;          printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
   /* We compute the life expectancy from trapezoids spaced every estepm months        fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
    * This is mainly to measure the difference between two models: for example  #endif
    * if stepm=24 months pijx are given only every 2 years and by summing them        u=(*cx)+GOLD*(*cx-*bx); 
    * we are calculating an estimate of the Life Expectancy assuming a linear        fu=(*func)(u); 
    * progression inbetween and thus overestimating or underestimating according      } /* end tests */
    * to the curvature of the survival function. If, for the same date, we      SHFT(*ax,*bx,*cx,u) 
    * estimate the model with stepm=1 month, we can keep estepm to 24 months      SHFT(*fa,*fb,*fc,fu) 
    * to compare the new estimate of Life expectancy with the same linear  #ifdef DEBUG
    * hypothesis. A more precise result, taking into account a more precise        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);
    * curvature will be obtained if estepm is as small as stepm. */        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);
   #endif
   /* For example we decided to compute the life expectancy with the smallest unit */    } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
   /* 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.  /*************** linmin ************************/
      Look at hpijx to understand the reason of that which relies in memory size  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
      and note for a fixed period like estepm months */  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
      survival function given by stepm (the optimization length). Unfortunately it  the value of func at the returned location p . This is actually all accomplished by calling the
      means that if the survival funtion is printed only each two years of age and if  routines mnbrak and brent .*/
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  int ncom; 
      results. So we changed our mind and took the option of the best precision.  double *pcom,*xicom;
   */  double (*nrfunc)(double []); 
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */   
   void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   agelim=AGESUP;  { 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double brent(double ax, double bx, double cx, 
     /* nhstepm age range expressed in number of stepm */                 double (*f)(double), double tol, double *xmin); 
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    double f1dim(double x); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     /* if (stepm >= YEARM) hstepm=1;*/                double *fc, double (*func)(double)); 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    int j; 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double xx,xmin,bx,ax; 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    double fx,fb,fa;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      double scale=10., axs, xxs, xxss; /* Scale added for infinity */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */   
     for(i=1; i<=nlstate;i++)    ncom=n; 
       for(j=1; j<=nlstate;j++)    pcom=vector(1,n); 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    xicom=vector(1,n); 
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    nrfunc=func; 
           /* 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]);*/    for (j=1;j<=n;j++) { 
         }      pcom[j]=p[j]; 
     fprintf(ficreseij,"%3.0f",age );      xicom[j]=xi[j]; 
     for(i=1; i<=nlstate;i++)    } 
       for(j=1; j<=nlstate;j++){  
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);    /* axs=0.0; */
       }    /* xxss=1; /\* 1 and using scale *\/ */
     fprintf(ficreseij,"\n");    xxs=1;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* do{ */
   }      ax=0.;
 }      xx= xxs;
       mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
 /************ Variance ******************/      /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)      /* xt[x,j]=pcom[j]+x*xicom[j]  f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and  f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j))   */
 {      /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
   /* Variance of health expectancies */      /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
   double **newm;      /* 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]]*/
   double **dnewm,**doldm;    /*   if (fx != fx){ */
   int i, j, nhstepm, hstepm, h, nstepm ;    /*    xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */
   int k, cptcode;    /*    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); */
   double *xp;    /*   } */
   double **gp, **gm;    /* }while(fx != fx); */
   double ***gradg, ***trgradg;  
   double ***p3mat;  #ifdef DEBUGLINMIN
   double age,agelim, hf;    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);
   int theta;  #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),*/
    fprintf(ficresvij,"# Covariances of life expectancies\n");    /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
   fprintf(ficresvij,"# Age");    /* fmin = f(p[j] + xmin * xi[j]) */
   for(i=1; i<=nlstate;i++)    /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
     for(j=1; j<=nlstate;j++)    /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  #ifdef DEBUG
   fprintf(ficresvij,"\n");    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   xp=vector(1,npar);  #endif
   dnewm=matrix(1,nlstate,1,npar);  #ifdef DEBUGLINMIN
   doldm=matrix(1,nlstate,1,nlstate);    printf("linmin end ");
    #endif
   if(estepm < stepm){    for (j=1;j<=n;j++) { 
     printf ("Problem %d lower than %d\n",estepm, stepm);      /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
   }      xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
   else  hstepm=estepm;        /* if(xxs <1.0) */
   /* For example we decided to compute the life expectancy with the smallest unit */      /*   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 ); */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      p[j] += xi[j]; /* Parameters values are updated accordingly */
      nhstepm is the number of hstepm from age to agelim    } 
      nstepm is the number of stepm from age to agelin.    /* printf("\n"); */
      Look at hpijx to understand the reason of that which relies in memory size  #ifdef DEBUGLINMIN
      and note for a fixed period like k years */    printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    for (j=1;j<=n;j++) { 
      survival function given by stepm (the optimization length). Unfortunately it      printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);
      means that if the survival funtion is printed only each two years of age and if      if(j % ncovmodel == 0)
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        printf("\n");
      results. So we changed our mind and took the option of the best precision.    }
   */  #endif
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    free_vector(xicom,1,n); 
   agelim = AGESUP;    free_vector(pcom,1,n); 
   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);  /*************** powell ************************/
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  /*
     gp=matrix(0,nhstepm,1,nlstate);  Minimization of a function func of n variables. Input consists of an initial starting point
     gm=matrix(0,nhstepm,1,nlstate);  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
   rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
     for(theta=1; theta <=npar; theta++){  such that failure to decrease by more than this amount on one iteration signals doneness. On
       for(i=1; i<=npar; i++){ /* Computes gradient */  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  function value at p , and iter is the number of iterations taken. The routine linmin is used.
       }   */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              double (*func)(double [])) 
   { 
       if (popbased==1) {    void linmin(double p[], double xi[], int n, double *fret, 
         for(i=1; i<=nlstate;i++)                double (*func)(double [])); 
           prlim[i][i]=probs[(int)age][i][ij];    int i,ibig,j; 
       }    double del,t,*pt,*ptt,*xit;
      double directest;
       for(j=1; j<= nlstate; j++){    double fp,fptt;
         for(h=0; h<=nhstepm; h++){    double *xits;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    int niterf, itmp;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }    pt=vector(1,n); 
       }    ptt=vector(1,n); 
        xit=vector(1,n); 
       for(i=1; i<=npar; i++) /* Computes gradient */    xits=vector(1,n); 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    *fret=(*func)(p); 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      for (j=1;j<=n;j++) pt[j]=p[j]; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      rcurr_time = time(NULL);  
      for (*iter=1;;++(*iter)) { 
       if (popbased==1) {      fp=(*fret); /* From former iteration or initial value */
         for(i=1; i<=nlstate;i++)      ibig=0; 
           prlim[i][i]=probs[(int)age][i][ij];      del=0.0; 
       }      rlast_time=rcurr_time;
       /* (void) gettimeofday(&curr_time,&tzp); */
       for(j=1; j<= nlstate; j++){      rcurr_time = time(NULL);  
         for(h=0; h<=nhstepm; h++){      curr_time = *localtime(&rcurr_time);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      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); */
       }      for (i=1;i<=n;i++) {
         printf(" %d %.12f",i, p[i]);
       for(j=1; j<= nlstate; j++)        fprintf(ficlog," %d %.12lf",i, p[i]);
         for(h=0; h<=nhstepm; h++){        fprintf(ficrespow," %.12lf", p[i]);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      }
         }      printf("\n");
     } /* End theta */      fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");fflush(ficrespow);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      if(*iter <=3){
         tml = *localtime(&rcurr_time);
     for(h=0; h<=nhstepm; h++)        strcpy(strcurr,asctime(&tml));
       for(j=1; j<=nlstate;j++)        rforecast_time=rcurr_time; 
         for(theta=1; theta <=npar; theta++)        itmp = strlen(strcurr);
           trgradg[h][j][theta]=gradg[h][theta][j];        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           strcurr[itmp-1]='\0';
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
     for(i=1;i<=nlstate;i++)        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       for(j=1;j<=nlstate;j++)        for(niterf=10;niterf<=30;niterf+=10){
         vareij[i][j][(int)age] =0.;          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
           forecast_time = *localtime(&rforecast_time);
     for(h=0;h<=nhstepm;h++){          strcpy(strfor,asctime(&forecast_time));
       for(k=0;k<=nhstepm;k++){          itmp = strlen(strfor);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          if(strfor[itmp-1]=='\n')
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          strfor[itmp-1]='\0';
         for(i=1;i<=nlstate;i++)          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);
           for(j=1;j<=nlstate;j++)          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);
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;        }
       }      }
     }      for (i=1;i<=n;i++) { /* For each direction i */
         for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
     fprintf(ficresvij,"%.0f ",age );        fptt=(*fret); 
     for(i=1; i<=nlstate;i++)  #ifdef DEBUG
       for(j=1; j<=nlstate;j++){            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
       }  #endif
     fprintf(ficresvij,"\n");            printf("%d",i);fflush(stdout); /* print direction (parameter) i */
     free_matrix(gp,0,nhstepm,1,nlstate);        fprintf(ficlog,"%d",i);fflush(ficlog);
     free_matrix(gm,0,nhstepm,1,nlstate);        linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);                                      /* Outputs are fret(new point p) p is updated and xit rescaled */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          /* because that direction will be replaced unless the gain del is small */
   } /* End age */          /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
            /* Unless the n directions are conjugate some gain in the determinant may be obtained */
   free_vector(xp,1,npar);          /* with the new direction. */
   free_matrix(doldm,1,nlstate,1,npar);          del=fabs(fptt-(*fret)); 
   free_matrix(dnewm,1,nlstate,1,nlstate);          ibig=i; 
         } 
 }  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
 /************ Variance of prevlim ******************/        fprintf(ficlog,"%d %.12e",i,(*fret));
 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)        for (j=1;j<=n;j++) {
 {          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   /* Variance of prevalence limit */          printf(" x(%d)=%.12e",j,xit[j]);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   double **newm;        }
   double **dnewm,**doldm;        for(j=1;j<=n;j++) {
   int i, j, nhstepm, hstepm;          printf(" p(%d)=%.12e",j,p[j]);
   int k, cptcode;          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
   double *xp;        }
   double *gp, *gm;        printf("\n");
   double **gradg, **trgradg;        fprintf(ficlog,"\n");
   double age,agelim;  #endif
   int theta;      } /* end loop on each direction i */
          /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
   fprintf(ficresvpl,"# Age");      /* New value of last point Pn is not computed, P(n-1) */
   for(i=1; i<=nlstate;i++)      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
       fprintf(ficresvpl," %1d-%1d",i,i);        /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
   fprintf(ficresvpl,"\n");        /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
         /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
   xp=vector(1,npar);        /* decreased of more than 3.84  */
   dnewm=matrix(1,nlstate,1,npar);        /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
   doldm=matrix(1,nlstate,1,nlstate);        /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
          /* By adding 10 parameters more the gain should be 18.31 */
   hstepm=1*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        /* Starting the program with initial values given by a former maximization will simply change */
   agelim = AGESUP;        /* the scales of the directions and the directions, because the are reset to canonical directions */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
     if (stepm >= YEARM) hstepm=1;  #ifdef DEBUG
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        int k[2],l;
     gradg=matrix(1,npar,1,nlstate);        k[0]=1;
     gp=vector(1,nlstate);        k[1]=-1;
     gm=vector(1,nlstate);        printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
     for(theta=1; theta <=npar; theta++){        for (j=1;j<=n;j++) {
       for(i=1; i<=npar; i++){ /* Computes gradient */          printf(" %.12e",p[j]);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          fprintf(ficlog," %.12e",p[j]);
       }        }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        printf("\n");
       for(i=1;i<=nlstate;i++)        fprintf(ficlog,"\n");
         gp[i] = prlim[i][i];        for(l=0;l<=1;l++) {
              for (j=1;j<=n;j++) {
       for(i=1; i<=npar; i++) /* Computes gradient */            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       for(i=1;i<=nlstate;i++)          }
         gm[i] = prlim[i][i];          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       for(i=1;i<=nlstate;i++)        }
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  #endif
     } /* End theta */  
   
     trgradg =matrix(1,nlstate,1,npar);        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
     for(j=1; j<=nlstate;j++)        free_vector(ptt,1,n); 
       for(theta=1; theta <=npar; theta++)        free_vector(pt,1,n); 
         trgradg[j][theta]=gradg[theta][j];        return; 
       } /* enough precision */ 
     for(i=1;i<=nlstate;i++)      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       varpl[i][(int)age] =0.;      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        ptt[j]=2.0*p[j]-pt[j]; 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        xit[j]=p[j]-pt[j]; 
     for(i=1;i<=nlstate;i++)        pt[j]=p[j]; 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      } 
       fptt=(*func)(ptt); /* f_3 */
     fprintf(ficresvpl,"%.0f ",age );  #ifdef POWELLF1F3
     for(i=1; i<=nlstate;i++)  #else
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
     fprintf(ficresvpl,"\n");  #endif
     free_vector(gp,1,nlstate);        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
     free_vector(gm,1,nlstate);        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
     free_matrix(gradg,1,npar,1,nlstate);        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
     free_matrix(trgradg,1,nlstate,1,npar);        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
   } /* End age */        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
         /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
   free_vector(xp,1,npar);        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
   free_matrix(doldm,1,nlstate,1,npar);  #ifdef NRCORIGINAL
   free_matrix(dnewm,1,nlstate,1,nlstate);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
   #else
 }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
         t= t- del*SQR(fp-fptt);
 /************ Variance of one-step probabilities  ******************/  #endif
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
 {  #ifdef DEBUG
   int i, j;        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);
   int k=0, cptcode;        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);
   double **dnewm,**doldm;        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
   double *xp;               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   double *gp, *gm;        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
   double **gradg, **trgradg;               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   double age,agelim, cov[NCOVMAX];        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);
   int theta;        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);
   char fileresprob[FILENAMELENGTH];  #endif
   #ifdef POWELLORIGINAL
   strcpy(fileresprob,"prob");        if (t < 0.0) { /* Then we use it for new direction */
   strcat(fileresprob,fileres);  #else
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        if (directest*t < 0.0) { /* Contradiction between both tests */
     printf("Problem with resultfile: %s\n", fileresprob);          printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
   }          printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);          fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
            fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
         } 
   xp=vector(1,npar);        if (directest < 0.0) { /* Then we use it for new direction */
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  #endif
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));  #ifdef DEBUGLINMIN
            printf("Before linmin in direction P%d-P0\n",n);
   cov[1]=1;          for (j=1;j<=n;j++) { 
   for (age=bage; age<=fage; age ++){            printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
     cov[2]=age;            if(j % ncovmodel == 0)
     gradg=matrix(1,npar,1,9);              printf("\n");
     trgradg=matrix(1,9,1,npar);          }
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  #endif
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
      #ifdef DEBUGLINMIN
     for(theta=1; theta <=npar; theta++){          for (j=1;j<=n;j++) { 
       for(i=1; i<=npar; i++)            printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            if(j % ncovmodel == 0)
                    printf("\n");
       pmij(pmmij,cov,ncovmodel,xp,nlstate);          }
      #endif
       k=0;          for (j=1;j<=n;j++) { 
       for(i=1; i<= (nlstate+ndeath); i++){            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
         for(j=1; j<=(nlstate+ndeath);j++){            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
            k=k+1;          }
           gp[k]=pmmij[i][j];          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);
       }  
   #ifdef DEBUG
       for(i=1; i<=npar; i++)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
              for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);            fprintf(ficlog," %.12e",xit[j]);
       k=0;          }
       for(i=1; i<=(nlstate+ndeath); i++){          printf("\n");
         for(j=1; j<=(nlstate+ndeath);j++){          fprintf(ficlog,"\n");
           k=k+1;  #endif
           gm[k]=pmmij[i][j];        } /* end of t or directest negative */
         }  #ifdef POWELLF1F3
       }  #else
            } /* end if (fptt < fp)  */
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  #endif
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      } /* loop iteration */ 
     }  } 
   
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  /**** Prevalence limit (stable or period prevalence)  ****************/
       for(theta=1; theta <=npar; theta++)  
       trgradg[j][theta]=gradg[theta][j];  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
    {
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);       matrix by transitions matrix until convergence is reached */
     
      pmij(pmmij,cov,ncovmodel,x,nlstate);    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
      k=0;    /* double **matprod2(); */ /* test */
      for(i=1; i<=(nlstate+ndeath); i++){    double **out, cov[NCOVMAX+1], **pmij();
        for(j=1; j<=(nlstate+ndeath);j++){    double **newm;
          k=k+1;    double agefin, delaymax=50 ; /* Max number of years to converge */
          gm[k]=pmmij[i][j];    
         }    for (ii=1;ii<=nlstate+ndeath;ii++)
      }      for (j=1;j<=nlstate+ndeath;j++){
              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      /*printf("\n%d ",(int)age);      }
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    
            cov[1]=1.;
     
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
      }*/    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       newm=savm;
   fprintf(ficresprob,"\n%d ",(int)age);      /* Covariates have to be included here again */
       cov[2]=agefin;
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      if(nagesqr==1)
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        cov[3]= agefin*agefin;;
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      for (k=1; k<=cptcovn;k++) {
   }        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])];
         /* 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])]); */
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      }
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2];
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      for (k=1; k<=cptcovprod;k++) /* Useless */
 }        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])];
  free_vector(xp,1,npar);      
 fclose(ficresprob);      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
 }      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
 /******************* Printing html file ***********/      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
  int lastpass, int stepm, int weightopt, char model[],\      
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \      savm=oldm;
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\      oldm=newm;
  char version[], int popforecast, int estepm ){      maxmax=0.;
   int jj1, k1, i1, cpt;      for(j=1;j<=nlstate;j++){
   FILE *fichtm;        min=1.;
   /*char optionfilehtm[FILENAMELENGTH];*/        max=0.;
         for(i=1; i<=nlstate; i++) {
   strcpy(optionfilehtm,optionfile);          sumnew=0;
   strcat(optionfilehtm,".htm");          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          prlim[i][j]= newm[i][j]/(1-sumnew);
     printf("Problem with %s \n",optionfilehtm), exit(0);          /*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]);
  fprintf(fichtm,"<body> <font size=\"2\">Imach, Version %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        maxmin=max-min;
 \n        maxmax=FMAX(maxmax,maxmin);
 Total number of observations=%d <br>\n      } /* j loop */
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      if(maxmax < ftolpl){
 <hr  size=\"2\" color=\"#EC5E5E\">        return prlim;
  <ul><li>Outputs files<br>\n      }
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    } /* age loop */
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n    return prlim; /* should not reach here */
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n  }
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n  
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n  /*************** transition probabilities ***************/ 
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,estepm);  
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
  fprintf(fichtm,"\n  {
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n    /* According to parameters values stored in x and the covariate's values stored in cov,
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n       computes the probability to be observed in state j being in state i by appying the
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n       model to the ncovmodel covariates (including constant and age).
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
        and, according on how parameters are entered, the position of the coefficient xij(nc) of the
  if(popforecast==1) fprintf(fichtm,"\n       ncth covariate in the global vector x is given by the formula:
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
         <br>",fileres,fileres,fileres,fileres);       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
  else       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
    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);       Outputs ps[i][j] the probability to be observed in j being in j according to
 fprintf(fichtm," <li>Graphs</li><p>");       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
     */
  m=cptcoveff;    double s1, lnpijopii;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    /*double t34;*/
     int i,j, nc, ii, jj;
  jj1=0;  
  for(k1=1; k1<=m;k1++){      for(i=1; i<= nlstate; i++){
    for(i1=1; i1<=ncodemax[k1];i1++){        for(j=1; j<i;j++){
        jj1++;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
        if (cptcovn > 0) {            /*lnpijopii += param[i][j][nc]*cov[nc];*/
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
          for (cpt=1; cpt<=cptcoveff;cpt++)  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);          }
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
        }  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>        }
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            for(j=i+1; j<=nlstate+ndeath;j++){
        for(cpt=1; cpt<nlstate;cpt++){          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
        }  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
     for(cpt=1; cpt<=nlstate;cpt++) {          }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
 interval) in state (%d): v%s%d%d.gif <br>        }
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        }
      }      
      for(cpt=1; cpt<=nlstate;cpt++) {      for(i=1; i<= nlstate; i++){
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        s1=0;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        for(j=1; j<i; j++){
      }          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
 health expectancies in states (1) and (2): e%s%d.gif<br>        }
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        for(j=i+1; j<=nlstate+ndeath; j++){
 fprintf(fichtm,"\n</body>");          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
    }          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
    }        }
 fclose(fichtm);        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
 }        ps[i][i]=1./(s1+1.);
         /* Computing other pijs */
 /******************* Gnuplot file **************/        for(j=1; j<i; j++)
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){          ps[i][j]= exp(ps[i][j])*ps[i][i];
         for(j=i+1; j<=nlstate+ndeath; j++)
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          ps[i][j]= exp(ps[i][j])*ps[i][i];
         /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   strcpy(optionfilegnuplot,optionfilefiname);      } /* end i */
   strcat(optionfilegnuplot,".gp.txt");      
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     printf("Problem with file %s",optionfilegnuplot);        for(jj=1; jj<= nlstate+ndeath; jj++){
   }          ps[ii][jj]=0;
           ps[ii][ii]=1;
 #ifdef windows        }
     fprintf(ficgp,"cd \"%s\" \n",pathc);      }
 #endif      
 m=pow(2,cptcoveff);      
        /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
  /* 1eme*/      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
   for (cpt=1; cpt<= nlstate ; cpt ++) {      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
    for (k1=1; k1<= m ; k1 ++) {      /*   } */
       /*   printf("\n "); */
 #ifdef windows      /* } */
     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",ageminpar,fage,fileres,k1-1,k1-1);      /* printf("\n ");printf("%lf ",cov[2]);*/
 #endif      /*
 #ifdef unix        for(i=1; i<= npar; i++) printf("%f ",x[i]);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);        goto end;*/
 #endif      return ps;
   }
 for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  /**************** Product of 2 matrices ******************/
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
     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 (i=1; i<= nlstate ; i ++) {    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /* in, b, out are matrice of pointers which should have been initialized 
 }       before: only the contents of out is modified. The function returns
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);       a pointer to pointers identical to out */
      for (i=1; i<= nlstate ; i ++) {    int i, j, k;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    for(i=nrl; i<= nrh; i++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(k=ncolol; k<=ncoloh; k++){
 }          out[i][k]=0.;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        for(j=ncl; j<=nch; j++)
 #ifdef unix          out[i][k] +=in[i][j]*b[j][k];
 fprintf(ficgp,"\nset ter gif small size 400,300");      }
 #endif    return out;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  }
    }  
   }  
   /*2 eme*/  /************* Higher Matrix Product ***************/
   
   for (k1=1; k1<= m ; k1 ++) {  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);  {
        /* Computes the transition matrix starting at age 'age' over 
     for (i=1; i<= nlstate+1 ; i ++) {       'nhstepm*hstepm*stepm' months (i.e. until
       k=2*i;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);       nhstepm*hstepm matrices. 
       for (j=1; j<= nlstate+1 ; j ++) {       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");       (typically every 2 years instead of every month which is too big 
   else fprintf(ficgp," \%%*lf (\%%*lf)");       for the memory).
 }         Model is determined by parameters x and covariates have to be 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");       included manually here. 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  
     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 ++) {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    int i, j, d, h, k;
         else fprintf(ficgp," \%%*lf (\%%*lf)");    double **out, cov[NCOVMAX+1];
 }      double **newm;
       fprintf(ficgp,"\" t\"\" w l 0,");    double agexact;
      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 ++) {    /* Hstepm could be zero and should return the unit matrix */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    for (i=1;i<=nlstate+ndeath;i++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for (j=1;j<=nlstate+ndeath;j++){
 }          oldm[i][j]=(i==j ? 1.0 : 0.0);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        po[i][j][0]=(i==j ? 1.0 : 0.0);
       else fprintf(ficgp,"\" t\"\" w l 0,");      }
     }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    for(h=1; h <=nhstepm; h++){
   }      for(d=1; d <=hstepm; d++){
          newm=savm;
   /*3eme*/        /* Covariates have to be included here again */
         cov[1]=1.;
   for (k1=1; k1<= m ; k1 ++) {        agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     for (cpt=1; cpt<= nlstate ; cpt ++) {        cov[2]=agexact;
       k=2+nlstate*(cpt-1);        if(nagesqr==1)
       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",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);          cov[3]= agexact*agexact;
       for (i=1; i< nlstate ; i ++) {        for (k=1; k<=cptcovn;k++) 
         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);          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])];
       }        for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
     }          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2];
     }        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])];
   /* CV preval stat */  
     for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<nlstate ; cpt ++) {        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       k=3;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
       for (i=1; i< nlstate ; i ++)        savm=oldm;
         fprintf(ficgp,"+$%d",k+i+1);        oldm=newm;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      }
            for(i=1; i<=nlstate+ndeath; i++)
       l=3+(nlstate+ndeath)*cpt;        for(j=1;j<=nlstate+ndeath;j++) {
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          po[i][j][h]=newm[i][j];
       for (i=1; i< nlstate ; i ++) {          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         l=3+(nlstate+ndeath)*cpt;        }
         fprintf(ficgp,"+$%d",l+i+1);      /*printf("h=%d ",h);*/
       }    } /* end h */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    /*     printf("\n H=%d \n",h); */
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    return po;
     }  }
   }    
    #ifdef NLOPT
   /* proba elementaires */    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
    for(i=1,jk=1; i <=nlstate; i++){    double fret;
     for(k=1; k <=(nlstate+ndeath); k++){    double *xt;
       if (k != i) {    int j;
         for(j=1; j <=ncovmodel; j++){    myfunc_data *d2 = (myfunc_data *) pd;
          /* xt = (p1-1); */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    xt=vector(1,n); 
           jk++;    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
           fprintf(ficgp,"\n");  
         }    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");
     for(jk=1; jk <=m; jk++) {   free_vector(xt,1,n);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    return fret;
    i=1;  }
    for(k2=1; k2<=nlstate; k2++) {  #endif
      k3=i;  
      for(k=1; k<=(nlstate+ndeath); k++) {  /*************** log-likelihood *************/
        if (k != k2){  double func( double *x)
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  {
 ij=1;    int i, ii, j, k, mi, d, kk;
         for(j=3; j <=ncovmodel; j++) {    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double **out;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    double sw; /* Sum of weights */
             ij++;    double lli; /* Individual log likelihood */
           }    int s1, s2;
           else    double bbh, survp;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    long ipmx;
         }    double agexact;
           fprintf(ficgp,")/(1");    /*extern weight */
            /* We are differentiating ll according to initial status */
         for(k1=1; k1 <=nlstate; k1++){      /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    /*for(i=1;i<imx;i++) 
 ij=1;      printf(" %d\n",s[4][i]);
           for(j=3; j <=ncovmodel; j++){    */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    ++countcallfunc;
             ij++;  
           }    cov[1]=1.;
           else  
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    for(k=1; k<=nlstate; k++) ll[k]=0.;
           }  
           fprintf(ficgp,")");    if(mle==1){
         }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        /* Computes the values of the ncovmodel covariates of the model
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
         i=i+ncovmodel;           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.
      }         */
    }        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);            cov[2+nagesqr+k]=covar[Tvar[k]][i];
    }        }
            /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
   fclose(ficgp);           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
 }  /* end gnuplot */           has been calculated etc */
         for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
 /*************** Moving average **************/            for (j=1;j<=nlstate+ndeath;j++){
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, cpt, cptcod;            }
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)          for(d=0; d<dh[mi][i]; d++){
       for (i=1; i<=nlstate;i++)            newm=savm;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
           mobaverage[(int)agedeb][i][cptcod]=0.;            cov[2]=agexact;
                if(nagesqr==1)
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){              cov[3]= agexact*agexact;
       for (i=1; i<=nlstate;i++){            for (kk=1; kk<=cptcovage;kk++) {
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
           for (cpt=0;cpt<=4;cpt++){            }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;            savm=oldm;
         }            oldm=newm;
       }          } /* end mult */
     }        
              /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 }          /* 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 
            * (in months) between two waves is not a multiple of stepm, we rounded to 
 /************** Forecasting ******************/           * the nearest (and in case of equal distance, to the lowest) interval but now
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){           * 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
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;           * probability in order to take into account the bias as a fraction of the way
   int *popage;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;           * -stepm/2 to stepm/2 .
   double *popeffectif,*popcount;           * For stepm=1 the results are the same as for previous versions of Imach.
   double ***p3mat;           * For stepm > 1 the results are less biased than in previous versions. 
   char fileresf[FILENAMELENGTH];           */
           s1=s[mw[mi][i]][i];
  agelim=AGESUP;          s2=s[mw[mi+1][i]][i];
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias bh is positive if real duration
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);           * is higher than the multiple of stepm and negative otherwise.
             */
            /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   strcpy(fileresf,"f");          if( s2 > nlstate){ 
   strcat(fileresf,fileres);            /* i.e. if s2 is a death state and if the date of death is known 
   if((ficresf=fopen(fileresf,"w"))==NULL) {               then the contribution to the likelihood is the probability to 
     printf("Problem with forecast resultfile: %s\n", fileresf);               die between last step unit time and current  step unit time, 
   }               which is also equal to probability to die before dh 
   printf("Computing forecasting: result on file '%s' \n", fileresf);               minus probability to die before dh-stepm . 
                In version up to 0.92 likelihood was computed
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          as if date of death was unknown. Death was treated as any other
           health state: the date of the interview describes the actual state
   if (mobilav==1) {          and not the date of a change in health state. The former idea was
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          to consider that at each interview the state was recorded
     movingaverage(agedeb, fage, ageminpar, mobaverage);          (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
   stepsize=(int) (stepm+YEARM-1)/YEARM;          contribution is smaller and very dependent of the step unit
   if (stepm<=12) stepsize=1;          stepm. It is no more the probability to die between last interview
            and month of death but the probability to survive from last
   agelim=AGESUP;          interview up to one month before death multiplied by the
            probability to die within a month. Thanks to Chris
   hstepm=1;          Jackson for correcting this bug.  Former versions increased
   hstepm=hstepm/stepm;          mortality artificially. The bad side is that we add another loop
   yp1=modf(dateintmean,&yp);          which slows down the processing. The difference can be up to 10%
   anprojmean=yp;          lower mortality.
   yp2=modf((yp1*12),&yp);            */
   mprojmean=yp;          /* If, at the beginning of the maximization mostly, the
   yp1=modf((yp2*30.5),&yp);             cumulative probability or probability to be dead is
   jprojmean=yp;             constant (ie = 1) over time d, the difference is equal to
   if(jprojmean==0) jprojmean=1;             0.  out[s1][3] = savm[s1][3]: probability, being at state
   if(mprojmean==0) jprojmean=1;             s1 at precedent wave, to be dead a month before current
               wave is equal to probability, being at state s1 at
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);             precedent wave, to be dead at mont of the current
               wave. Then the observed probability (that this person died)
   for(cptcov=1;cptcov<=i2;cptcov++){             is null according to current estimated parameter. In fact,
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){             it should be very low but not zero otherwise the log go to
       k=k+1;             infinity.
       fprintf(ficresf,"\n#******");          */
       for(j=1;j<=cptcoveff;j++) {  /* #ifdef INFINITYORIGINAL */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
       }  /* #else */
       fprintf(ficresf,"******\n");  /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
       fprintf(ficresf,"# StartingAge FinalAge");  /*          lli=log(mytinydouble); */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  /*        else */
        /*          lli=log(out[s1][s2] - savm[s1][s2]); */
        /* #endif */
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {              lli=log(out[s1][s2] - savm[s1][s2]);
         fprintf(ficresf,"\n");  
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            } else if  (s2==-2) {
             for (j=1,survp=0. ; j<=nlstate; j++) 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            /*survp += out[s1][j]; */
           nhstepm = nhstepm/hstepm;            lli= log(survp);
                    }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          
           oldm=oldms;savm=savms;          else if  (s2==-4) { 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              for (j=3,survp=0. ; j<=nlstate; j++)  
                      survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           for (h=0; h<=nhstepm; h++){            lli= log(survp); 
             if (h==(int) (calagedate+YEARM*cpt)) {          } 
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);  
             }          else if  (s2==-5) { 
             for(j=1; j<=nlstate+ndeath;j++) {            for (j=1,survp=0. ; j<=2; j++)  
               kk1=0.;kk2=0;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
               for(i=1; i<=nlstate;i++) {                          lli= log(survp); 
                 if (mobilav==1)          } 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          
                 else {          else{
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                 }            /*  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 */
                          } 
               }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
               if (h==(int)(calagedate+12*cpt)){          /*if(lli ==000.0)*/
                 fprintf(ficresf," %.3f", kk1);          /*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); */
                                  ipmx +=1;
               }          sw += weight[i];
             }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           }          /* if (lli < log(mytinydouble)){ */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
         }          /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
       }          /* } */
     }        } /* end of wave */
   }      } /* end of individual */
            }  else if(mle==2){
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
   fclose(ficresf);        for(mi=1; mi<= wav[i]-1; mi++){
 }          for (ii=1;ii<=nlstate+ndeath;ii++)
 /************** Forecasting ******************/            for (j=1;j<=nlstate+ndeath;j++){
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            }
   int *popage;          for(d=0; d<=dh[mi][i]; d++){
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            newm=savm;
   double *popeffectif,*popcount;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double ***p3mat,***tabpop,***tabpopprev;            cov[2]=agexact;
   char filerespop[FILENAMELENGTH];            if(nagesqr==1)
               cov[3]= agexact*agexact;
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for (kk=1; kk<=cptcovage;kk++) {
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
   agelim=AGESUP;            }
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            savm=oldm;
              oldm=newm;
            } /* end mult */
   strcpy(filerespop,"pop");        
   strcat(filerespop,fileres);          s1=s[mw[mi][i]][i];
   if((ficrespop=fopen(filerespop,"w"))==NULL) {          s2=s[mw[mi+1][i]][i];
     printf("Problem with forecast resultfile: %s\n", filerespop);          bbh=(double)bh[mi][i]/(double)stepm; 
   }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   printf("Computing forecasting: result on file '%s' \n", filerespop);          ipmx +=1;
           sw += weight[i];
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
   if (mobilav==1) {      } /* end of individual */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    }  else if(mle==3){  /* exponential inter-extrapolation */
     movingaverage(agedeb, fage, ageminpar, mobaverage);      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++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for (ii=1;ii<=nlstate+ndeath;ii++)
   if (stepm<=12) stepsize=1;            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   agelim=AGESUP;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
   hstepm=1;          for(d=0; d<dh[mi][i]; d++){
   hstepm=hstepm/stepm;            newm=savm;
              agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
   if (popforecast==1) {            cov[2]=agexact;
     if((ficpop=fopen(popfile,"r"))==NULL) {            if(nagesqr==1)
       printf("Problem with population file : %s\n",popfile);exit(0);              cov[3]= agexact*agexact;
     }            for (kk=1; kk<=cptcovage;kk++) {
     popage=ivector(0,AGESUP);              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
     popeffectif=vector(0,AGESUP);            }
     popcount=vector(0,AGESUP);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                             1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     i=1;              savm=oldm;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;            oldm=newm;
              } /* end mult */
     imx=i;        
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          s1=s[mw[mi][i]][i];
   }          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
   for(cptcov=1;cptcov<=i2;cptcov++){          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 */
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          ipmx +=1;
       k=k+1;          sw += weight[i];
       fprintf(ficrespop,"\n#******");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(j=1;j<=cptcoveff;j++) {        } /* end of wave */
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      } /* end of individual */
       }    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       fprintf(ficrespop,"******\n");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       fprintf(ficrespop,"# Age");        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);        for(mi=1; mi<= wav[i]-1; mi++){
       if (popforecast==1)  fprintf(ficrespop," [Population]");          for (ii=1;ii<=nlstate+ndeath;ii++)
                  for (j=1;j<=nlstate+ndeath;j++){
       for (cpt=0; cpt<=0;cpt++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                savm[ii][j]=(ii==j ? 1.0 : 0.0);
                    }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          for(d=0; d<dh[mi][i]; d++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            newm=savm;
           nhstepm = nhstepm/hstepm;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                      cov[2]=agexact;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            if(nagesqr==1)
           oldm=oldms;savm=savms;              cov[3]= agexact*agexact;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              for (kk=1; kk<=cptcovage;kk++) {
                      cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
           for (h=0; h<=nhstepm; h++){            }
             if (h==(int) (calagedate+YEARM*cpt)) {          
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             for(j=1; j<=nlstate+ndeath;j++) {            savm=oldm;
               kk1=0.;kk2=0;            oldm=newm;
               for(i=1; i<=nlstate;i++) {                        } /* end mult */
                 if (mobilav==1)        
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          s1=s[mw[mi][i]][i];
                 else {          s2=s[mw[mi+1][i]][i];
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          if( s2 > nlstate){ 
                 }            lli=log(out[s1][s2] - savm[s1][s2]);
               }          }else{
               if (h==(int)(calagedate+12*cpt)){            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          }
                   /*fprintf(ficrespop," %.3f", kk1);          ipmx +=1;
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/          sw += weight[i];
               }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             }  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
             for(i=1; i<=nlstate;i++){        } /* end of wave */
               kk1=0.;      } /* end of individual */
                 for(j=1; j<=nlstate;j++){    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                 }        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];        for(mi=1; mi<= wav[i]-1; mi++){
             }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);              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;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {            for (kk=1; kk<=cptcovage;kk++) {
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){            }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          
           nhstepm = nhstepm/hstepm;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                                   1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            savm=oldm;
           oldm=oldms;savm=savms;            oldm=newm;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            } /* end mult */
           for (h=0; h<=nhstepm; h++){        
             if (h==(int) (calagedate+YEARM*cpt)) {          s1=s[mw[mi][i]][i];
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          s2=s[mw[mi+1][i]][i];
             }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
             for(j=1; j<=nlstate+ndeath;j++) {          ipmx +=1;
               kk1=0.;kk2=0;          sw += weight[i];
               for(i=1; i<=nlstate;i++) {                        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
               }        } /* end of wave */
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);      } /* end of individual */
             }    } /* End of if */
           }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       }    return -l;
    }  }
   }  
    /*************** log-likelihood *************/
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  double funcone( double *x)
   {
   if (popforecast==1) {    /* Same as likeli but slower because of a lot of printf and if */
     free_ivector(popage,0,AGESUP);    int i, ii, j, k, mi, d, kk;
     free_vector(popeffectif,0,AGESUP);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     free_vector(popcount,0,AGESUP);    double **out;
   }    double lli; /* Individual log likelihood */
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double llt;
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int s1, s2;
   fclose(ficrespop);    double bbh, survp;
 }    double agexact;
     /*extern weight */
 /***********************************************/    /* We are differentiating ll according to initial status */
 /**************** Main Program *****************/    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 /***********************************************/    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
 int main(int argc, char *argv[])    */
 {    cov[1]=1.;
   
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   double agedeb, agefin,hf;  
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    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 fret;      for(mi=1; mi<= wav[i]-1; mi++){
   double **xi,tmp,delta;        for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
   double dum; /* Dummy variable */            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double ***p3mat;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int *indx;          }
   char line[MAXLINE], linepar[MAXLINE];        for(d=0; d<dh[mi][i]; d++){
   char title[MAXLINE];          newm=savm;
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];          cov[2]=agexact;
            if(nagesqr==1)
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];            cov[3]= agexact*agexact;
           for (kk=1; kk<=cptcovage;kk++) {
   char filerest[FILENAMELENGTH];            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
   char fileregp[FILENAMELENGTH];          }
   char popfile[FILENAMELENGTH];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   int firstobs=1, lastobs=10;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int sdeb, sfin; /* Status at beginning and end */                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   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;        bbh=(double)bh[mi][i]/(double)stepm; 
   double ftolpl=FTOL;        /* bias is positive if real duration
   double **prlim;         * is higher than the multiple of stepm and negative otherwise.
   double *severity;         */
   double ***param; /* Matrix of parameters */        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   double  *p;          lli=log(out[s1][s2] - savm[s1][s2]);
   double **matcov; /* Matrix of covariance */        } else if  (s2==-2) {
   double ***delti3; /* Scale */          for (j=1,survp=0. ; j<=nlstate; j++) 
   double *delti; /* Scale */            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   double ***eij, ***vareij;          lli= log(survp);
   double **varpl; /* Variances of prevalence limits by age */        }else if (mle==1){
   double *epj, vepp;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double kk1, kk2;        } else if(mle==2){
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
          } else if(mle==3){  /* exponential inter-extrapolation */
           lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   char version[80]="Imach version 0.8a, March 2002, INED-EUROREVES ";        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   char *alph[]={"a","a","b","c","d","e"}, str[4];          lli=log(out[s1][s2]); /* Original formula */
         } else{  /* mle=0 back to 1 */
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   char z[1]="c", occ;          /*lli=log(out[s1][s2]); */ /* Original formula */
 #include <sys/time.h>        } /* End of if */
 #include <time.h>        ipmx +=1;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        sw += weight[i];
          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /* long total_usecs;        /*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]); */
   struct timeval start_time, end_time;        if(globpr){
            fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */   %11.6f %11.6f %11.6f ", \
   getcwd(pathcd, size);                  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]);
   printf("\n%s",version);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   if(argc <=1){            llt +=ll[k]*gipmx/gsw;
     printf("\nEnter the parameter file name: ");            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     scanf("%s",pathtot);          }
   }          fprintf(ficresilk," %10.6f\n", -llt);
   else{        }
     strcpy(pathtot,argv[1]);      } /* end of wave */
   }    } /* end of individual */
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   /*cygwin_split_path(pathtot,path,optionfile);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   /* cutv(path,optionfile,pathtot,'\\');*/    if(globpr==0){ /* First time we count the contributions and weights */
       gipmx=ipmx;
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);      gsw=sw;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    }
   chdir(path);    return -l;
   replace(pathc,path);  }
   
 /*-------- arguments in the command line --------*/  
   /*************** function likelione ***********/
   strcpy(fileres,"r");  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   strcat(fileres, optionfilefiname);  {
   strcat(fileres,".txt");    /* Other files have txt extension */    /* This routine should help understanding what is done with 
        the selection of individuals/waves and
   /*---------arguments file --------*/       to check the exact contribution to the likelihood.
        Plotting could be done.
   if((ficpar=fopen(optionfile,"r"))==NULL)    {     */
     printf("Problem with optionfile %s\n",optionfile);    int k;
     goto end;  
   }    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
   strcpy(filereso,"o");      strcat(fileresilk,fileres);
   strcat(filereso,fileres);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   if((ficparo=fopen(filereso,"w"))==NULL) {        printf("Problem with resultfile: %s\n", fileresilk);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   }      }
       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");
   /* Reads comments: lines beginning with '#' */      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   while((c=getc(ficpar))=='#' && c!= EOF){      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     ungetc(c,ficpar);      for(k=1; k<=nlstate; k++) 
     fgets(line, MAXLINE, ficpar);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     puts(line);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     fputs(line,ficparo);    }
   }  
   ungetc(c,ficpar);    *fretone=(*funcone)(p);
     if(*globpri !=0){
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);      fclose(ficresilk);
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);      fflush(fichtm); 
 while((c=getc(ficpar))=='#' && c!= EOF){    } 
     ungetc(c,ficpar);    return;
     fgets(line, MAXLINE, ficpar);  }
     puts(line);  
     fputs(line,ficparo);  
   }  /*********** Maximum Likelihood Estimation ***************/
   ungetc(c,ficpar);  
    void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
      {
   covar=matrix(0,NCOVMAX,1,n);    int i,j, iter=0;
   cptcovn=0;    double **xi;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    double fret;
     double fretone; /* Only one call to likelihood */
   ncovmodel=2+cptcovn;    /*  char filerespow[FILENAMELENGTH];*/
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
    #ifdef NLOPT
   /* Read guess parameters */    int creturn;
   /* Reads comments: lines beginning with '#' */    nlopt_opt opt;
   while((c=getc(ficpar))=='#' && c!= EOF){    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
     ungetc(c,ficpar);    double *lb;
     fgets(line, MAXLINE, ficpar);    double minf; /* the minimum objective value, upon return */
     puts(line);    double * p1; /* Shifted parameters from 0 instead of 1 */
     fputs(line,ficparo);    myfunc_data dinst, *d = &dinst;
   }  #endif
   ungetc(c,ficpar);  
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    xi=matrix(1,npar,1,npar);
     for(i=1; i <=nlstate; i++)    for (i=1;i<=npar;i++)
     for(j=1; j <=nlstate+ndeath-1; j++){      for (j=1;j<=npar;j++)
       fscanf(ficpar,"%1d%1d",&i1,&j1);        xi[i][j]=(i==j ? 1.0 : 0.0);
       fprintf(ficparo,"%1d%1d",i1,j1);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       printf("%1d%1d",i,j);    strcpy(filerespow,"pow"); 
       for(k=1; k<=ncovmodel;k++){    strcat(filerespow,fileres);
         fscanf(ficpar," %lf",&param[i][j][k]);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf(" %lf",param[i][j][k]);      printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficparo," %lf",param[i][j][k]);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }    }
       fscanf(ficpar,"\n");    fprintf(ficrespow,"# Powell\n# iter -2*LL");
       printf("\n");    for (i=1;i<=nlstate;i++)
       fprintf(ficparo,"\n");      for(j=1;j<=nlstate+ndeath;j++)
     }        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
      fprintf(ficrespow,"\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  #ifdef POWELL
     powell(p,xi,npar,ftol,&iter,&fret,func);
   p=param[1][1];  #endif
    
   /* Reads comments: lines beginning with '#' */  #ifdef NLOPT
   while((c=getc(ficpar))=='#' && c!= EOF){  #ifdef NEWUOA
     ungetc(c,ficpar);    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
     fgets(line, MAXLINE, ficpar);  #else
     puts(line);    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
     fputs(line,ficparo);  #endif
   }    lb=vector(0,npar-1);
   ungetc(c,ficpar);    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
     nlopt_set_lower_bounds(opt, lb);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    nlopt_set_initial_step1(opt, 0.1);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    
   for(i=1; i <=nlstate; i++){    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
     for(j=1; j <=nlstate+ndeath-1; j++){    d->function = func;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
       printf("%1d%1d",i,j);    nlopt_set_min_objective(opt, myfunc, d);
       fprintf(ficparo,"%1d%1d",i1,j1);    nlopt_set_xtol_rel(opt, ftol);
       for(k=1; k<=ncovmodel;k++){    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
         fscanf(ficpar,"%le",&delti3[i][j][k]);      printf("nlopt failed! %d\n",creturn); 
         printf(" %le",delti3[i][j][k]);    }
         fprintf(ficparo," %le",delti3[i][j][k]);    else {
       }      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
       fscanf(ficpar,"\n");      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
       printf("\n");      iter=1; /* not equal */
       fprintf(ficparo,"\n");    }
     }    nlopt_destroy(opt);
   }  #endif
   delti=delti3[1][1];    free_matrix(xi,1,npar,1,npar);
      fclose(ficrespow);
   /* Reads comments: lines beginning with '#' */    printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     ungetc(c,ficpar);    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     fgets(line, MAXLINE, ficpar);  
     puts(line);  }
     fputs(line,ficparo);  
   }  /**** Computes Hessian and covariance matrix ***/
   ungetc(c,ficpar);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
    {
   matcov=matrix(1,npar,1,npar);    double  **a,**y,*x,pd;
   for(i=1; i <=npar; i++){    double **hess;
     fscanf(ficpar,"%s",&str);    int i, j;
     printf("%s",str);    int *indx;
     fprintf(ficparo,"%s",str);  
     for(j=1; j <=i; j++){    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
       fscanf(ficpar," %le",&matcov[i][j]);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
       printf(" %.5le",matcov[i][j]);    void lubksb(double **a, int npar, int *indx, double b[]) ;
       fprintf(ficparo," %.5le",matcov[i][j]);    void ludcmp(double **a, int npar, int *indx, double *d) ;
     }    double gompertz(double p[]);
     fscanf(ficpar,"\n");    hess=matrix(1,npar,1,npar);
     printf("\n");  
     fprintf(ficparo,"\n");    printf("\nCalculation of the hessian matrix. Wait...\n");
   }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   for(i=1; i <=npar; i++)    for (i=1;i<=npar;i++){
     for(j=i+1;j<=npar;j++)      printf("%d",i);fflush(stdout);
       matcov[i][j]=matcov[j][i];      fprintf(ficlog,"%d",i);fflush(ficlog);
         
   printf("\n");       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       
       /*  printf(" %f ",p[i]);
     /*-------- Rewriting paramater file ----------*/          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
      strcpy(rfileres,"r");    /* "Rparameterfile */    }
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    
      strcat(rfileres,".");    /* */    for (i=1;i<=npar;i++) {
      strcat(rfileres,optionfilext);    /* Other files have txt extension */      for (j=1;j<=npar;j++)  {
     if((ficres =fopen(rfileres,"w"))==NULL) {        if (j>i) { 
       printf("Problem writing new parameter file: %s\n", fileres);goto end;          printf(".%d%d",i,j);fflush(stdout);
     }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     fprintf(ficres,"#%s\n",version);          hess[i][j]=hessij(p,delti,i,j,func,npar);
              
     /*-------- data file ----------*/          hess[j][i]=hess[i][j];    
     if((fic=fopen(datafile,"r"))==NULL)    {          /*printf(" %lf ",hess[i][j]);*/
       printf("Problem with datafile: %s\n", datafile);goto end;        }
     }      }
     }
     n= lastobs;    printf("\n");
     severity = vector(1,maxwav);    fprintf(ficlog,"\n");
     outcome=imatrix(1,maxwav+1,1,n);  
     num=ivector(1,n);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     moisnais=vector(1,n);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     annais=vector(1,n);    
     moisdc=vector(1,n);    a=matrix(1,npar,1,npar);
     andc=vector(1,n);    y=matrix(1,npar,1,npar);
     agedc=vector(1,n);    x=vector(1,npar);
     cod=ivector(1,n);    indx=ivector(1,npar);
     weight=vector(1,n);    for (i=1;i<=npar;i++)
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     mint=matrix(1,maxwav,1,n);    ludcmp(a,npar,indx,&pd);
     anint=matrix(1,maxwav,1,n);  
     s=imatrix(1,maxwav+1,1,n);    for (j=1;j<=npar;j++) {
     adl=imatrix(1,maxwav+1,1,n);          for (i=1;i<=npar;i++) x[i]=0;
     tab=ivector(1,NCOVMAX);      x[j]=1;
     ncodemax=ivector(1,8);      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
     i=1;        matcov[i][j]=x[i];
     while (fgets(line, MAXLINE, fic) != NULL)    {      }
       if ((i >= firstobs) && (i <=lastobs)) {    }
          
         for (j=maxwav;j>=1;j--){    printf("\n#Hessian matrix#\n");
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    fprintf(ficlog,"\n#Hessian matrix#\n");
           strcpy(line,stra);    for (i=1;i<=npar;i++) { 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      for (j=1;j<=npar;j++) { 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        printf("%.3e ",hess[i][j]);
         }        fprintf(ficlog,"%.3e ",hess[i][j]);
              }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      printf("\n");
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      fprintf(ficlog,"\n");
     }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    /* Recompute Inverse */
     for (i=1;i<=npar;i++)
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         for (j=ncovcol;j>=1;j--){    ludcmp(a,npar,indx,&pd);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }    /*  printf("\n#Hessian matrix recomputed#\n");
         num[i]=atol(stra);  
            for (j=1;j<=npar;j++) {
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){      for (i=1;i<=npar;i++) x[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])); ij=ij+1;}*/      x[j]=1;
       lubksb(a,npar,indx,x);
         i=i+1;      for (i=1;i<=npar;i++){ 
       }        y[i][j]=x[i];
     }        printf("%.3e ",y[i][j]);
     /* printf("ii=%d", ij);        fprintf(ficlog,"%.3e ",y[i][j]);
        scanf("%d",i);*/      }
   imx=i-1; /* Number of individuals */      printf("\n");
       fprintf(ficlog,"\n");
   /* for (i=1; i<=imx; i++){    }
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    */
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;  
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    free_matrix(a,1,npar,1,npar);
     }*/    free_matrix(y,1,npar,1,npar);
      free_vector(x,1,npar);
   /* for (i=1; i<=imx; i++){    free_ivector(indx,1,npar);
      if (s[4][i]==9)  s[4][i]=-1;    free_matrix(hess,1,npar,1,npar);
      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]));}  
   */  
    }
   /* Calculation of the number of parameter from char model*/  
   Tvar=ivector(1,15);  /*************** hessian matrix ****************/
   Tprod=ivector(1,15);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   Tvaraff=ivector(1,15);  {
   Tvard=imatrix(1,15,1,2);    int i;
   Tage=ivector(1,15);          int l=1, lmax=20;
        double k1,k2;
   if (strlen(model) >1){    double p2[MAXPARM+1]; /* identical to x */
     j=0, j1=0, k1=1, k2=1;    double res;
     j=nbocc(model,'+');    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     j1=nbocc(model,'*');    double fx;
     cptcovn=j+1;    int k=0,kmax=10;
     cptcovprod=j1;    double l1;
      
     strcpy(modelsav,model);    fx=func(x);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    for (i=1;i<=npar;i++) p2[i]=x[i];
       printf("Error. Non available option model=%s ",model);    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
       goto end;      l1=pow(10,l);
     }      delts=delt;
          for(k=1 ; k <kmax; k=k+1){
     for(i=(j+1); i>=1;i--){        delt = delta*(l1*k);
       cutv(stra,strb,modelsav,'+');        p2[theta]=x[theta] +delt;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        p2[theta]=x[theta]-delt;
       /*scanf("%d",i);*/        k2=func(p2)-fx;
       if (strchr(strb,'*')) {        /*res= (k1-2.0*fx+k2)/delt/delt; */
         cutv(strd,strc,strb,'*');        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         if (strcmp(strc,"age")==0) {        
           cptcovprod--;  #ifdef DEBUGHESS
           cutv(strb,stre,strd,'V');        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);
           Tvar[i]=atoi(stre);        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);
           cptcovage++;  #endif
             Tage[cptcovage]=i;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
             /*printf("stre=%s ", stre);*/        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         }          k=kmax;
         else if (strcmp(strd,"age")==0) {        }
           cptcovprod--;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           cutv(strb,stre,strc,'V');          k=kmax; l=lmax*10;
           Tvar[i]=atoi(stre);        }
           cptcovage++;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           Tage[cptcovage]=i;          delts=delt;
         }        }
         else {      }
           cutv(strb,stre,strc,'V');    }
           Tvar[i]=ncovcol+k1;    delti[theta]=delts;
           cutv(strb,strc,strd,'V');    return res; 
           Tprod[k1]=i;    
           Tvard[k1][1]=atoi(strc);  }
           Tvard[k1][2]=atoi(stre);  
           Tvar[cptcovn+k2]=Tvard[k1][1];  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  {
           for (k=1; k<=lastobs;k++)    int i;
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    int l=1, lmax=20;
           k1++;    double k1,k2,k3,k4,res,fx;
           k2=k2+2;    double p2[MAXPARM+1];
         }    int k;
       }  
       else {    fx=func(x);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    for (k=1; k<=2; k++) {
        /*  scanf("%d",i);*/      for (i=1;i<=npar;i++) p2[i]=x[i];
       cutv(strd,strc,strb,'V');      p2[thetai]=x[thetai]+delti[thetai]/k;
       Tvar[i]=atoi(strc);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       }      k1=func(p2)-fx;
       strcpy(modelsav,stra);      
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      p2[thetai]=x[thetai]+delti[thetai]/k;
         scanf("%d",i);*/      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     }      k2=func(p2)-fx;
 }    
        p2[thetai]=x[thetai]-delti[thetai]/k;
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   printf("cptcovprod=%d ", cptcovprod);      k3=func(p2)-fx;
   scanf("%d ",i);*/    
     fclose(fic);      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     /*  if(mle==1){*/      k4=func(p2)-fx;
     if (weightopt != 1) { /* Maximisation without weights*/      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       for(i=1;i<=n;i++) weight[i]=1.0;  #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);
     /*-calculation of age at interview from date of interview and age at death -*/      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);
     agev=matrix(1,maxwav,1,imx);  #endif
     }
     for (i=1; i<=imx; i++) {    return res;
       for(m=2; (m<= maxwav); m++) {  }
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  
          anint[m][i]=9999;  /************** Inverse of matrix **************/
          s[m][i]=-1;  void ludcmp(double **a, int n, int *indx, double *d) 
        }  { 
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    int i,imax,j,k; 
       }    double big,dum,sum,temp; 
     }    double *vv; 
    
     for (i=1; i<=imx; i++)  {    vv=vector(1,n); 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    *d=1.0; 
       for(m=1; (m<= maxwav); m++){    for (i=1;i<=n;i++) { 
         if(s[m][i] >0){      big=0.0; 
           if (s[m][i] >= nlstate+1) {      for (j=1;j<=n;j++) 
             if(agedc[i]>0)        if ((temp=fabs(a[i][j])) > big) big=temp; 
               if(moisdc[i]!=99 && andc[i]!=9999)      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
                 agev[m][i]=agedc[i];      vv[i]=1.0/big; 
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    } 
            else {    for (j=1;j<=n;j++) { 
               if (andc[i]!=9999){      for (i=1;i<j;i++) { 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        sum=a[i][j]; 
               agev[m][i]=-1;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
               }        a[i][j]=sum; 
             }      } 
           }      big=0.0; 
           else if(s[m][i] !=9){ /* Should no more exist */      for (i=j;i<=n;i++) { 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        sum=a[i][j]; 
             if(mint[m][i]==99 || anint[m][i]==9999)        for (k=1;k<j;k++) 
               agev[m][i]=1;          sum -= a[i][k]*a[k][j]; 
             else if(agev[m][i] <agemin){        a[i][j]=sum; 
               agemin=agev[m][i];        if ( (dum=vv[i]*fabs(sum)) >= big) { 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/          big=dum; 
             }          imax=i; 
             else if(agev[m][i] >agemax){        } 
               agemax=agev[m][i];      } 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      if (j != imax) { 
             }        for (k=1;k<=n;k++) { 
             /*agev[m][i]=anint[m][i]-annais[i];*/          dum=a[imax][k]; 
             /*   agev[m][i] = age[i]+2*m;*/          a[imax][k]=a[j][k]; 
           }          a[j][k]=dum; 
           else { /* =9 */        } 
             agev[m][i]=1;        *d = -(*d); 
             s[m][i]=-1;        vv[imax]=vv[j]; 
           }      } 
         }      indx[j]=imax; 
         else /*= 0 Unknown */      if (a[j][j] == 0.0) a[j][j]=TINY; 
           agev[m][i]=1;      if (j != n) { 
       }        dum=1.0/(a[j][j]); 
            for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     }      } 
     for (i=1; i<=imx; i++)  {    } 
       for(m=1; (m<= maxwav); m++){    free_vector(vv,1,n);  /* Doesn't work */
         if (s[m][i] > (nlstate+ndeath)) {  ;
           printf("Error: Wrong value in nlstate or ndeath\n");    } 
           goto end;  
         }  void lubksb(double **a, int n, int *indx, double b[]) 
       }  { 
     }    int i,ii=0,ip,j; 
     double sum; 
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);   
     for (i=1;i<=n;i++) { 
     free_vector(severity,1,maxwav);      ip=indx[i]; 
     free_imatrix(outcome,1,maxwav+1,1,n);      sum=b[ip]; 
     free_vector(moisnais,1,n);      b[ip]=b[i]; 
     free_vector(annais,1,n);      if (ii) 
     /* free_matrix(mint,1,maxwav,1,n);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
        free_matrix(anint,1,maxwav,1,n);*/      else if (sum) ii=i; 
     free_vector(moisdc,1,n);      b[i]=sum; 
     free_vector(andc,1,n);    } 
     for (i=n;i>=1;i--) { 
          sum=b[i]; 
     wav=ivector(1,imx);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      b[i]=sum/a[i][i]; 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    } 
      } 
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  void pstamp(FILE *fichier)
   {
     fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
       Tcode=ivector(1,100);  }
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  
       ncodemax[1]=1;  /************ Frequencies ********************/
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  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[])
        {  /* Some frequencies */
    codtab=imatrix(1,100,1,10);    
    h=0;    int i, m, jk, j1, bool, z1,j;
    m=pow(2,cptcoveff);    int first;
      double ***freq; /* Frequencies */
    for(k=1;k<=cptcoveff; k++){    double *pp, **prop;
      for(i=1; i <=(m/pow(2,k));i++){    double pos,posprop, k2, dateintsum=0,k2cpt=0;
        for(j=1; j <= ncodemax[k]; j++){    char fileresp[FILENAMELENGTH];
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    
            h++;    pp=vector(1,nlstate);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    prop=matrix(1,nlstate,iagemin,iagemax+3);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/    strcpy(fileresp,"p");
          }    strcat(fileresp,fileres);
        }    if((ficresp=fopen(fileresp,"w"))==NULL) {
      }      printf("Problem with prevalence resultfile: %s\n", fileresp);
    }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);      exit(0);
       codtab[1][2]=1;codtab[2][2]=2; */    }
    /* for(i=1; i <=m ;i++){    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
       for(k=1; k <=cptcovn; k++){    j1=0;
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    
       }    j=cptcoveff;
       printf("\n");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       }  
       scanf("%d",i);*/    first=1;
      
    /* Calculates basic frequencies. Computes observed prevalence at single age    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
        and prints on file fileres'p'. */    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
     /*    j1++; */
        for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
            /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          scanf("%d", i);*/
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for (i=-5; i<=nlstate+ndeath; i++)  
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for (jk=-5; jk<=nlstate+ndeath; jk++)  
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for(m=iagemin; m <= iagemax+3; m++)
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              freq[i][jk][m]=0;
              
     /* For Powell, parameters are in a vector p[] starting at p[1]        for (i=1; i<=nlstate; i++)  
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          for(m=iagemin; m <= iagemax+3; m++)
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */            prop[i][m]=0;
         
     if(mle==1){        dateintsum=0;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        k2cpt=0;
     }        for (i=1; i<=imx; i++) {
              bool=1;
     /*--------- results files --------------*/          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);            for (z1=1; z1<=cptcoveff; z1++)       
                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 */
    jk=1;                bool=0;
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");                /* 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", 
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
    for(i=1,jk=1; i <=nlstate; i++){                  j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
      for(k=1; k <=(nlstate+ndeath); k++){                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
        if (k != i)              } 
          {          }
            printf("%d%d ",i,k);   
            fprintf(ficres,"%1d%1d ",i,k);          if (bool==1){
            for(j=1; j <=ncovmodel; j++){            for(m=firstpass; m<=lastpass; m++){
              printf("%f ",p[jk]);              k2=anint[m][i]+(mint[m][i]/12.);
              fprintf(ficres,"%f ",p[jk]);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
              jk++;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
            }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
            printf("\n");                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
            fprintf(ficres,"\n");                if (m<lastpass) {
          }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
      }                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
    }                }
  if(mle==1){                
     /* Computing hessian and covariance matrix */                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     ftolhess=ftol; /* Usually correct */                  dateintsum=dateintsum+k2;
     hesscov(matcov, p, npar, delti, ftolhess, func);                  k2cpt++;
  }                }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");                /*}*/
     printf("# Scales (for hessian or gradient estimation)\n");            }
      for(i=1,jk=1; i <=nlstate; i++){          }
       for(j=1; j <=nlstate+ndeath; j++){        } /* end i */
         if (j!=i) {         
           fprintf(ficres,"%1d%1d",i,j);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
           printf("%1d%1d",i,j);        pstamp(ficresp);
           for(k=1; k<=ncovmodel;k++){        if  (cptcovn>0) {
             printf(" %.5e",delti[jk]);          fprintf(ficresp, "\n#********** Variable "); 
             fprintf(ficres," %.5e",delti[jk]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             jk++;          fprintf(ficresp, "**********\n#");
           }          fprintf(ficlog, "\n#********** Variable "); 
           printf("\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
           fprintf(ficres,"\n");          fprintf(ficlog, "**********\n#");
         }        }
       }        for(i=1; i<=nlstate;i++) 
      }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
            fprintf(ficresp, "\n");
     k=1;        
     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");        for(i=iagemin; i <= iagemax+3; i++){
     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");          if(i==iagemax+3){
     for(i=1;i<=npar;i++){            fprintf(ficlog,"Total");
       /*  if (k>nlstate) k=1;          }else{
       i1=(i-1)/(ncovmodel*nlstate)+1;            if(first==1){
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);              first=0;
       printf("%s%d%d",alph[k],i1,tab[i]);*/              printf("See log file for details...\n");
       fprintf(ficres,"%3d",i);            }
       printf("%3d",i);            fprintf(ficlog,"Age %d", i);
       for(j=1; j<=i;j++){          }
         fprintf(ficres," %.5e",matcov[i][j]);          for(jk=1; jk <=nlstate ; jk++){
         printf(" %.5e",matcov[i][j]);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       }              pp[jk] += freq[jk][m][i]; 
       fprintf(ficres,"\n");          }
       printf("\n");          for(jk=1; jk <=nlstate ; jk++){
       k++;            for(m=-1, pos=0; m <=0 ; m++)
     }              pos += freq[jk][m][i];
                if(pp[jk]>=1.e-10){
     while((c=getc(ficpar))=='#' && c!= EOF){              if(first==1){
       ungetc(c,ficpar);                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       fgets(line, MAXLINE, ficpar);              }
       puts(line);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       fputs(line,ficparo);            }else{
     }              if(first==1)
     ungetc(c,ficpar);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     estepm=0;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     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;          for(jk=1; jk <=nlstate ; jk++){
       fage = agemaxpar;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     }              pp[jk] += freq[jk][m][i];
              }       
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);            pos += pp[jk];
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);            posprop += prop[jk][i];
            }
     while((c=getc(ficpar))=='#' && c!= EOF){          for(jk=1; jk <=nlstate ; jk++){
     ungetc(c,ficpar);            if(pos>=1.e-5){
     fgets(line, MAXLINE, ficpar);              if(first==1)
     puts(line);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     fputs(line,ficparo);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   }            }else{
   ungetc(c,ficpar);              if(first==1)
                  printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   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( i <= iagemax){
                    if(pos>=1.e-5){
   while((c=getc(ficpar))=='#' && c!= EOF){                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     ungetc(c,ficpar);                /*probs[i][jk][j1]= pp[jk]/pos;*/
     fgets(line, MAXLINE, ficpar);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     puts(line);              }
     fputs(line,ficparo);              else
   }                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   ungetc(c,ficpar);            }
            }
           
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          for(jk=-1; jk <=nlstate+ndeath; jk++)
    dateprev2=anprev2+mprev2/12.+jprev2/365.;            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
   fscanf(ficpar,"pop_based=%d\n",&popbased);              if(first==1)
   fprintf(ficparo,"pop_based=%d\n",popbased);                  printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   fprintf(ficres,"pop_based=%d\n",popbased);                  fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                }
   while((c=getc(ficpar))=='#' && c!= EOF){          if(i <= iagemax)
     ungetc(c,ficpar);            fprintf(ficresp,"\n");
     fgets(line, MAXLINE, ficpar);          if(first==1)
     puts(line);            printf("Others in log...\n");
     fputs(line,ficparo);          fprintf(ficlog,"\n");
   }        }
   ungetc(c,ficpar);        /*}*/
     }
   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);    dateintmean=dateintsum/k2cpt; 
 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);   
 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);    fclose(ficresp);
     free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
 while((c=getc(ficpar))=='#' && c!= EOF){    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     ungetc(c,ficpar);    /* End of Freq */
     fgets(line, MAXLINE, ficpar);  }
     puts(line);  
     fputs(line,ficparo);  /************ 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)
   ungetc(c,ficpar);  {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);       in each health status at the date of interview (if between dateprev1 and dateprev2).
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);       We still use firstpass and lastpass as another selection.
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    */
    
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    int i, m, jk, j1, bool, z1,j;
   
 /*------------ gnuplot -------------*/    double **prop;
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);    double posprop; 
      double  y2; /* in fractional years */
 /*------------ free_vector  -------------*/    int iagemin, iagemax;
  chdir(path);    int first; /** to stop verbosity which is redirected to log file */
    
  free_ivector(wav,1,imx);    iagemin= (int) agemin;
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    iagemax= (int) agemax;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      /*pp=vector(1,nlstate);*/
  free_ivector(num,1,n);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
  free_vector(agedc,1,n);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    j1=0;
  fclose(ficparo);    
  fclose(ficres);    /*j=cptcoveff;*/
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
 /*--------- index.htm --------*/    
     first=1;
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
       /*for(i1=1; i1<=ncodemax[k1];i1++){
          j1++;*/
   /*--------------- Prevalence limit --------------*/        
          for (i=1; i<=nlstate; i++)  
   strcpy(filerespl,"pl");          for(m=iagemin; m <= iagemax+3; m++)
   strcat(filerespl,fileres);            prop[i][m]=0.0;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {       
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        for (i=1; i<=imx; i++) { /* Each individual */
   }          bool=1;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          if  (cptcovn>0) {
   fprintf(ficrespl,"#Prevalence limit\n");            for (z1=1; z1<=cptcoveff; z1++) 
   fprintf(ficrespl,"#Age ");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) 
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);                bool=0;
   fprintf(ficrespl,"\n");          } 
            if (bool==1) { 
   prlim=matrix(1,nlstate,1,nlstate);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                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); 
   k=0;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   agebase=ageminpar;                  /*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]]);*/
   agelim=agemaxpar;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   ftolpl=1.e-10;                  prop[s[m][i]][iagemax+3] += weight[i]; 
   i1=cptcoveff;                } 
   if (cptcovn < 1){i1=1;}              }
             } /* end selection of waves */
   for(cptcov=1;cptcov<=i1;cptcov++){          }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        }
         k=k+1;        for(i=iagemin; i <= iagemax+3; i++){  
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         fprintf(ficrespl,"\n#******");            posprop += prop[jk][i]; 
         for(j=1;j<=cptcoveff;j++)          } 
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          
         fprintf(ficrespl,"******\n");          for(jk=1; jk <=nlstate ; jk++){     
                    if( i <=  iagemax){ 
         for (age=agebase; age<=agelim; age++){              if(posprop>=1.e-5){ 
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                probs[i][jk][j1]= prop[jk][i]/posprop;
           fprintf(ficrespl,"%.0f",age );              } else{
           for(i=1; i<=nlstate;i++)                if(first==1){
           fprintf(ficrespl," %.5f", prlim[i][i]);                  first=0;
           fprintf(ficrespl,"\n");                  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]);
         }                }
       }              }
     }            } 
   fclose(ficrespl);          }/* end jk */ 
         }/* end i */ 
   /*------------- h Pij x at various ages ------------*/      /*} *//* end i1 */
      } /* end j1 */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    /*free_vector(pp,1,nlstate);*/
   }    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   printf("Computing pij: result on file '%s' \n", filerespij);  }  /* End of prevalence */
    
   stepsize=(int) (stepm+YEARM-1)/YEARM;  /************* Waves Concatenation ***************/
   /*if (stepm<=24) stepsize=2;*/  
   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)
   agelim=AGESUP;  {
   hstepm=stepsize*YEARM; /* Every year of age */    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */       Death is a valid wave (if date is known).
         mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   k=0;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   for(cptcov=1;cptcov<=i1;cptcov++){       and mw[mi+1][i]. dh depends on stepm.
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       */
       k=k+1;  
         fprintf(ficrespij,"\n#****** ");    int i, mi, m;
         for(j=1;j<=cptcoveff;j++)    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       double sum=0., jmean=0.;*/
         fprintf(ficrespij,"******\n");    int first;
            int j, k=0,jk, ju, jl;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    double sum=0.;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    first=0;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    jmin=100000;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    jmax=-1;
           oldm=oldms;savm=savms;    jmean=0.;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      for(i=1; i<=imx; i++){
           fprintf(ficrespij,"# Age");      mi=0;
           for(i=1; i<=nlstate;i++)      m=firstpass;
             for(j=1; j<=nlstate+ndeath;j++)      while(s[m][i] <= nlstate){
               fprintf(ficrespij," %1d-%1d",i,j);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
           fprintf(ficrespij,"\n");          mw[++mi][i]=m;
           for (h=0; h<=nhstepm; h++){        if(m >=lastpass)
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          break;
             for(i=1; i<=nlstate;i++)        else
               for(j=1; j<=nlstate+ndeath;j++)          m++;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      }/* end while */
             fprintf(ficrespij,"\n");      if (s[m][i] > nlstate){
           }        mi++;     /* Death is another wave */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /* if(mi==0)  never been interviewed correctly before death */
           fprintf(ficrespij,"\n");           /* Only death is a correct wave */
         }        mw[mi][i]=m;
     }      }
   }  
       wav[i]=mi;
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/      if(mi==0){
         nbwarn++;
   fclose(ficrespij);        if(first==0){
           printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           first=1;
   /*---------- Forecasting ------------------*/        }
   if((stepm == 1) && (strcmp(model,".")==0)){        if(first==1){
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],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);      } /* end mi==0 */
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    } /* End individuals */
     free_vector(weight,1,n);}  
   else{    for(i=1; i<=imx; i++){
     erreur=108;      for(mi=1; mi<wav[i];mi++){
     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);        if (stepm <=0)
   }          dh[mi][i]=1;
          else{
           if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   /*---------- Health expectancies and variances ------------*/            if (agedc[i] < 2*AGESUP) {
               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   strcpy(filerest,"t");              if(j==0) j=1;  /* Survives at least one month after exam */
   strcat(filerest,fileres);              else if(j<0){
   if((ficrest=fopen(filerest,"w"))==NULL) {                nberr++;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   }                j=1; /* Temporary Dangerous patch */
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                 fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
   strcpy(filerese,"e");              }
   strcat(filerese,fileres);              k=k+1;
   if((ficreseij=fopen(filerese,"w"))==NULL) {              if (j >= jmax){
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                jmax=j;
   }                ijmax=i;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);              }
               if (j <= jmin){
  strcpy(fileresv,"v");                jmin=j;
   strcat(fileresv,fileres);                ijmin=i;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {              }
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);              sum=sum+j;
   }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
   k=0;          }
   for(cptcov=1;cptcov<=i1;cptcov++){          else{
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       k=k+1;  /*        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]); */
       fprintf(ficrest,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)            k=k+1;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            if (j >= jmax) {
       fprintf(ficrest,"******\n");              jmax=j;
               ijmax=i;
       fprintf(ficreseij,"\n#****** ");            }
       for(j=1;j<=cptcoveff;j++)            else if (j <= jmin){
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              jmin=j;
       fprintf(ficreseij,"******\n");              ijmin=i;
             }
       fprintf(ficresvij,"\n#****** ");            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       for(j=1;j<=cptcoveff;j++)            /*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]);*/
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            if(j<0){
       fprintf(ficresvij,"******\n");              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]);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);              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]);
       oldm=oldms;savm=savms;            }
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);              sum=sum+j;
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          }
       oldm=oldms;savm=savms;          jk= j/stepm;
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);          jl= j -jk*stepm;
              ju= j -(jk+1)*stepm;
           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
              if(jl==0){
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");              dh[mi][i]=jk;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);              bh[mi][i]=0;
       fprintf(ficrest,"\n");            }else{ /* We want a negative bias in order to only have interpolation ie
                     * to avoid the price of an extra matrix product in likelihood */
       epj=vector(1,nlstate+1);              dh[mi][i]=jk+1;
       for(age=bage; age <=fage ;age++){              bh[mi][i]=ju;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            }
         if (popbased==1) {          }else{
           for(i=1; i<=nlstate;i++)            if(jl <= -ju){
             prlim[i][i]=probs[(int)age][i][k];              dh[mi][i]=jk;
         }              bh[mi][i]=jl;       /* bias is positive if real duration
                                           * is higher than the multiple of stepm and negative otherwise.
         fprintf(ficrest," %4.0f",age);                                   */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){            }
           for(i=1, epj[j]=0.;i <=nlstate;i++) {            else{
             epj[j] += prlim[i][i]*eij[i][j][(int)age];              dh[mi][i]=jk+1;
           }              bh[mi][i]=ju;
           epj[nlstate+1] +=epj[j];            }
         }            if(dh[mi][i]==0){
         for(i=1, vepp=0.;i <=nlstate;i++)              dh[mi][i]=1; /* At least one step */
           for(j=1;j <=nlstate;j++)              bh[mi][i]=ju; /* At least one step */
             vepp += vareij[i][j][(int)age];              /*  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);*/
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));            }
         for(j=1;j <=nlstate;j++){          } /* end if mle */
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));        }
         }      } /* end wave */
         fprintf(ficrest,"\n");    }
       }    jmean=sum/k;
     }    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
   }    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
    }
   fclose(ficreseij);  
   fclose(ficresvij);  /*********** Tricode ****************************/
   fclose(ficrest);  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   fclose(ficpar);  {
   free_vector(epj,1,nlstate+1);    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
      /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
   /*------- Variance limit prevalence------*/       * Boring subroutine which should only output nbcode[Tvar[j]][k]
      * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
   strcpy(fileresvpl,"vpl");     * nbcode[Tvar[j]][1]= 
   strcat(fileresvpl,fileres);    */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     exit(0);    int modmaxcovj=0; /* Modality max of covariates j */
   }    int cptcode=0; /* Modality max of covariates j */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    int modmincovj=0; /* Modality min of covariates j */
   
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){    cptcoveff=0; 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   
       k=k+1;    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
       fprintf(ficresvpl,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)    /* Loop on covariates without age and products */
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
       fprintf(ficresvpl,"******\n");      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 
       varpl=matrix(1,nlstate,(int) bage, (int) fage);                                 modality of this covariate Vj*/ 
       oldm=oldms;savm=savms;        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                                      * 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
   fclose(ficresvpl);                                        modality of the nth covariate of individual i. */
         if (ij > modmaxcovj)
   /*---------- End : free ----------------*/          modmaxcovj=ij; 
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        else if (ij < modmincovj) 
            modmincovj=ij; 
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        if ((ij < -1) && (ij > NCOVMAX)){
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
            exit(1);
          }else
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        /* 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
   free_matrix(matcov,1,npar,1,npar);           female is 1, then modmaxcovj=1.*/
   free_vector(delti,1,npar);      } /* end for loop on individuals i */
   free_matrix(agev,1,maxwav,1,imx);      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
       cptcode=modmaxcovj;
   if(erreur >0)      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
     printf("End of Imach with error or warning %d\n",erreur);     /*for (i=0; i<=cptcode; i++) {*/
   else   printf("End of Imach\n");      for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        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]);
   /* 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);*/        if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
   /*printf("Total time was %d uSec.\n", total_usecs);*/          if( k != -1){
   /*------ End -----------*/            ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th
                                covariate for which somebody answered excluding 
                                undefined. Usually 2: 0 and 1. */
  end:          }
 #ifdef windows          ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
   /* chdir(pathcd);*/                               covariate for which somebody answered including 
 #endif                               undefined. Usually 3: -1, 0 and 1. */
  /*system("wgnuplot graph.plt");*/        }
  /*system("../gp37mgw/wgnuplot graph.plt");*/        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
  /*system("cd ../gp37mgw");*/           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      } /* Ndum[-1] number of undefined modalities */
  strcpy(plotcmd,GNUPLOTPROGRAM);  
  strcat(plotcmd," ");      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
  strcat(plotcmd,optionfilegnuplot);      /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. 
  system(plotcmd);         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;
 #ifdef windows         There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
   while (z[0] != 'q') {         which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
     /* chdir(path); */         defining two dummy variables: variables V1_1 and V1_2.
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");         nbcode[Tvar[j]][ij]=k;
     scanf("%s",z);         nbcode[Tvar[j]][1]=0;
     if (z[0] == 'c') system("./imach");         nbcode[Tvar[j]][2]=1;
     else if (z[0] == 'e') system(optionfilehtm);         nbcode[Tvar[j]][3]=2;
     else if (z[0] == 'g') system(plotcmd);         To be continued (not working yet).
     else if (z[0] == 'q') exit(0);      */
   }      ij=0; /* ij is similar to i but can jump over null modalities */
 #endif      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(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");
     /* 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,"\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.png\"> <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.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\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></br>this page is important in order to visualize confidence intervals and especially correlation between disability and recovery</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,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,Tvar[Tage[k]])]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])];
           
       
           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,"\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 png small size 320, 240");
                       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.png\">\
   %s%d%1d%1d-%1d%1d.png</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.png\"> ",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.png\"",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 \"%s%d%1d%1d-%1d%1d.png\";replot;",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 fileres[], 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(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"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(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"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\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- 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.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">", 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) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",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(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"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(fileres,"cve"),subdirf2(fileres,"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(fileres,"stde"),subdirf2(fileres,"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(fileres,"v"),subdirf2(fileres,"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(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"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.png <br>\
   <img src=\"%s%d_%d.png\">",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.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      /* } /\* end i1 *\/ */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], 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;
   /*   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.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"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(fileres,"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*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*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.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         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 ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         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+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         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,");
       }
     }
     
     /*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.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"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(fileres,"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(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* 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.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\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 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<=2;ng++){ /* Number of graphics: first is probabilities second is incidence 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.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\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){
                if(ng==2)
                  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);
                else
                  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);
                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,Tvar[j-2])]);
                      ij++;
                    }
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                }
                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,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,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* 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,fileres);
     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,fileres);
     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 fileres[], 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.png\">");
     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 fileres[], 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.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\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,fileres);
       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,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           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,fileres);
       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(fileres,".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,fileres);
     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]\n", model)) !=EOF){
       if (num_filled != 1) {
         printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
         fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
         model[0]='\0';
         goto end;
       }
       else{
         if (model[0]=='+'){
           for(i=1; i<=strlen(model);i++)
             modeltemp[i-1]=model[i];
         }
         strcpy(model,modeltemp); 
       }
       printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout);
     }
     /* 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", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);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,fileres);
       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(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       printinghtmlmort(fileres,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(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,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(fileres, 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,fileres);
       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]][codtab[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,fileres);
       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,fileres);
       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,fileres);
       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,fileres);
       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]][codtab[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]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[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]][codtab[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; /* 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 e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               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",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];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               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,fileres);
       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]][codtab[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.1.36  
changed lines
  Added in v.1.198


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