Diff for /imach/src/imach.c between versions 1.20 and 1.177

version 1.20, 2002/02/20 17:22:01 version 1.177, 2015/01/03 18:40:56
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.177  2015/01/03 18:40:56  brouard
   individuals from different ages are interviewed on their health status    Summary: Still testing ilc32 on OSX
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.176  2015/01/03 16:45:04  brouard
   Health expectancies are computed from the transistions observed between    *** empty log message ***
   waves and are computed for each degree of severity of disability (number  
   of life states). More degrees you consider, more time is necessary to    Revision 1.175  2015/01/03 16:33:42  brouard
   reach the Maximum Likelihood of the parameters involved in the model.    *** empty log message ***
   The simplest model is the multinomial logistic model where pij is  
   the probabibility to be observed in state j at the second wave conditional    Revision 1.174  2015/01/03 16:15:49  brouard
   to be observed in state i at the first wave. Therefore the model is:    Summary: Still in cross-compilation
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'  
   is a covariate. If you want to have a more complex model than "constant and    Revision 1.173  2015/01/03 12:06:26  brouard
   age", you should modify the program where the markup    Summary: trying to detect cross-compilation
     *Covariates have to be included here again* invites you to do it.  
   More covariates you add, less is the speed of the convergence.    Revision 1.172  2014/12/27 12:07:47  brouard
     Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   The advantage that this computer programme claims, comes from that if the  
   delay between waves is not identical for each individual, or if some    Revision 1.171  2014/12/23 13:26:59  brouard
   individual missed an interview, the information is not rounded or lost, but    Summary: Back from Visual C
   taken into account using an interpolation or extrapolation.  
   hPijx is the probability to be    Still problem with utsname.h on Windows
   observed in state i at age x+h conditional to the observed state i at age  
   x. The delay 'h' can be split into an exact number (nh*stepm) of    Revision 1.170  2014/12/23 11:17:12  brouard
   unobserved intermediate  states. This elementary transition (by month or    Summary: Cleaning some \%% back to %%
   quarter trimester, semester or year) is model as a multinomial logistic.  
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    The escape was mandatory for a specific compiler (which one?), but too many warnings.
   and the contribution of each individual to the likelihood is simply hPijx.  
     Revision 1.169  2014/12/22 23:08:31  brouard
   Also this programme outputs the covariance matrix of the parameters but also    Summary: 0.98p
   of the life expectancies. It also computes the prevalence limits.  
      Outputs some informations on compiler used, OS etc. Testing on different platforms.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.168  2014/12/22 15:17:42  brouard
   This software have been partly granted by Euro-REVES, a concerted action    Summary: update
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.167  2014/12/22 13:50:56  brouard
   software can be distributed freely for non commercial use. Latest version    Summary: Testing uname and compiler version and if compiled 32 or 64
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Testing on Linux 64
    
 #include <math.h>    Revision 1.166  2014/12/22 11:40:47  brouard
 #include <stdio.h>    *** empty log message ***
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.165  2014/12/16 11:20:36  brouard
     Summary: After compiling on Visual C
 #define MAXLINE 256  
 #define FILENAMELENGTH 80    * imach.c (Module): Merging 1.61 to 1.162
 /*#define DEBUG*/  
 #define windows    Revision 1.164  2014/12/16 10:52:11  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     * imach.c (Module): Merging 1.61 to 1.162
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.163  2014/12/16 10:30:11  brouard
     * imach.c (Module): Merging 1.61 to 1.162
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.162  2014/09/25 11:43:39  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Summary: temporary backup 0.99!
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.1  2014/09/16 11:06:58  brouard
 #define YEARM 12. /* Number of months per year */    Summary: With some code (wrong) for nlopt
 #define AGESUP 130  
 #define AGEBASE 40    Author:
   
     Revision 1.161  2014/09/15 20:41:41  brouard
 int nvar;    Summary: Problem with macro SQR on Intel compiler
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.160  2014/09/02 09:24:05  brouard
 int nlstate=2; /* Number of live states */    *** empty log message ***
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.159  2014/09/01 10:34:10  brouard
 int popbased=0;    Summary: WIN32
     Author: Brouard
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.158  2014/08/27 17:11:51  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    *** empty log message ***
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.157  2014/08/27 16:26:55  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Summary: Preparing windows Visual studio version
 double jmean; /* Mean space between 2 waves */    Author: Brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    In order to compile on Visual studio, time.h is now correct and time_t
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    and tm struct should be used. difftime should be used but sometimes I
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    just make the differences in raw time format (time(&now).
 FILE *ficreseij;    Trying to suppress #ifdef LINUX
   char filerese[FILENAMELENGTH];    Add xdg-open for __linux in order to open default browser.
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    Revision 1.156  2014/08/25 20:10:10  brouard
  FILE  *ficresvpl;    *** empty log message ***
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.155  2014/08/25 18:32:34  brouard
 #define NR_END 1    Summary: New compile, minor changes
 #define FREE_ARG char*    Author: Brouard
 #define FTOL 1.0e-10  
     Revision 1.154  2014/06/20 17:32:08  brouard
 #define NRANSI    Summary: Outputs now all graphs of convergence to period prevalence
 #define ITMAX 200  
     Revision 1.153  2014/06/20 16:45:46  brouard
 #define TOL 2.0e-4    Summary: If 3 live state, convergence to period prevalence on same graph
     Author: Brouard
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.152  2014/06/18 17:54:09  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Summary: open browser, use gnuplot on same dir than imach if not found in the path
   
 #define GOLD 1.618034    Revision 1.151  2014/06/18 16:43:30  brouard
 #define GLIMIT 100.0    *** empty log message ***
 #define TINY 1.0e-20  
     Revision 1.150  2014/06/18 16:42:35  brouard
 static double maxarg1,maxarg2;    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Author: brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.149  2014/06/18 15:51:14  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Summary: Some fixes in parameter files errors
 #define rint(a) floor(a+0.5)    Author: Nicolas Brouard
   
 static double sqrarg;    Revision 1.148  2014/06/17 17:38:48  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Summary: Nothing new
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Author: Brouard
   
 int imx;    Just a new packaging for OS/X version 0.98nS
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.147  2014/06/16 10:33:11  brouard
     *** empty log message ***
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.146  2014/06/16 10:20:28  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Summary: Merge
 double **pmmij, ***probs, ***mobaverage;    Author: Brouard
 double dateintmean=0;  
     Merge, before building revised version.
 double *weight;  
 int **s; /* Status */    Revision 1.145  2014/06/10 21:23:15  brouard
 double *agedc, **covar, idx;    Summary: Debugging with valgrind
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Author: Nicolas Brouard
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Lot of changes in order to output the results with some covariates
 double ftolhess; /* Tolerance for computing hessian */    After the Edimburgh REVES conference 2014, it seems mandatory to
     improve the code.
 /**************** split *************************/    No more memory valgrind error but a lot has to be done in order to
 static  int split( char *path, char *dirc, char *name )    continue the work of splitting the code into subroutines.
 {    Also, decodemodel has been improved. Tricode is still not
    char *s;                             /* pointer */    optimal. nbcode should be improved. Documentation has been added in
    int  l1, l2;                         /* length counters */    the source code.
   
    l1 = strlen( path );                 /* length of path */    Revision 1.143  2014/01/26 09:45:38  brouard
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
    s = strrchr( path, '\\' );           /* find last / */  
    if ( s == NULL ) {                   /* no directory, so use current */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #if     defined(__bsd__)                /* get current working directory */    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
       extern char       *getwd( );  
     Revision 1.142  2014/01/26 03:57:36  brouard
       if ( getwd( dirc ) == NULL ) {    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 #else  
       extern char       *getcwd( );    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.141  2014/01/26 02:42:01  brouard
 #endif    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
          return( GLOCK_ERROR_GETCWD );  
       }    Revision 1.140  2011/09/02 10:37:54  brouard
       strcpy( name, path );             /* we've got it */    Summary: times.h is ok with mingw32 now.
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Revision 1.139  2010/06/14 07:50:17  brouard
       l2 = strlen( s );                 /* length of filename */    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Revision 1.138  2010/04/30 18:19:40  brouard
       dirc[l1-l2] = 0;                  /* add zero */    *** empty log message ***
    }  
    l1 = strlen( dirc );                 /* length of directory */    Revision 1.137  2010/04/29 18:11:38  brouard
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    (Module): Checking covariates for more complex models
    return( 0 );                         /* we're done */    than V1+V2. A lot of change to be done. Unstable.
 }  
     Revision 1.136  2010/04/26 20:30:53  brouard
     (Module): merging some libgsl code. Fixing computation
 /******************************************/    of likelione (using inter/intrapolation if mle = 0) in order to
     get same likelihood as if mle=1.
 void replace(char *s, char*t)    Some cleaning of code and comments added.
 {  
   int i;    Revision 1.135  2009/10/29 15:33:14  brouard
   int lg=20;    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   i=0;  
   lg=strlen(t);    Revision 1.134  2009/10/29 13:18:53  brouard
   for(i=0; i<= lg; i++) {    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Revision 1.133  2009/07/06 10:21:25  brouard
   }    just nforces
 }  
     Revision 1.132  2009/07/06 08:22:05  brouard
 int nbocc(char *s, char occ)    Many tings
 {  
   int i,j=0;    Revision 1.131  2009/06/20 16:22:47  brouard
   int lg=20;    Some dimensions resccaled
   i=0;  
   lg=strlen(s);    Revision 1.130  2009/05/26 06:44:34  brouard
   for(i=0; i<= lg; i++) {    (Module): Max Covariate is now set to 20 instead of 8. A
   if  (s[i] == occ ) j++;    lot of cleaning with variables initialized to 0. Trying to make
   }    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   return j;  
 }    Revision 1.129  2007/08/31 13:49:27  lievre
     Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 void cutv(char *u,char *v, char*t, char occ)  
 {    Revision 1.128  2006/06/30 13:02:05  brouard
   int i,lg,j,p=0;    (Module): Clarifications on computing e.j
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    Revision 1.127  2006/04/28 18:11:50  brouard
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    (Module): Yes the sum of survivors was wrong since
   }    imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
   lg=strlen(t);    (Module): In order to speed up (in case of numerous covariates) we
   for(j=0; j<p; j++) {    compute health expectancies (without variances) in a first step
     (u[j] = t[j]);    and then all the health expectancies with variances or standard
   }    deviation (needs data from the Hessian matrices) which slows the
      u[p]='\0';    computation.
     In the future we should be able to stop the program is only health
    for(j=0; j<= lg; j++) {    expectancies and graph are needed without standard deviations.
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }    Revision 1.126  2006/04/28 17:23:28  brouard
 }    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
 /********************** nrerror ********************/    loop. Now we define nhstepma in the age loop.
     Version 0.98h
 void nrerror(char error_text[])  
 {    Revision 1.125  2006/04/04 15:20:31  lievre
   fprintf(stderr,"ERREUR ...\n");    Errors in calculation of health expectancies. Age was not initialized.
   fprintf(stderr,"%s\n",error_text);    Forecasting file added.
   exit(1);  
 }    Revision 1.124  2006/03/22 17:13:53  lievre
 /*********************** vector *******************/    Parameters are printed with %lf instead of %f (more numbers after the comma).
 double *vector(int nl, int nh)    The log-likelihood is printed in the log file
 {  
   double *v;    Revision 1.123  2006/03/20 10:52:43  brouard
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    * imach.c (Module): <title> changed, corresponds to .htm file
   if (!v) nrerror("allocation failure in vector");    name. <head> headers where missing.
   return v-nl+NR_END;  
 }    * imach.c (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
 /************************ free vector ******************/    otherwise the weight is truncated).
 void free_vector(double*v, int nl, int nh)    Modification of warning when the covariates values are not 0 or
 {    1.
   free((FREE_ARG)(v+nl-NR_END));    Version 0.98g
 }  
     Revision 1.122  2006/03/20 09:45:41  brouard
 /************************ivector *******************************/    (Module): Weights can have a decimal point as for
 int *ivector(long nl,long nh)    English (a comma might work with a correct LC_NUMERIC environment,
 {    otherwise the weight is truncated).
   int *v;    Modification of warning when the covariates values are not 0 or
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    1.
   if (!v) nrerror("allocation failure in ivector");    Version 0.98g
   return v-nl+NR_END;  
 }    Revision 1.121  2006/03/16 17:45:01  lievre
     * imach.c (Module): Comments concerning covariates added
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)    * imach.c (Module): refinements in the computation of lli if
 {    status=-2 in order to have more reliable computation if stepm is
   free((FREE_ARG)(v+nl-NR_END));    not 1 month. Version 0.98f
 }  
     Revision 1.120  2006/03/16 15:10:38  lievre
 /******************* imatrix *******************************/    (Module): refinements in the computation of lli if
 int **imatrix(long nrl, long nrh, long ncl, long nch)    status=-2 in order to have more reliable computation if stepm is
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    not 1 month. Version 0.98f
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Revision 1.119  2006/03/15 17:42:26  brouard
   int **m;    (Module): Bug if status = -2, the loglikelihood was
      computed as likelihood omitting the logarithm. Version O.98e
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    Revision 1.118  2006/03/14 18:20:07  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): varevsij Comments added explaining the second
   m += NR_END;    table of variances if popbased=1 .
   m -= nrl;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
      (Module): Function pstamp added
      (Module): Version 0.98d
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    Revision 1.117  2006/03/14 17:16:22  brouard
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    (Module): varevsij Comments added explaining the second
   m[nrl] += NR_END;    table of variances if popbased=1 .
   m[nrl] -= ncl;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
      (Module): Function pstamp added
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    (Module): Version 0.98d
    
   /* return pointer to array of pointers to rows */    Revision 1.116  2006/03/06 10:29:27  brouard
   return m;    (Module): Variance-covariance wrong links and
 }    varian-covariance of ej. is needed (Saito).
   
 /****************** free_imatrix *************************/    Revision 1.115  2006/02/27 12:17:45  brouard
 void free_imatrix(m,nrl,nrh,ncl,nch)    (Module): One freematrix added in mlikeli! 0.98c
       int **m;  
       long nch,ncl,nrh,nrl;    Revision 1.114  2006/02/26 12:57:58  brouard
      /* free an int matrix allocated by imatrix() */    (Module): Some improvements in processing parameter
 {    filename with strsep.
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));    Revision 1.113  2006/02/24 14:20:24  brouard
 }    (Module): Memory leaks checks with valgrind and:
     datafile was not closed, some imatrix were not freed and on matrix
 /******************* matrix *******************************/    allocation too.
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {    Revision 1.112  2006/01/30 09:55:26  brouard
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   double **m;  
     Revision 1.111  2006/01/25 20:38:18  brouard
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    (Module): Lots of cleaning and bugs added (Gompertz)
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): Comments can be added in data file. Missing date values
   m += NR_END;    can be a simple dot '.'.
   m -= nrl;  
     Revision 1.110  2006/01/25 00:51:50  brouard
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    (Module): Lots of cleaning and bugs added (Gompertz)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.109  2006/01/24 19:37:15  brouard
   m[nrl] -= ncl;    (Module): Comments (lines starting with a #) are allowed in data.
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Revision 1.108  2006/01/19 18:05:42  lievre
   return m;    Gnuplot problem appeared...
 }    To be fixed
   
 /*************************free matrix ************************/    Revision 1.107  2006/01/19 16:20:37  brouard
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    Test existence of gnuplot in imach path
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Revision 1.106  2006/01/19 13:24:36  brouard
   free((FREE_ARG)(m+nrl-NR_END));    Some cleaning and links added in html output
 }  
     Revision 1.105  2006/01/05 20:23:19  lievre
 /******************* ma3x *******************************/    *** empty log message ***
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {    Revision 1.104  2005/09/30 16:11:43  lievre
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    (Module): sump fixed, loop imx fixed, and simplifications.
   double ***m;    (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
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    (instead of missing=-1 in earlier versions) and his/her
   if (!m) nrerror("allocation failure 1 in matrix()");    contributions to the likelihood is 1 - Prob of dying from last
   m += NR_END;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   m -= nrl;    the healthy state at last known wave). Version is 0.98
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Revision 1.103  2005/09/30 15:54:49  lievre
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    (Module): sump fixed, loop imx fixed, and simplifications.
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.102  2004/09/15 17:31:30  brouard
     Add the possibility to read data file including tab characters.
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
     Revision 1.101  2004/09/15 10:38:38  brouard
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    Fix on curr_time
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;    Revision 1.100  2004/07/12 18:29:06  brouard
   m[nrl][ncl] -= nll;    Add version for Mac OS X. Just define UNIX in Makefile
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;    Revision 1.99  2004/06/05 08:57:40  brouard
      *** empty log message ***
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    Revision 1.98  2004/05/16 15:05:56  brouard
     for (j=ncl+1; j<=nch; j++)    New version 0.97 . First attempt to estimate force of mortality
       m[i][j]=m[i][j-1]+nlay;    directly from the data i.e. without the need of knowing the health
   }    state at each age, but using a Gompertz model: log u =a + b*age .
   return m;    This is the basic analysis of mortality and should be done before any
 }    other analysis, in order to test if the mortality estimated from the
     cross-longitudinal survey is different from the mortality estimated
 /*************************free ma3x ************************/    from other sources like vital statistic data.
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {    The same imach parameter file can be used but the option for mle should be -3.
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Agnès, who wrote this part of the code, tried to keep most of the
   free((FREE_ARG)(m+nrl-NR_END));    former routines in order to include the new code within the former code.
 }  
     The output is very simple: only an estimate of the intercept and of
 /***************** f1dim *************************/    the slope with 95% confident intervals.
 extern int ncom;  
 extern double *pcom,*xicom;    Current limitations:
 extern double (*nrfunc)(double []);    A) Even if you enter covariates, i.e. with the
      model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 double f1dim(double x)    B) There is no computation of Life Expectancy nor Life Table.
 {  
   int j;    Revision 1.97  2004/02/20 13:25:42  lievre
   double f;    Version 0.96d. Population forecasting command line is (temporarily)
   double *xt;    suppressed.
    
   xt=vector(1,ncom);    Revision 1.96  2003/07/15 15:38:55  brouard
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   f=(*nrfunc)(xt);    rewritten within the same printf. Workaround: many printfs.
   free_vector(xt,1,ncom);  
   return f;    Revision 1.95  2003/07/08 07:54:34  brouard
 }    * imach.c (Repository):
     (Repository): Using imachwizard code to output a more meaningful covariance
 /*****************brent *************************/    matrix (cov(a12,c31) instead of numbers.
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {    Revision 1.94  2003/06/27 13:00:02  brouard
   int iter;    Just cleaning
   double a,b,d,etemp;  
   double fu,fv,fw,fx;    Revision 1.93  2003/06/25 16:33:55  brouard
   double ftemp;    (Module): On windows (cygwin) function asctime_r doesn't
   double p,q,r,tol1,tol2,u,v,w,x,xm;    exist so I changed back to asctime which exists.
   double e=0.0;    (Module): Version 0.96b
    
   a=(ax < cx ? ax : cx);    Revision 1.92  2003/06/25 16:30:45  brouard
   b=(ax > cx ? ax : cx);    (Module): On windows (cygwin) function asctime_r doesn't
   x=w=v=bx;    exist so I changed back to asctime which exists.
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {    Revision 1.91  2003/06/25 15:30:29  brouard
     xm=0.5*(a+b);    * imach.c (Repository): Duplicated warning errors corrected.
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    (Repository): Elapsed time after each iteration is now output. It
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    helps to forecast when convergence will be reached. Elapsed time
     printf(".");fflush(stdout);    is stamped in powell.  We created a new html file for the graphs
 #ifdef DEBUG    concerning matrix of covariance. It has extension -cov.htm.
     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);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    Revision 1.90  2003/06/24 12:34:15  brouard
 #endif    (Module): Some bugs corrected for windows. Also, when
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    mle=-1 a template is output in file "or"mypar.txt with the design
       *xmin=x;    of the covariance matrix to be input.
       return fx;  
     }    Revision 1.89  2003/06/24 12:30:52  brouard
     ftemp=fu;    (Module): Some bugs corrected for windows. Also, when
     if (fabs(e) > tol1) {    mle=-1 a template is output in file "or"mypar.txt with the design
       r=(x-w)*(fx-fv);    of the covariance matrix to be input.
       q=(x-v)*(fx-fw);  
       p=(x-v)*q-(x-w)*r;    Revision 1.88  2003/06/23 17:54:56  brouard
       q=2.0*(q-r);    * 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.
       if (q > 0.0) p = -p;  
       q=fabs(q);    Revision 1.87  2003/06/18 12:26:01  brouard
       etemp=e;    Version 0.96
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    Revision 1.86  2003/06/17 20:04:08  brouard
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    (Module): Change position of html and gnuplot routines and added
       else {    routine fileappend.
         d=p/q;  
         u=x+d;    Revision 1.85  2003/06/17 13:12:43  brouard
         if (u-a < tol2 || b-u < tol2)    * imach.c (Repository): Check when date of death was earlier that
           d=SIGN(tol1,xm-x);    current date of interview. It may happen when the death was just
       }    prior to the death. In this case, dh was negative and likelihood
     } else {    was wrong (infinity). We still send an "Error" but patch by
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    assuming that the date of death was just one stepm after the
     }    interview.
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    (Repository): Because some people have very long ID (first column)
     fu=(*f)(u);    we changed int to long in num[] and we added a new lvector for
     if (fu <= fx) {    memory allocation. But we also truncated to 8 characters (left
       if (u >= x) a=x; else b=x;    truncation)
       SHFT(v,w,x,u)    (Repository): No more line truncation errors.
         SHFT(fv,fw,fx,fu)  
         } else {    Revision 1.84  2003/06/13 21:44:43  brouard
           if (u < x) a=u; else b=u;    * imach.c (Repository): Replace "freqsummary" at a correct
           if (fu <= fw || w == x) {    place. It differs from routine "prevalence" which may be called
             v=w;    many times. Probs is memory consuming and must be used with
             w=u;    parcimony.
             fv=fw;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {    Revision 1.83  2003/06/10 13:39:11  lievre
             v=u;    *** empty log message ***
             fv=fu;  
           }    Revision 1.82  2003/06/05 15:57:20  brouard
         }    Add log in  imach.c and  fullversion number is now printed.
   }  
   nrerror("Too many iterations in brent");  */
   *xmin=x;  /*
   return fx;     Interpolated Markov Chain
 }  
     Short summary of the programme:
 /****************** mnbrak ***********************/    
     This program computes Healthy Life Expectancies from
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
             double (*func)(double))    first survey ("cross") where individuals from different ages are
 {    interviewed on their health status or degree of disability (in the
   double ulim,u,r,q, dum;    case of a health survey which is our main interest) -2- at least a
   double fu;    second wave of interviews ("longitudinal") which measure each change
      (if any) in individual health status.  Health expectancies are
   *fa=(*func)(*ax);    computed from the time spent in each health state according to a
   *fb=(*func)(*bx);    model. More health states you consider, more time is necessary to reach the
   if (*fb > *fa) {    Maximum Likelihood of the parameters involved in the model.  The
     SHFT(dum,*ax,*bx,dum)    simplest model is the multinomial logistic model where pij is the
       SHFT(dum,*fb,*fa,dum)    probability to be observed in state j at the second wave
       }    conditional to be observed in state i at the first wave. Therefore
   *cx=(*bx)+GOLD*(*bx-*ax);    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   *fc=(*func)(*cx);    'age' is age and 'sex' is a covariate. If you want to have a more
   while (*fb > *fc) {    complex model than "constant and age", you should modify the program
     r=(*bx-*ax)*(*fb-*fc);    where the markup *Covariates have to be included here again* invites
     q=(*bx-*cx)*(*fb-*fa);    you to do it.  More covariates you add, slower the
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    convergence.
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  
     ulim=(*bx)+GLIMIT*(*cx-*bx);    The advantage of this computer programme, compared to a simple
     if ((*bx-u)*(u-*cx) > 0.0) {    multinomial logistic model, is clear when the delay between waves is not
       fu=(*func)(u);    identical for each individual. Also, if a individual missed an
     } else if ((*cx-u)*(u-ulim) > 0.0) {    intermediate interview, the information is lost, but taken into
       fu=(*func)(u);    account using an interpolation or extrapolation.  
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    hPijx is the probability to be observed in state i at age x+h
           SHFT(*fb,*fc,fu,(*func)(u))    conditional to the observed state i at age x. The delay 'h' can be
           }    split into an exact number (nh*stepm) of unobserved intermediate
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    states. This elementary transition (by month, quarter,
       u=ulim;    semester or year) is modelled as a multinomial logistic.  The hPx
       fu=(*func)(u);    matrix is simply the matrix product of nh*stepm elementary matrices
     } else {    and the contribution of each individual to the likelihood is simply
       u=(*cx)+GOLD*(*cx-*bx);    hPijx.
       fu=(*func)(u);  
     }    Also this programme outputs the covariance matrix of the parameters but also
     SHFT(*ax,*bx,*cx,u)    of the life expectancies. It also computes the period (stable) prevalence. 
       SHFT(*fa,*fb,*fc,fu)    
       }    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 }             Institut national d'études démographiques, Paris.
     This software have been partly granted by Euro-REVES, a concerted action
 /*************** linmin ************************/    from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
 int ncom;    software can be distributed freely for non commercial use. Latest version
 double *pcom,*xicom;    can be accessed at http://euroreves.ined.fr/imach .
 double (*nrfunc)(double []);  
      Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 {    
   double brent(double ax, double bx, double cx,    **********************************************************************/
                double (*f)(double), double tol, double *xmin);  /*
   double f1dim(double x);    main
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    read parameterfile
               double *fc, double (*func)(double));    read datafile
   int j;    concatwav
   double xx,xmin,bx,ax;    freqsummary
   double fx,fb,fa;    if (mle >= 1)
        mlikeli
   ncom=n;    print results files
   pcom=vector(1,n);    if mle==1 
   xicom=vector(1,n);       computes hessian
   nrfunc=func;    read end of parameter file: agemin, agemax, bage, fage, estepm
   for (j=1;j<=n;j++) {        begin-prev-date,...
     pcom[j]=p[j];    open gnuplot file
     xicom[j]=xi[j];    open html file
   }    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
   ax=0.0;     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
   xx=1.0;                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      freexexit2 possible for memory heap.
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG    h Pij x                         | pij_nom  ficrestpij
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
 #endif         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
   for (j=1;j<=n;j++) {         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
     xi[j] *= xmin;  
     p[j] += xi[j];         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
   }         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
   free_vector(xicom,1,n);    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   free_vector(pcom,1,n);     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
 }     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   
 /*************** powell ************************/    forecasting if prevfcast==1 prevforecast call prevalence()
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    health expectancies
             double (*func)(double []))    Variance-covariance of DFLE
 {    prevalence()
   void linmin(double p[], double xi[], int n, double *fret,     movingaverage()
               double (*func)(double []));    varevsij() 
   int i,ibig,j;    if popbased==1 varevsij(,popbased)
   double del,t,*pt,*ptt,*xit;    total life expectancies
   double fp,fptt;    Variance of period (stable) prevalence
   double *xits;   end
   pt=vector(1,n);  */
   ptt=vector(1,n);  
   xit=vector(1,n);  #define POWELL /* Instead of NLOPT */
   xits=vector(1,n);  
   *fret=(*func)(p);  #include <math.h>
   for (j=1;j<=n;j++) pt[j]=p[j];  #include <stdio.h>
   for (*iter=1;;++(*iter)) {  #include <stdlib.h>
     fp=(*fret);  #include <string.h>
     ibig=0;  
     del=0.0;  #ifdef _WIN32
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  #include <io.h>
     for (i=1;i<=n;i++)  #include <windows.h>
       printf(" %d %.12f",i, p[i]);  #include <tchar.h>
     printf("\n");  #else
     for (i=1;i<=n;i++) {  #include <unistd.h>
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  #endif
       fptt=(*fret);  
 #ifdef DEBUG  #include <limits.h>
       printf("fret=%lf \n",*fret);  #include <sys/types.h>
 #endif  
       printf("%d",i);fflush(stdout);  #if defined(__GNUC__)
       linmin(p,xit,n,fret,func);  #include <sys/utsname.h> /* Doesn't work on Windows */
       if (fabs(fptt-(*fret)) > del) {  #endif
         del=fabs(fptt-(*fret));  
         ibig=i;  #include <sys/stat.h>
       }  #include <errno.h>
 #ifdef DEBUG  /* extern int errno; */
       printf("%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {  /* #ifdef LINUX */
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  /* #include <time.h> */
         printf(" x(%d)=%.12e",j,xit[j]);  /* #include "timeval.h" */
       }  /* #else */
       for(j=1;j<=n;j++)  /* #include <sys/time.h> */
         printf(" p=%.12e",p[j]);  /* #endif */
       printf("\n");  
 #endif  #include <time.h>
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #ifdef GSL
 #ifdef DEBUG  #include <gsl/gsl_errno.h>
       int k[2],l;  #include <gsl/gsl_multimin.h>
       k[0]=1;  #endif
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++)  #ifdef NLOPT
         printf(" %.12e",p[j]);  #include <nlopt.h>
       printf("\n");  typedef struct {
       for(l=0;l<=1;l++) {    double (* function)(double [] );
         for (j=1;j<=n;j++) {  } myfunc_data ;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  #endif
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  
         }  /* #include <libintl.h> */
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  /* #define _(String) gettext (String) */
       }  
 #endif  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   
   #define GNUPLOTPROGRAM "gnuplot"
       free_vector(xit,1,n);  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       free_vector(xits,1,n);  #define FILENAMELENGTH 132
       free_vector(ptt,1,n);  
       free_vector(pt,1,n);  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       return;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
     for (j=1;j<=n;j++) {  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
       ptt[j]=2.0*p[j]-pt[j];  
       xit[j]=p[j]-pt[j];  #define NINTERVMAX 8
       pt[j]=p[j];  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
     }  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
     fptt=(*func)(ptt);  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
     if (fptt < fp) {  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  #define MAXN 20000
       if (t < 0.0) {  #define YEARM 12. /**< Number of months per year */
         linmin(p,xit,n,fret,func);  #define AGESUP 130
         for (j=1;j<=n;j++) {  #define AGEBASE 40
           xi[j][ibig]=xi[j][n];  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
           xi[j][n]=xit[j];  #ifdef _WIN32
         }  #define DIRSEPARATOR '\\'
 #ifdef DEBUG  #define CHARSEPARATOR "\\"
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #define ODIRSEPARATOR '/'
         for(j=1;j<=n;j++)  #else
           printf(" %.12e",xit[j]);  #define DIRSEPARATOR '/'
         printf("\n");  #define CHARSEPARATOR "/"
 #endif  #define ODIRSEPARATOR '\\'
       }  #endif
     }  
   }  /* $Id$ */
 }  /* $State$ */
   
 /**** Prevalence limit ****************/  char version[]="Imach version 0.98p, December 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
   char fullversion[]="$Revision$ $Date$"; 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  char strstart[80];
 {  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
      matrix by transitions matrix until convergence is reached */  int nvar=0, nforce=0; /* Number of variables, number of forces */
   /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   int i, ii,j,k;  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
   double min, max, maxmin, maxmax,sumnew=0.;  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
   double **matprod2();  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
   double **out, cov[NCOVMAX], **pmij();  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
   double **newm;  int cptcovprodnoage=0; /**< Number of covariate products without age */   
   double agefin, delaymax=50 ; /* Max number of years to converge */  int cptcoveff=0; /* Total number of covariates to vary for printing results */
   int cptcov=0; /* Working variable */
   for (ii=1;ii<=nlstate+ndeath;ii++)  int npar=NPARMAX;
     for (j=1;j<=nlstate+ndeath;j++){  int nlstate=2; /* Number of live states */
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  int ndeath=1; /* Number of dead states */
     }  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
    cov[1]=1.;  
    int *wav; /* Number of waves for this individuual 0 is possible */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  int maxwav=0; /* Maxim number of waves */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     newm=savm;  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
     /* Covariates have to be included here again */  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
      cov[2]=agefin;                     to the likelihood and the sum of weights (done by funcone)*/
    int mle=1, weightopt=0;
       for (k=1; k<=cptcovn;k++) {  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       }             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       for (k=1; k<=cptcovage;k++)  int countcallfunc=0;  /* Count the number of calls to func */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  double jmean=1; /* Mean space between 2 waves */
       for (k=1; k<=cptcovprod;k++)  double **matprod2(); /* test */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  /*FILE *fic ; */ /* Used in readdata only */
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog, *ficrespow;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  int globpr=0; /* Global variable for printing or not */
   double fretone; /* Only one call to likelihood */
     savm=oldm;  long ipmx=0; /* Number of contributions */
     oldm=newm;  double sw; /* Sum of weights */
     maxmax=0.;  char filerespow[FILENAMELENGTH];
     for(j=1;j<=nlstate;j++){  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       min=1.;  FILE *ficresilk;
       max=0.;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       for(i=1; i<=nlstate; i++) {  FILE *ficresprobmorprev;
         sumnew=0;  FILE *fichtm, *fichtmcov; /* Html File */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  FILE *ficreseij;
         prlim[i][j]= newm[i][j]/(1-sumnew);  char filerese[FILENAMELENGTH];
         max=FMAX(max,prlim[i][j]);  FILE *ficresstdeij;
         min=FMIN(min,prlim[i][j]);  char fileresstde[FILENAMELENGTH];
       }  FILE *ficrescveij;
       maxmin=max-min;  char filerescve[FILENAMELENGTH];
       maxmax=FMAX(maxmax,maxmin);  FILE  *ficresvij;
     }  char fileresv[FILENAMELENGTH];
     if(maxmax < ftolpl){  FILE  *ficresvpl;
       return prlim;  char fileresvpl[FILENAMELENGTH];
     }  char title[MAXLINE];
   }  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 }  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 /*************** transition probabilities ***************/  char command[FILENAMELENGTH];
   int  outcmd=0;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  
 {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   double s1, s2;  
   /*double t34;*/  char filelog[FILENAMELENGTH]; /* Log file */
   int i,j,j1, nc, ii, jj;  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
     for(i=1; i<= nlstate; i++){  char popfile[FILENAMELENGTH];
     for(j=1; j<i;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  /* struct timezone tzp; */
       }  /* extern int gettimeofday(); */
       ps[i][j]=s2;  struct tm tml, *gmtime(), *localtime();
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }  extern time_t time();
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  struct tm start_time, end_time, curr_time, last_time, forecast_time;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  struct tm tm;
       }  
       ps[i][j]=(s2);  char strcurr[80], strfor[80];
     }  
   }  char *endptr;
     /*ps[3][2]=1;*/  long lval;
   double dval;
   for(i=1; i<= nlstate; i++){  
      s1=0;  #define NR_END 1
     for(j=1; j<i; j++)  #define FREE_ARG char*
       s1+=exp(ps[i][j]);  #define FTOL 1.0e-10
     for(j=i+1; j<=nlstate+ndeath; j++)  
       s1+=exp(ps[i][j]);  #define NRANSI 
     ps[i][i]=1./(s1+1.);  #define ITMAX 200 
     for(j=1; j<i; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  #define TOL 2.0e-4 
     for(j=i+1; j<=nlstate+ndeath; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  #define CGOLD 0.3819660 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  #define ZEPS 1.0e-10 
   } /* end i */  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  #define GOLD 1.618034 
     for(jj=1; jj<= nlstate+ndeath; jj++){  #define GLIMIT 100.0 
       ps[ii][jj]=0;  #define TINY 1.0e-20 
       ps[ii][ii]=1;  
     }  static double maxarg1,maxarg2;
   }  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     for(jj=1; jj<= nlstate+ndeath; jj++){  #define rint(a) floor(a+0.5)
      printf("%lf ",ps[ii][jj]);  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
    }  /* #define mytinydouble 1.0e-16 */
     printf("\n ");  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
     }  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
     printf("\n ");printf("%lf ",cov[2]);*/  /* static double dsqrarg; */
 /*  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  static double sqrarg;
   goto end;*/  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     return ps;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 }  int agegomp= AGEGOMP;
   
 /**************** Product of 2 matrices ******************/  int imx; 
   int stepm=1;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  /* Stepm, step in month: minimum step interpolation*/
 {  
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  int estepm;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   /* in, b, out are matrice of pointers which should have been initialized  
      before: only the contents of out is modified. The function returns  int m,nb;
      a pointer to pointers identical to out */  long *num;
   long i, j, k;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   for(i=nrl; i<= nrh; i++)  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     for(k=ncolol; k<=ncoloh; k++)  double **pmmij, ***probs;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  double *ageexmed,*agecens;
         out[i][k] +=in[i][j]*b[j][k];  double dateintmean=0;
   
   return out;  double *weight;
 }  int **s; /* Status */
   double *agedc;
   double  **covar; /**< covar[j,i], value of jth covariate for individual i,
 /************* Higher Matrix Product ***************/                    * covar=matrix(0,NCOVMAX,1,n); 
                     * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  double  idx; 
 {  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  int *Ndum; /** Freq of modality (tricode */
      duration (i.e. until  int **codtab; /**< codtab=imatrix(1,100,1,10); */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  double *lsurv, *lpop, *tpop;
      (typically every 2 years instead of every month which is too big).  
      Model is determined by parameters x and covariates have to be  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
      included manually here.  double ftolhess; /**< Tolerance for computing hessian */
   
      */  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   int i, j, d, h, k;  {
   double **out, cov[NCOVMAX];    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   double **newm;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     */ 
   /* Hstepm could be zero and should return the unit matrix */    char  *ss;                            /* pointer */
   for (i=1;i<=nlstate+ndeath;i++)    int   l1, l2;                         /* length counters */
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);    l1 = strlen(path );                   /* length of path */
       po[i][j][0]=(i==j ? 1.0 : 0.0);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   for(h=1; h <=nhstepm; h++){      strcpy( name, path );               /* we got the fullname name because no directory */
     for(d=1; d <=hstepm; d++){      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       newm=savm;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       /* Covariates have to be included here again */      /* get current working directory */
       cov[1]=1.;      /*    extern  char* getcwd ( char *buf , int len);*/
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        return( GLOCK_ERROR_GETCWD );
       for (k=1; k<=cptcovage;k++)      }
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      /* got dirc from getcwd*/
       for (k=1; k<=cptcovprod;k++)      printf(" DIRC = %s \n",dirc);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      strcpy( name, ss );         /* save file name */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      strncpy( dirc, path, l1 - l2 );     /* now the directory */
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      dirc[l1-l2] = 0;                    /* add zero */
       savm=oldm;      printf(" DIRC2 = %s \n",dirc);
       oldm=newm;    }
     }    /* We add a separator at the end of dirc if not exists */
     for(i=1; i<=nlstate+ndeath; i++)    l1 = strlen( dirc );                  /* length of directory */
       for(j=1;j<=nlstate+ndeath;j++) {    if( dirc[l1-1] != DIRSEPARATOR ){
         po[i][j][h]=newm[i][j];      dirc[l1] =  DIRSEPARATOR;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      dirc[l1+1] = 0; 
          */      printf(" DIRC3 = %s \n",dirc);
       }    }
   } /* end h */    ss = strrchr( name, '.' );            /* find last / */
   return po;    if (ss >0){
 }      ss++;
       strcpy(ext,ss);                     /* save extension */
       l1= strlen( name);
 /*************** log-likelihood *************/      l2= strlen(ss)+1;
 double func( double *x)      strncpy( finame, name, l1-l2);
 {      finame[l1-l2]= 0;
   int i, ii, j, k, mi, d, kk;    }
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;    return( 0 );                          /* we're done */
   double sw; /* Sum of weights */  }
   double lli; /* Individual log likelihood */  
   long ipmx;  
   /*extern weight */  /******************************************/
   /* We are differentiating ll according to initial status */  
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  void replace_back_to_slash(char *s, char*t)
   /*for(i=1;i<imx;i++)  {
     printf(" %d\n",s[4][i]);    int i;
   */    int lg=0;
   cov[1]=1.;    i=0;
     lg=strlen(t);
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for(i=0; i<= lg; i++) {
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      (s[i] = t[i]);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      if (t[i]== '\\') s[i]='/';
     for(mi=1; mi<= wav[i]-1; mi++){    }
       for (ii=1;ii<=nlstate+ndeath;ii++)  }
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
       for(d=0; d<dh[mi][i]; d++){  char *trimbb(char *out, char *in)
         newm=savm;  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    char *s;
         for (kk=1; kk<=cptcovage;kk++) {    s=out;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    while (*in != '\0'){
         }      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
                in++;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      }
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      *out++ = *in++;
         savm=oldm;    }
         oldm=newm;    *out='\0';
            return s;
          }
       } /* end mult */  
        char *cutl(char *blocc, char *alocc, char *in, char occ)
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  {
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
       ipmx +=1;       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       sw += weight[i];       gives blocc="abcdef2ghi" and alocc="j".
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;       If occ is not found blocc is null and alocc is equal to in. Returns blocc
     } /* end of wave */    */
   } /* end of individual */    char *s, *t;
     t=in;s=in;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    while ((*in != occ) && (*in != '\0')){
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      *alocc++ = *in++;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    }
   return -l;    if( *in == occ){
 }      *(alocc)='\0';
       s=++in;
     }
 /*********** Maximum Likelihood Estimation ***************/   
     if (s == t) {/* occ not found */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      *(alocc-(in-s))='\0';
 {      in=s;
   int i,j, iter;    }
   double **xi,*delti;    while ( *in != '\0'){
   double fret;      *blocc++ = *in++;
   xi=matrix(1,npar,1,npar);    }
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)    *blocc='\0';
       xi[i][j]=(i==j ? 1.0 : 0.0);    return t;
   printf("Powell\n");  }
   powell(p,xi,npar,ftol,&iter,&fret,func);  char *cutv(char *blocc, char *alocc, char *in, char occ)
   {
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
        gives blocc="abcdef2ghi" and alocc="j".
 }       If occ is not found blocc is null and alocc is equal to in. Returns alocc
     */
 /**** Computes Hessian and covariance matrix ***/    char *s, *t;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    t=in;s=in;
 {    while (*in != '\0'){
   double  **a,**y,*x,pd;      while( *in == occ){
   double **hess;        *blocc++ = *in++;
   int i, j,jk;        s=in;
   int *indx;      }
       *blocc++ = *in++;
   double hessii(double p[], double delta, int theta, double delti[]);    }
   double hessij(double p[], double delti[], int i, int j);    if (s == t) /* occ not found */
   void lubksb(double **a, int npar, int *indx, double b[]) ;      *(blocc-(in-s))='\0';
   void ludcmp(double **a, int npar, int *indx, double *d) ;    else
       *(blocc-(in-s)-1)='\0';
   hess=matrix(1,npar,1,npar);    in=s;
     while ( *in != '\0'){
   printf("\nCalculation of the hessian matrix. Wait...\n");      *alocc++ = *in++;
   for (i=1;i<=npar;i++){    }
     printf("%d",i);fflush(stdout);  
     hess[i][i]=hessii(p,ftolhess,i,delti);    *alocc='\0';
     /*printf(" %f ",p[i]);*/    return s;
     /*printf(" %lf ",hess[i][i]);*/  }
   }  
    int nbocc(char *s, char occ)
   for (i=1;i<=npar;i++) {  {
     for (j=1;j<=npar;j++)  {    int i,j=0;
       if (j>i) {    int lg=20;
         printf(".%d%d",i,j);fflush(stdout);    i=0;
         hess[i][j]=hessij(p,delti,i,j);    lg=strlen(s);
         hess[j][i]=hess[i][j];        for(i=0; i<= lg; i++) {
         /*printf(" %lf ",hess[i][j]);*/    if  (s[i] == occ ) j++;
       }    }
     }    return j;
   }  }
   printf("\n");  
   /* void cutv(char *u,char *v, char*t, char occ) */
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  /* { */
    /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   a=matrix(1,npar,1,npar);  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   y=matrix(1,npar,1,npar);  /*      gives u="abcdef2ghi" and v="j" *\/ */
   x=vector(1,npar);  /*   int i,lg,j,p=0; */
   indx=ivector(1,npar);  /*   i=0; */
   for (i=1;i<=npar;i++)  /*   lg=strlen(t); */
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  /*   for(j=0; j<=lg-1; j++) { */
   ludcmp(a,npar,indx,&pd);  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   /*   } */
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  /*   for(j=0; j<p; j++) { */
     x[j]=1;  /*     (u[j] = t[j]); */
     lubksb(a,npar,indx,x);  /*   } */
     for (i=1;i<=npar;i++){  /*      u[p]='\0'; */
       matcov[i][j]=x[i];  
     }  /*    for(j=0; j<= lg; j++) { */
   }  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   /*   } */
   printf("\n#Hessian matrix#\n");  /* } */
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++) {  #ifdef _WIN32
       printf("%.3e ",hess[i][j]);  char * strsep(char **pp, const char *delim)
     }  {
     printf("\n");    char *p, *q;
   }           
     if ((p = *pp) == NULL)
   /* Recompute Inverse */      return 0;
   for (i=1;i<=npar;i++)    if ((q = strpbrk (p, delim)) != NULL)
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    {
   ludcmp(a,npar,indx,&pd);      *pp = q + 1;
       *q = '\0';
   /*  printf("\n#Hessian matrix recomputed#\n");    }
     else
   for (j=1;j<=npar;j++) {      *pp = 0;
     for (i=1;i<=npar;i++) x[i]=0;    return p;
     x[j]=1;  }
     lubksb(a,npar,indx,x);  #endif
     for (i=1;i<=npar;i++){  
       y[i][j]=x[i];  /********************** nrerror ********************/
       printf("%.3e ",y[i][j]);  
     }  void nrerror(char error_text[])
     printf("\n");  {
   }    fprintf(stderr,"ERREUR ...\n");
   */    fprintf(stderr,"%s\n",error_text);
     exit(EXIT_FAILURE);
   free_matrix(a,1,npar,1,npar);  }
   free_matrix(y,1,npar,1,npar);  /*********************** vector *******************/
   free_vector(x,1,npar);  double *vector(int nl, int nh)
   free_ivector(indx,1,npar);  {
   free_matrix(hess,1,npar,1,npar);    double *v;
     v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
 }    return v-nl+NR_END;
   }
 /*************** hessian matrix ****************/  
 double hessii( double x[], double delta, int theta, double delti[])  /************************ free vector ******************/
 {  void free_vector(double*v, int nl, int nh)
   int i;  {
   int l=1, lmax=20;    free((FREE_ARG)(v+nl-NR_END));
   double k1,k2;  }
   double p2[NPARMAX+1];  
   double res;  /************************ivector *******************************/
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  int *ivector(long nl,long nh)
   double fx;  {
   int k=0,kmax=10;    int *v;
   double l1;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     if (!v) nrerror("allocation failure in ivector");
   fx=func(x);    return v-nl+NR_END;
   for (i=1;i<=npar;i++) p2[i]=x[i];  }
   for(l=0 ; l <=lmax; l++){  
     l1=pow(10,l);  /******************free ivector **************************/
     delts=delt;  void free_ivector(int *v, long nl, long nh)
     for(k=1 ; k <kmax; k=k+1){  {
       delt = delta*(l1*k);    free((FREE_ARG)(v+nl-NR_END));
       p2[theta]=x[theta] +delt;  }
       k1=func(p2)-fx;  
       p2[theta]=x[theta]-delt;  /************************lvector *******************************/
       k2=func(p2)-fx;  long *lvector(long nl,long nh)
       /*res= (k1-2.0*fx+k2)/delt/delt; */  {
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    long *v;
          v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 #ifdef DEBUG    if (!v) nrerror("allocation failure in ivector");
       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);    return v-nl+NR_END;
 #endif  }
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  /******************free lvector **************************/
         k=kmax;  void free_lvector(long *v, long nl, long nh)
       }  {
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    free((FREE_ARG)(v+nl-NR_END));
         k=kmax; l=lmax*10.;  }
       }  
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  /******************* imatrix *******************************/
         delts=delt;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       }       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     }  { 
   }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   delti[theta]=delts;    int **m; 
   return res;    
      /* allocate pointers to rows */ 
 }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
 double hessij( double x[], double delti[], int thetai,int thetaj)    m += NR_END; 
 {    m -= nrl; 
   int i;    
   int l=1, l1, lmax=20;    
   double k1,k2,k3,k4,res,fx;    /* allocate rows and set pointers to them */ 
   double p2[NPARMAX+1];    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   int k;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     m[nrl] += NR_END; 
   fx=func(x);    m[nrl] -= ncl; 
   for (k=1; k<=2; k++) {    
     for (i=1;i<=npar;i++) p2[i]=x[i];    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     p2[thetai]=x[thetai]+delti[thetai]/k;    
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    /* return pointer to array of pointers to rows */ 
     k1=func(p2)-fx;    return m; 
    } 
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  /****************** free_imatrix *************************/
     k2=func(p2)-fx;  void free_imatrix(m,nrl,nrh,ncl,nch)
          int **m;
     p2[thetai]=x[thetai]-delti[thetai]/k;        long nch,ncl,nrh,nrl; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;       /* free an int matrix allocated by imatrix() */ 
     k3=func(p2)-fx;  { 
      free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     p2[thetai]=x[thetai]-delti[thetai]/k;    free((FREE_ARG) (m+nrl-NR_END)); 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  } 
     k4=func(p2)-fx;  
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  /******************* matrix *******************************/
 #ifdef DEBUG  double **matrix(long nrl, long nrh, long ncl, long nch)
     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    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   }    double **m;
   return res;  
 }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 /************** Inverse of matrix **************/    m += NR_END;
 void ludcmp(double **a, int n, int *indx, double *d)    m -= nrl;
 {  
   int i,imax,j,k;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double big,dum,sum,temp;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double *vv;    m[nrl] += NR_END;
      m[nrl] -= ncl;
   vv=vector(1,n);  
   *d=1.0;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   for (i=1;i<=n;i++) {    return m;
     big=0.0;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
     for (j=1;j<=n;j++)  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
       if ((temp=fabs(a[i][j])) > big) big=temp;  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");     */
     vv[i]=1.0/big;  }
   }  
   for (j=1;j<=n;j++) {  /*************************free matrix ************************/
     for (i=1;i<j;i++) {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       sum=a[i][j];  {
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       a[i][j]=sum;    free((FREE_ARG)(m+nrl-NR_END));
     }  }
     big=0.0;  
     for (i=j;i<=n;i++) {  /******************* ma3x *******************************/
       sum=a[i][j];  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       for (k=1;k<j;k++)  {
         sum -= a[i][k]*a[k][j];    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       a[i][j]=sum;    double ***m;
       if ( (dum=vv[i]*fabs(sum)) >= big) {  
         big=dum;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         imax=i;    if (!m) nrerror("allocation failure 1 in matrix()");
       }    m += NR_END;
     }    m -= nrl;
     if (j != imax) {  
       for (k=1;k<=n;k++) {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         dum=a[imax][k];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         a[imax][k]=a[j][k];    m[nrl] += NR_END;
         a[j][k]=dum;    m[nrl] -= ncl;
       }  
       *d = -(*d);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       vv[imax]=vv[j];  
     }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     indx[j]=imax;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     if (a[j][j] == 0.0) a[j][j]=TINY;    m[nrl][ncl] += NR_END;
     if (j != n) {    m[nrl][ncl] -= nll;
       dum=1.0/(a[j][j]);    for (j=ncl+1; j<=nch; j++) 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      m[nrl][j]=m[nrl][j-1]+nlay;
     }    
   }    for (i=nrl+1; i<=nrh; i++) {
   free_vector(vv,1,n);  /* Doesn't work */      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 ;      for (j=ncl+1; j<=nch; j++) 
 }        m[i][j]=m[i][j-1]+nlay;
     }
 void lubksb(double **a, int n, int *indx, double b[])    return m; 
 {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   int i,ii=0,ip,j;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   double sum;    */
    }
   for (i=1;i<=n;i++) {  
     ip=indx[i];  /*************************free ma3x ************************/
     sum=b[ip];  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     b[ip]=b[i];  {
     if (ii)    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     else if (sum) ii=i;    free((FREE_ARG)(m+nrl-NR_END));
     b[i]=sum;  }
   }  
   for (i=n;i>=1;i--) {  /*************** function subdirf ***********/
     sum=b[i];  char *subdirf(char fileres[])
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  {
     b[i]=sum/a[i][i];    /* Caution optionfilefiname is hidden */
   }    strcpy(tmpout,optionfilefiname);
 }    strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
 /************ Frequencies ********************/    return tmpout;
 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)  }
 {  /* Some frequencies */  
    /*************** function subdirf2 ***********/
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  char *subdirf2(char fileres[], char *preop)
   double ***freq; /* Frequencies */  {
   double *pp;    
   double pos, k2, dateintsum=0,k2cpt=0;    /* Caution optionfilefiname is hidden */
   FILE *ficresp;    strcpy(tmpout,optionfilefiname);
   char fileresp[FILENAMELENGTH];    strcat(tmpout,"/");
     strcat(tmpout,preop);
   pp=vector(1,nlstate);    strcat(tmpout,fileres);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    return tmpout;
   strcpy(fileresp,"p");  }
   strcat(fileresp,fileres);  
   if((ficresp=fopen(fileresp,"w"))==NULL) {  /*************** function subdirf3 ***********/
     printf("Problem with prevalence resultfile: %s\n", fileresp);  char *subdirf3(char fileres[], char *preop, char *preop2)
     exit(0);  {
   }    
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    /* Caution optionfilefiname is hidden */
   j1=0;    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
   j=cptcoveff;    strcat(tmpout,preop);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    strcat(tmpout,preop2);
     strcat(tmpout,fileres);
   for(k1=1; k1<=j;k1++){    return tmpout;
    for(i1=1; i1<=ncodemax[k1];i1++){  }
        j1++;  
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  char *asc_diff_time(long time_sec, char ascdiff[])
          scanf("%d", i);*/  {
         for (i=-1; i<=nlstate+ndeath; i++)      long sec_left, days, hours, minutes;
          for (jk=-1; jk<=nlstate+ndeath; jk++)      days = (time_sec) / (60*60*24);
            for(m=agemin; m <= agemax+3; m++)    sec_left = (time_sec) % (60*60*24);
              freq[i][jk][m]=0;    hours = (sec_left) / (60*60) ;
     sec_left = (sec_left) %(60*60);
         dateintsum=0;    minutes = (sec_left) /60;
         k2cpt=0;    sec_left = (sec_left) % (60);
        for (i=1; i<=imx; i++) {    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
          bool=1;    return ascdiff;
          if  (cptcovn>0) {  }
            for (z1=1; z1<=cptcoveff; z1++)  
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  /***************** f1dim *************************/
                bool=0;  extern int ncom; 
          }  extern double *pcom,*xicom;
          if (bool==1) {  extern double (*nrfunc)(double []); 
            for(m=firstpass; m<=lastpass; m++){   
              k2=anint[m][i]+(mint[m][i]/12.);  double f1dim(double x) 
              if ((k2>=dateprev1) && (k2<=dateprev2)) {  { 
                if(agev[m][i]==0) agev[m][i]=agemax+1;    int j; 
                if(agev[m][i]==1) agev[m][i]=agemax+2;    double f;
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    double *xt; 
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];   
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    xt=vector(1,ncom); 
                  dateintsum=dateintsum+k2;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
                  k2cpt++;    f=(*nrfunc)(xt); 
                }    free_vector(xt,1,ncom); 
     return f; 
              }  } 
            }  
          }  /*****************brent *************************/
        }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
         if  (cptcovn>0) {  { 
          fprintf(ficresp, "\n#********** Variable ");    int iter; 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double a,b,d,etemp;
        fprintf(ficresp, "**********\n#");    double fu=0,fv,fw,fx;
         }    double ftemp=0.;
        for(i=1; i<=nlstate;i++)    double p,q,r,tol1,tol2,u,v,w,x,xm; 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    double e=0.0; 
        fprintf(ficresp, "\n");   
            a=(ax < cx ? ax : cx); 
   for(i=(int)agemin; i <= (int)agemax+3; i++){    b=(ax > cx ? ax : cx); 
     if(i==(int)agemax+3)    x=w=v=bx; 
       printf("Total");    fw=fv=fx=(*f)(x); 
     else    for (iter=1;iter<=ITMAX;iter++) { 
       printf("Age %d", i);      xm=0.5*(a+b); 
     for(jk=1; jk <=nlstate ; jk++){      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         pp[jk] += freq[jk][m][i];      printf(".");fflush(stdout);
     }      fprintf(ficlog,".");fflush(ficlog);
     for(jk=1; jk <=nlstate ; jk++){  #ifdef DEBUGBRENT
       for(m=-1, pos=0; m <=0 ; m++)      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);
         pos += freq[jk][m][i];      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       if(pp[jk]>=1.e-10)      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  #endif
       else      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        *xmin=x; 
     }        return fx; 
       } 
      for(jk=1; jk <=nlstate ; jk++){      ftemp=fu;
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      if (fabs(e) > tol1) { 
         pp[jk] += freq[jk][m][i];        r=(x-w)*(fx-fv); 
      }        q=(x-v)*(fx-fw); 
         p=(x-v)*q-(x-w)*r; 
     for(jk=1,pos=0; jk <=nlstate ; jk++)        q=2.0*(q-r); 
       pos += pp[jk];        if (q > 0.0) p = -p; 
     for(jk=1; jk <=nlstate ; jk++){        q=fabs(q); 
       if(pos>=1.e-5)        etemp=e; 
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        e=d; 
       else        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       if( i <= (int) agemax){        else { 
         if(pos>=1.e-5){          d=p/q; 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          u=x+d; 
           probs[i][jk][j1]= pp[jk]/pos;          if (u-a < tol2 || b-u < tol2) 
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/            d=SIGN(tol1,xm-x); 
         }        } 
       else      } else { 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       }      } 
     }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     for(jk=-1; jk <=nlstate+ndeath; jk++)      fu=(*f)(u); 
       for(m=-1; m <=nlstate+ndeath; m++)      if (fu <= fx) { 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        if (u >= x) a=x; else b=x; 
     if(i <= (int) agemax)        SHFT(v,w,x,u) 
       fprintf(ficresp,"\n");          SHFT(fv,fw,fx,fu) 
     printf("\n");          } else { 
     }            if (u < x) a=u; else b=u; 
     }            if (fu <= fw || w == x) { 
  }              v=w; 
   dateintmean=dateintsum/k2cpt;              w=u; 
                fv=fw; 
   fclose(ficresp);              fw=fu; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            } else if (fu <= fv || v == x || v == w) { 
   free_vector(pp,1,nlstate);              v=u; 
               fv=fu; 
   /* End of Freq */            } 
 }          } 
     } 
 /************ Prevalence ********************/    nrerror("Too many iterations in brent"); 
 void prevalence(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 calagedate)    *xmin=x; 
 {  /* Some frequencies */    return fx; 
    } 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */  /****************** mnbrak ***********************/
   double *pp;  
   double pos, k2;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               double (*func)(double)) 
   pp=vector(1,nlstate);  { 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    double ulim,u,r,q, dum;
      double fu; 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);   
   j1=0;    *fa=(*func)(*ax); 
      *fb=(*func)(*bx); 
   j=cptcoveff;    if (*fb > *fa) { 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      SHFT(dum,*ax,*bx,dum) 
          SHFT(dum,*fb,*fa,dum) 
  for(k1=1; k1<=j;k1++){        } 
     for(i1=1; i1<=ncodemax[k1];i1++){    *cx=(*bx)+GOLD*(*bx-*ax); 
       j1++;    *fc=(*func)(*cx); 
      while (*fb > *fc) { /* Declining fa, fb, fc */
       for (i=-1; i<=nlstate+ndeath; i++)        r=(*bx-*ax)*(*fb-*fc); 
         for (jk=-1; jk<=nlstate+ndeath; jk++)        q=(*bx-*cx)*(*fb-*fa); 
           for(m=agemin; m <= agemax+3; m++)      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
             freq[i][jk][m]=0;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
            ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
       for (i=1; i<=imx; i++) {      if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
         bool=1;        fu=(*func)(u); 
         if  (cptcovn>0) {  #ifdef DEBUG
           for (z1=1; z1<=cptcoveff; z1++)        /* f(x)=A(x-u)**2+f(u) */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        double A, fparabu; 
               bool=0;        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
         }        fparabu= *fa - A*(*ax-u)*(*ax-u);
         if (bool==1) {        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);
           for(m=firstpass; m<=lastpass; m++){        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);
             k2=anint[m][i]+(mint[m][i]/12.);  #endif 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
               if(agev[m][i]==0) agev[m][i]=agemax+1;        fu=(*func)(u); 
               if(agev[m][i]==1) agev[m][i]=agemax+2;        if (fu < *fc) { 
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];              SHFT(*fb,*fc,fu,(*func)(u)) 
             }            } 
           }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
         }        u=ulim; 
       }        fu=(*func)(u); 
            } else { 
         for(i=(int)agemin; i <= (int)agemax+3; i++){        u=(*cx)+GOLD*(*cx-*bx); 
           for(jk=1; jk <=nlstate ; jk++){        fu=(*func)(u); 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      } 
               pp[jk] += freq[jk][m][i];      SHFT(*ax,*bx,*cx,u) 
           }        SHFT(*fa,*fb,*fc,fu) 
           for(jk=1; jk <=nlstate ; jk++){        } 
             for(m=-1, pos=0; m <=0 ; m++)  } 
             pos += freq[jk][m][i];  
         }  /*************** linmin ************************/
          /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
          for(jk=1; jk <=nlstate ; jk++){  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
              pp[jk] += freq[jk][m][i];  the value of func at the returned location p . This is actually all accomplished by calling the
          }  routines mnbrak and brent .*/
            int ncom; 
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  double *pcom,*xicom;
   double (*nrfunc)(double []); 
          for(jk=1; jk <=nlstate ; jk++){             
            if( i <= (int) agemax){  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
              if(pos>=1.e-5){  { 
                probs[i][jk][j1]= pp[jk]/pos;    double brent(double ax, double bx, double cx, 
              }                 double (*f)(double), double tol, double *xmin); 
            }    double f1dim(double x); 
          }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                          double *fc, double (*func)(double)); 
         }    int j; 
     }    double xx,xmin,bx,ax; 
   }    double fx,fb,fa;
     
      ncom=n; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    pcom=vector(1,n); 
   free_vector(pp,1,nlstate);    xicom=vector(1,n); 
      nrfunc=func; 
 }  /* End of Freq */    for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
 /************* Waves Concatenation ***************/      xicom[j]=xi[j]; 
     } 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    ax=0.0; 
 {    xx=1.0; 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
      Death is a valid wave (if date is known).    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  #ifdef DEBUG
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
      and mw[mi+1][i]. dh depends on stepm.    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
      */  #endif
     for (j=1;j<=n;j++) { 
   int i, mi, m;      xi[j] *= xmin; 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      p[j] += xi[j]; 
      double sum=0., jmean=0.;*/    } 
     free_vector(xicom,1,n); 
   int j, k=0,jk, ju, jl;    free_vector(pcom,1,n); 
   double sum=0.;  } 
   jmin=1e+5;  
   jmax=-1;  
   jmean=0.;  /*************** powell ************************/
   for(i=1; i<=imx; i++){  /*
     mi=0;  Minimization of a function func of n variables. Input consists of an initial starting point
     m=firstpass;  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
     while(s[m][i] <= nlstate){  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
       if(s[m][i]>=1)  such that failure to decrease by more than this amount on one iteration signals doneness. On
         mw[++mi][i]=m;  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
       if(m >=lastpass)  function value at p , and iter is the number of iterations taken. The routine linmin is used.
         break;   */
       else  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         m++;              double (*func)(double [])) 
     }/* end while */  { 
     if (s[m][i] > nlstate){    void linmin(double p[], double xi[], int n, double *fret, 
       mi++;     /* Death is another wave */                double (*func)(double [])); 
       /* if(mi==0)  never been interviewed correctly before death */    int i,ibig,j; 
          /* Only death is a correct wave */    double del,t,*pt,*ptt,*xit;
       mw[mi][i]=m;    double fp,fptt;
     }    double *xits;
     int niterf, itmp;
     wav[i]=mi;  
     if(mi==0)    pt=vector(1,n); 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    ptt=vector(1,n); 
   }    xit=vector(1,n); 
     xits=vector(1,n); 
   for(i=1; i<=imx; i++){    *fret=(*func)(p); 
     for(mi=1; mi<wav[i];mi++){    for (j=1;j<=n;j++) pt[j]=p[j]; 
       if (stepm <=0)      rcurr_time = time(NULL);  
         dh[mi][i]=1;    for (*iter=1;;++(*iter)) { 
       else{      fp=(*fret); 
         if (s[mw[mi+1][i]][i] > nlstate) {      ibig=0; 
           if (agedc[i] < 2*AGESUP) {      del=0.0; 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      rlast_time=rcurr_time;
           if(j==0) j=1;  /* Survives at least one month after exam */      /* (void) gettimeofday(&curr_time,&tzp); */
           k=k+1;      rcurr_time = time(NULL);  
           if (j >= jmax) jmax=j;      curr_time = *localtime(&rcurr_time);
           if (j <= jmin) jmin=j;      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
           sum=sum+j;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
           /* if (j<10) printf("j=%d num=%d ",j,i); */  /*     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]);
         else{        fprintf(ficlog," %d %.12lf",i, p[i]);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        fprintf(ficrespow," %.12lf", p[i]);
           k=k+1;      }
           if (j >= jmax) jmax=j;      printf("\n");
           else if (j <= jmin)jmin=j;      fprintf(ficlog,"\n");
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */      fprintf(ficrespow,"\n");fflush(ficrespow);
           sum=sum+j;      if(*iter <=3){
         }        tml = *localtime(&rcurr_time);
         jk= j/stepm;        strcpy(strcurr,asctime(&tml));
         jl= j -jk*stepm;        rforecast_time=rcurr_time; 
         ju= j -(jk+1)*stepm;        itmp = strlen(strcurr);
         if(jl <= -ju)        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           dh[mi][i]=jk;          strcurr[itmp-1]='\0';
         else        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
           dh[mi][i]=jk+1;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
         if(dh[mi][i]==0)        for(niterf=10;niterf<=30;niterf+=10){
           dh[mi][i]=1; /* At least one step */          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
       }          forecast_time = *localtime(&rforecast_time);
     }          strcpy(strfor,asctime(&forecast_time));
   }          itmp = strlen(strfor);
   jmean=sum/k;          if(strfor[itmp-1]=='\n')
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          strfor[itmp-1]='\0';
  }          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
 /*********** Tricode ****************************/          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);
 void tricode(int *Tvar, int **nbcode, int imx)        }
 {      }
   int Ndum[20],ij=1, k, j, i;      for (i=1;i<=n;i++) { 
   int cptcode=0;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   cptcoveff=0;        fptt=(*fret); 
    #ifdef DEBUG
   for (k=0; k<19; k++) Ndum[k]=0;            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
   for (k=1; k<=7; k++) ncodemax[k]=0;            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
   #endif
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        printf("%d",i);fflush(stdout);
     for (i=1; i<=imx; i++) {        fprintf(ficlog,"%d",i);fflush(ficlog);
       ij=(int)(covar[Tvar[j]][i]);        linmin(p,xit,n,fret,func); 
       Ndum[ij]++;        if (fabs(fptt-(*fret)) > del) { 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          del=fabs(fptt-(*fret)); 
       if (ij > cptcode) cptcode=ij;          ibig=i; 
     }        } 
   #ifdef DEBUG
     for (i=0; i<=cptcode; i++) {        printf("%d %.12e",i,(*fret));
       if(Ndum[i]!=0) ncodemax[j]++;        fprintf(ficlog,"%d %.12e",i,(*fret));
     }        for (j=1;j<=n;j++) {
     ij=1;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           printf(" x(%d)=%.12e",j,xit[j]);
           fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     for (i=1; i<=ncodemax[j]; i++) {        }
       for (k=0; k<=19; k++) {        for(j=1;j<=n;j++) {
         if (Ndum[k] != 0) {          printf(" p(%d)=%.12e",j,p[j]);
           nbcode[Tvar[j]][ij]=k;          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
           ij++;        }
         }        printf("\n");
         if (ij > ncodemax[j]) break;        fprintf(ficlog,"\n");
       }    #endif
     }      } /* end i */
   }        if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   #ifdef DEBUG
  for (k=0; k<19; k++) Ndum[k]=0;        int k[2],l;
         k[0]=1;
  for (i=1; i<=ncovmodel-2; i++) {        k[1]=-1;
       ij=Tvar[i];        printf("Max: %.12e",(*func)(p));
       Ndum[ij]++;        fprintf(ficlog,"Max: %.12e",(*func)(p));
     }        for (j=1;j<=n;j++) {
           printf(" %.12e",p[j]);
  ij=1;          fprintf(ficlog," %.12e",p[j]);
  for (i=1; i<=10; i++) {        }
    if((Ndum[i]!=0) && (i<=ncov)){        printf("\n");
      Tvaraff[ij]=i;        fprintf(ficlog,"\n");
      ij++;        for(l=0;l<=1;l++) {
    }          for (j=1;j<=n;j++) {
  }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
              printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     cptcoveff=ij-1;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 }          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 /*********** Health Expectancies ****************/          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)  #endif
 {  
   /* Health expectancies */  
   int i, j, nhstepm, hstepm, h;        free_vector(xit,1,n); 
   double age, agelim,hf;        free_vector(xits,1,n); 
   double ***p3mat;        free_vector(ptt,1,n); 
          free_vector(pt,1,n); 
   fprintf(ficreseij,"# Health expectancies\n");        return; 
   fprintf(ficreseij,"# Age");      } 
   for(i=1; i<=nlstate;i++)      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     for(j=1; j<=nlstate;j++)      for (j=1;j<=n;j++) { /* Computes an extrapolated point */
       fprintf(ficreseij," %1d-%1d",i,j);        ptt[j]=2.0*p[j]-pt[j]; 
   fprintf(ficreseij,"\n");        xit[j]=p[j]-pt[j]; 
         pt[j]=p[j]; 
   hstepm=1*YEARM; /*  Every j years of age (in month) */      } 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      fptt=(*func)(ptt); 
       if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
   agelim=AGESUP;        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
     /* nhstepm age range expressed in number of stepm */        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
     /* Typically if 20 years = 20*12/6=40 stepm */        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
     if (stepm >= YEARM) hstepm=1;        /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */        /* Thus we compare delta(2h) with observed f1-f3 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /* or best gain on one ancient line 'del' with total  */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        /* gain f1-f2 = f1 - f2 - 'del' with del  */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
         t= t- del*SQR(fp-fptt);
     for(i=1; i<=nlstate;i++)        printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
       for(j=1; j<=nlstate;j++)        fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){  #ifdef DEBUG
           eij[i][j][(int)age] +=p3mat[i][j][h];        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
         }               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
            fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
     hf=1;               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
     if (stepm >= YEARM) hf=stepm/YEARM;        printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
     fprintf(ficreseij,"%.0f",age );        fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
     for(i=1; i<=nlstate;i++)  #endif
       for(j=1; j<=nlstate;j++){        if (t < 0.0) { /* Then we use it for last direction */
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
       }          for (j=1;j<=n;j++) { 
     fprintf(ficreseij,"\n");            xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
   }          }
 }          printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
           fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
 /************ Variance ******************/  
 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)  #ifdef DEBUG
 {          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   /* Variance of health expectancies */          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          for(j=1;j<=n;j++){
   double **newm;            printf(" %.12e",xit[j]);
   double **dnewm,**doldm;            fprintf(ficlog," %.12e",xit[j]);
   int i, j, nhstepm, hstepm, h;          }
   int k, cptcode;          printf("\n");
   double *xp;          fprintf(ficlog,"\n");
   double **gp, **gm;  #endif
   double ***gradg, ***trgradg;        } /* end of t negative */
   double ***p3mat;      } /* end if (fptt < fp)  */
   double age,agelim;    } 
   int theta;  } 
   
    fprintf(ficresvij,"# Covariances of life expectancies\n");  /**** Prevalence limit (stable or period prevalence)  ****************/
   fprintf(ficresvij,"# Age");  
   for(i=1; i<=nlstate;i++)  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     for(j=1; j<=nlstate;j++)  {
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   fprintf(ficresvij,"\n");       matrix by transitions matrix until convergence is reached */
     
   xp=vector(1,npar);    int i, ii,j,k;
   dnewm=matrix(1,nlstate,1,npar);    double min, max, maxmin, maxmax,sumnew=0.;
   doldm=matrix(1,nlstate,1,nlstate);    /* double **matprod2(); */ /* test */
      double **out, cov[NCOVMAX+1], **pmij();
   hstepm=1*YEARM; /* Every year of age */    double **newm;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    double agefin, delaymax=50 ; /* Max number of years to converge */
   agelim = AGESUP;    
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    for (ii=1;ii<=nlstate+ndeath;ii++)
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      for (j=1;j<=nlstate+ndeath;j++){
     if (stepm >= YEARM) hstepm=1;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    cov[1]=1.;
     gp=matrix(0,nhstepm,1,nlstate);    
     gm=matrix(0,nhstepm,1,nlstate);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     for(theta=1; theta <=npar; theta++){      newm=savm;
       for(i=1; i<=npar; i++){ /* Computes gradient */      /* Covariates have to be included here again */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      cov[2]=agefin;
       }      
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        for (k=1; k<=cptcovn;k++) {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
       if (popbased==1) {      }
         for(i=1; i<=nlstate;i++)      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
           prlim[i][i]=probs[(int)age][i][ij];      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
       }      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
            
       for(j=1; j<= nlstate; j++){      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         for(h=0; h<=nhstepm; h++){      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         }      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
       }      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
          
       for(i=1; i<=npar; i++) /* Computes gradient */      savm=oldm;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      oldm=newm;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        maxmax=0.;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      for(j=1;j<=nlstate;j++){
         min=1.;
       if (popbased==1) {        max=0.;
         for(i=1; i<=nlstate;i++)        for(i=1; i<=nlstate; i++) {
           prlim[i][i]=probs[(int)age][i][ij];          sumnew=0;
       }          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           prlim[i][j]= newm[i][j]/(1-sumnew);
       for(j=1; j<= nlstate; j++){          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
         for(h=0; h<=nhstepm; h++){          max=FMAX(max,prlim[i][j]);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          min=FMIN(min,prlim[i][j]);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        }
         }        maxmin=max-min;
       }        maxmax=FMAX(maxmax,maxmin);
       } /* j loop */
       for(j=1; j<= nlstate; j++)      if(maxmax < ftolpl){
         for(h=0; h<=nhstepm; h++){        return prlim;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      }
         }    } /* age loop */
     } /* End theta */    return prlim; /* should not reach here */
   }
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  
   /*************** transition probabilities ***************/ 
     for(h=0; h<=nhstepm; h++)  
       for(j=1; j<=nlstate;j++)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         for(theta=1; theta <=npar; theta++)  {
           trgradg[h][j][theta]=gradg[h][theta][j];    /* According to parameters values stored in x and the covariate's values stored in cov,
        computes the probability to be observed in state j being in state i by appying the
     for(i=1;i<=nlstate;i++)       model to the ncovmodel covariates (including constant and age).
       for(j=1;j<=nlstate;j++)       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
         vareij[i][j][(int)age] =0.;       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
     for(h=0;h<=nhstepm;h++){       ncth covariate in the global vector x is given by the formula:
       for(k=0;k<=nhstepm;k++){       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
         for(i=1;i<=nlstate;i++)       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
           for(j=1;j<=nlstate;j++)       Outputs ps[i][j] the probability to be observed in j being in j according to
             vareij[i][j][(int)age] += doldm[i][j];       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
       }    */
     }    double s1, lnpijopii;
     h=1;    /*double t34;*/
     if (stepm >= YEARM) h=stepm/YEARM;    int i,j, nc, ii, jj;
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)      for(i=1; i<= nlstate; i++){
       for(j=1; j<=nlstate;j++){        for(j=1; j<i;j++){
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       }            /*lnpijopii += param[i][j][nc]*cov[nc];*/
     fprintf(ficresvij,"\n");            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
     free_matrix(gp,0,nhstepm,1,nlstate);  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     free_matrix(gm,0,nhstepm,1,nlstate);          }
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
   } /* End age */        for(j=i+1; j<=nlstate+ndeath;j++){
            for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
   free_vector(xp,1,npar);            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
   free_matrix(doldm,1,nlstate,1,npar);            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
   free_matrix(dnewm,1,nlstate,1,nlstate);  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
           }
 }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         }
 /************ 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)      
 {      for(i=1; i<= nlstate; i++){
   /* Variance of prevalence limit */        s1=0;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        for(j=1; j<i; j++){
   double **newm;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   double **dnewm,**doldm;          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   int i, j, nhstepm, hstepm;        }
   int k, cptcode;        for(j=i+1; j<=nlstate+ndeath; j++){
   double *xp;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   double *gp, *gm;          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   double **gradg, **trgradg;        }
   double age,agelim;        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
   int theta;        ps[i][i]=1./(s1+1.);
            /* Computing other pijs */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");        for(j=1; j<i; j++)
   fprintf(ficresvpl,"# Age");          ps[i][j]= exp(ps[i][j])*ps[i][i];
   for(i=1; i<=nlstate;i++)        for(j=i+1; j<=nlstate+ndeath; j++)
       fprintf(ficresvpl," %1d-%1d",i,i);          ps[i][j]= exp(ps[i][j])*ps[i][i];
   fprintf(ficresvpl,"\n");        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       } /* end i */
   xp=vector(1,npar);      
   dnewm=matrix(1,nlstate,1,npar);      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   doldm=matrix(1,nlstate,1,nlstate);        for(jj=1; jj<= nlstate+ndeath; jj++){
            ps[ii][jj]=0;
   hstepm=1*YEARM; /* Every year of age */          ps[ii][ii]=1;
   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;      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
     gradg=matrix(1,npar,1,nlstate);      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
     gp=vector(1,nlstate);      /*   } */
     gm=vector(1,nlstate);      /*   printf("\n "); */
       /* } */
     for(theta=1; theta <=npar; theta++){      /* printf("\n ");printf("%lf ",cov[2]);*/
       for(i=1; i<=npar; i++){ /* Computes gradient */      /*
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       }        goto end;*/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      return ps;
       for(i=1;i<=nlstate;i++)  }
         gp[i] = prlim[i][i];  
      /**************** Product of 2 matrices ******************/
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  {
       for(i=1;i<=nlstate;i++)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         gm[i] = prlim[i][i];       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
       for(i=1;i<=nlstate;i++)       before: only the contents of out is modified. The function returns
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];       a pointer to pointers identical to out */
     } /* End theta */    int i, j, k;
     for(i=nrl; i<= nrh; i++)
     trgradg =matrix(1,nlstate,1,npar);      for(k=ncolol; k<=ncoloh; k++){
         out[i][k]=0.;
     for(j=1; j<=nlstate;j++)        for(j=ncl; j<=nch; j++)
       for(theta=1; theta <=npar; theta++)          out[i][k] +=in[i][j]*b[j][k];
         trgradg[j][theta]=gradg[theta][j];      }
     return out;
     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);  /************* Higher Matrix Product ***************/
     for(i=1;i<=nlstate;i++)  
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   {
     fprintf(ficresvpl,"%.0f ",age );    /* Computes the transition matrix starting at age 'age' over 
     for(i=1; i<=nlstate;i++)       'nhstepm*hstepm*stepm' months (i.e. until
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     fprintf(ficresvpl,"\n");       nhstepm*hstepm matrices. 
     free_vector(gp,1,nlstate);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     free_vector(gm,1,nlstate);       (typically every 2 years instead of every month which is too big 
     free_matrix(gradg,1,npar,1,nlstate);       for the memory).
     free_matrix(trgradg,1,nlstate,1,npar);       Model is determined by parameters x and covariates have to be 
   } /* End age */       included manually here. 
   
   free_vector(xp,1,npar);       */
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);    int i, j, d, h, k;
     double **out, cov[NCOVMAX+1];
 }    double **newm;
   
 /************ Variance of one-step probabilities  ******************/    /* Hstepm could be zero and should return the unit matrix */
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    for (i=1;i<=nlstate+ndeath;i++)
 {      for (j=1;j<=nlstate+ndeath;j++){
   int i, j;        oldm[i][j]=(i==j ? 1.0 : 0.0);
   int k=0, cptcode;        po[i][j][0]=(i==j ? 1.0 : 0.0);
   double **dnewm,**doldm;      }
   double *xp;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   double *gp, *gm;    for(h=1; h <=nhstepm; h++){
   double **gradg, **trgradg;      for(d=1; d <=hstepm; d++){
   double age,agelim, cov[NCOVMAX];        newm=savm;
   int theta;        /* Covariates have to be included here again */
   char fileresprob[FILENAMELENGTH];        cov[1]=1.;
         cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   strcpy(fileresprob,"prob");        for (k=1; k<=cptcovn;k++) 
   strcat(fileresprob,fileres);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        for (k=1; k<=cptcovage;k++)
     printf("Problem with resultfile: %s\n", fileresprob);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   }        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
    
   
   xp=vector(1,npar);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                       pmij(pmmij,cov,ncovmodel,x,nlstate));
   cov[1]=1;        savm=oldm;
   for (age=bage; age<=fage; age ++){        oldm=newm;
     cov[2]=age;      }
     gradg=matrix(1,npar,1,9);      for(i=1; i<=nlstate+ndeath; i++)
     trgradg=matrix(1,9,1,npar);        for(j=1;j<=nlstate+ndeath;j++) {
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          po[i][j][h]=newm[i][j];
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
            }
     for(theta=1; theta <=npar; theta++){      /*printf("h=%d ",h);*/
       for(i=1; i<=npar; i++)    } /* end h */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  /*     printf("\n H=%d \n",h); */
          return po;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  }
      
       k=0;  #ifdef NLOPT
       for(i=1; i<= (nlstate+ndeath); i++){    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
         for(j=1; j<=(nlstate+ndeath);j++){    double fret;
            k=k+1;    double *xt;
           gp[k]=pmmij[i][j];    int j;
         }    myfunc_data *d2 = (myfunc_data *) pd;
       }  /* xt = (p1-1); */
     xt=vector(1,n); 
       for(i=1; i<=npar; i++)    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
        fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
     /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    printf("Function = %.12lf ",fret);
       k=0;    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
       for(i=1; i<=(nlstate+ndeath); i++){    printf("\n");
         for(j=1; j<=(nlstate+ndeath);j++){   free_vector(xt,1,n);
           k=k+1;    return fret;
           gm[k]=pmmij[i][j];  }
         }  #endif
       }  
        /*************** log-likelihood *************/
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  double func( double *x)
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    {
     }    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    double **out;
       for(theta=1; theta <=npar; theta++)    double sw; /* Sum of weights */
       trgradg[j][theta]=gradg[theta][j];    double lli; /* Individual log likelihood */
      int s1, s2;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    double bbh, survp;
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    long ipmx;
     /*extern weight */
      pmij(pmmij,cov,ncovmodel,x,nlstate);    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      k=0;    /*for(i=1;i<imx;i++) 
      for(i=1; i<=(nlstate+ndeath); i++){      printf(" %d\n",s[4][i]);
        for(j=1; j<=(nlstate+ndeath);j++){    */
          k=k+1;  
          gm[k]=pmmij[i][j];    ++countcallfunc;
         }  
      }    cov[1]=1.;
        
      /*printf("\n%d ",(int)age);    for(k=1; k<=nlstate; k++) ll[k]=0.;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  
            if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        /* Computes the values of the ncovmodel covariates of the model
      }*/           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
            Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
   fprintf(ficresprob,"\n%d ",(int)age);           to be observed in j being in i according to the model.
          */
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          cov[2+k]=covar[Tvar[k]][i];
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        }
   }        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
            is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));           has been calculated etc */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        for(mi=1; mi<= wav[i]-1; mi++){
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            for (j=1;j<=nlstate+ndeath;j++){
 }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  free_vector(xp,1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 fclose(ficresprob);            }
  exit(0);          for(d=0; d<dh[mi][i]; d++){
 }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 /***********************************************/            for (kk=1; kk<=cptcovage;kk++) {
 /**************** Main Program *****************/              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
 /***********************************************/            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 /*int main(int argc, char *argv[])*/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 int main()            savm=oldm;
 {            oldm=newm;
           } /* end mult */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        
   double agedeb, agefin,hf;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   double agemin=1.e20, agemax=-1.e20;          /* 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 
   double fret;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   double **xi,tmp,delta;           * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
   double dum; /* Dummy variable */           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   double ***p3mat;           * probability in order to take into account the bias as a fraction of the way
   int *indx;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   char line[MAXLINE], linepar[MAXLINE];           * -stepm/2 to stepm/2 .
   char title[MAXLINE];           * For stepm=1 the results are the same as for previous versions of Imach.
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];           * For stepm > 1 the results are less biased than in previous versions. 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];           */
   char filerest[FILENAMELENGTH];          s1=s[mw[mi][i]][i];
   char fileregp[FILENAMELENGTH];          s2=s[mw[mi+1][i]][i];
   char popfile[FILENAMELENGTH];          bbh=(double)bh[mi][i]/(double)stepm; 
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          /* bias bh is positive if real duration
   int firstobs=1, lastobs=10;           * is higher than the multiple of stepm and negative otherwise.
   int sdeb, sfin; /* Status at beginning and end */           */
   int c,  h , cpt,l;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   int ju,jl, mi;          if( s2 > nlstate){ 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            /* i.e. if s2 is a death state and if the date of death is known 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;               then the contribution to the likelihood is the probability to 
   int mobilav=0,popforecast=0;               die between last step unit time and current  step unit time, 
   int hstepm, nhstepm;               which is also equal to probability to die before dh 
   int *popage;/*boolprev=0 if date and zero if wave*/               minus probability to die before dh-stepm . 
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;               In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
   double bage, fage, age, agelim, agebase;          health state: the date of the interview describes the actual state
   double ftolpl=FTOL;          and not the date of a change in health state. The former idea was
   double **prlim;          to consider that at each interview the state was recorded
   double *severity;          (healthy, disable or death) and IMaCh was corrected; but when we
   double ***param; /* Matrix of parameters */          introduced the exact date of death then we should have modified
   double  *p;          the contribution of an exact death to the likelihood. This new
   double **matcov; /* Matrix of covariance */          contribution is smaller and very dependent of the step unit
   double ***delti3; /* Scale */          stepm. It is no more the probability to die between last interview
   double *delti; /* Scale */          and month of death but the probability to survive from last
   double ***eij, ***vareij;          interview up to one month before death multiplied by the
   double **varpl; /* Variances of prevalence limits by age */          probability to die within a month. Thanks to Chris
   double *epj, vepp;          Jackson for correcting this bug.  Former versions increased
   double kk1, kk2;          mortality artificially. The bad side is that we add another loop
   double *popeffectif,*popcount;          which slows down the processing. The difference can be up to 10%
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;          lower mortality.
   double yp,yp1,yp2;            */
             lli=log(out[s1][s2] - savm[s1][s2]);
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";  
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
           } else if  (s2==-2) {
             for (j=1,survp=0. ; j<=nlstate; j++) 
   char z[1]="c", occ;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 #include <sys/time.h>            /*survp += out[s1][j]; */
 #include <time.h>            lli= log(survp);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          }
            
   /* long total_usecs;          else if  (s2==-4) { 
   struct timeval start_time, end_time;            for (j=3,survp=0. ; j<=nlstate; j++)  
                survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */            lli= log(survp); 
           } 
   
   printf("\nIMACH, Version 0.7");          else if  (s2==-5) { 
   printf("\nEnter the parameter file name: ");            for (j=1,survp=0. ; j<=2; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 #ifdef windows            lli= log(survp); 
   scanf("%s",pathtot);          } 
   getcwd(pathcd, size);          
   /*cygwin_split_path(pathtot,path,optionfile);          else{
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   /* cutv(path,optionfile,pathtot,'\\');*/            /*  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 */
           } 
 split(pathtot, path,optionfile);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   chdir(path);          /*if(lli ==000.0)*/
   replace(pathc,path);          /*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); */
 #endif          ipmx +=1;
 #ifdef unix          sw += weight[i];
   scanf("%s",optionfile);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 #endif        } /* end of wave */
       } /* end of individual */
 /*-------- arguments in the command line --------*/    }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   strcpy(fileres,"r");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   strcat(fileres, optionfile);        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   /*---------arguments file --------*/            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     printf("Problem with optionfile %s\n",optionfile);            }
     goto end;          for(d=0; d<=dh[mi][i]; d++){
   }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   strcpy(filereso,"o");            for (kk=1; kk<=cptcovage;kk++) {
   strcat(filereso,fileres);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   if((ficparo=fopen(filereso,"w"))==NULL) {            }
     printf("Problem with Output resultfile: %s\n", filereso);goto end;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   /* Reads comments: lines beginning with '#' */            oldm=newm;
   while((c=getc(ficpar))=='#' && c!= EOF){          } /* end mult */
     ungetc(c,ficpar);        
     fgets(line, MAXLINE, ficpar);          s1=s[mw[mi][i]][i];
     puts(line);          s2=s[mw[mi+1][i]][i];
     fputs(line,ficparo);          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 */
   ungetc(c,ficpar);          ipmx +=1;
           sw += weight[i];
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);        } /* end of wave */
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);      } /* end of individual */
 while((c=getc(ficpar))=='#' && c!= EOF){    }  else if(mle==3){  /* exponential inter-extrapolation */
     ungetc(c,ficpar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     fgets(line, MAXLINE, ficpar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     puts(line);        for(mi=1; mi<= wav[i]-1; mi++){
     fputs(line,ficparo);          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
   ungetc(c,ficpar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
                }
   covar=matrix(0,NCOVMAX,1,n);          for(d=0; d<dh[mi][i]; d++){
   cptcovn=0;            newm=savm;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   ncovmodel=2+cptcovn;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */            }
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* Read guess parameters */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /* Reads comments: lines beginning with '#' */            savm=oldm;
   while((c=getc(ficpar))=='#' && c!= EOF){            oldm=newm;
     ungetc(c,ficpar);          } /* end mult */
     fgets(line, MAXLINE, ficpar);        
     puts(line);          s1=s[mw[mi][i]][i];
     fputs(line,ficparo);          s2=s[mw[mi+1][i]][i];
   }          bbh=(double)bh[mi][i]/(double)stepm; 
   ungetc(c,ficpar);          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 */
            ipmx +=1;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          sw += weight[i];
     for(i=1; i <=nlstate; i++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(j=1; j <=nlstate+ndeath-1; j++){        } /* end of wave */
       fscanf(ficpar,"%1d%1d",&i1,&j1);      } /* end of individual */
       fprintf(ficparo,"%1d%1d",i1,j1);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       printf("%1d%1d",i,j);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(k=1; k<=ncovmodel;k++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         fscanf(ficpar," %lf",&param[i][j][k]);        for(mi=1; mi<= wav[i]-1; mi++){
         printf(" %lf",param[i][j][k]);          for (ii=1;ii<=nlstate+ndeath;ii++)
         fprintf(ficparo," %lf",param[i][j][k]);            for (j=1;j<=nlstate+ndeath;j++){
       }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       fscanf(ficpar,"\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       printf("\n");            }
       fprintf(ficparo,"\n");          for(d=0; d<dh[mi][i]; d++){
     }            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   p=param[1][1];            }
            
   /* Reads comments: lines beginning with '#' */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   while((c=getc(ficpar))=='#' && c!= EOF){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     ungetc(c,ficpar);            savm=oldm;
     fgets(line, MAXLINE, ficpar);            oldm=newm;
     puts(line);          } /* end mult */
     fputs(line,ficparo);        
   }          s1=s[mw[mi][i]][i];
   ungetc(c,ficpar);          s2=s[mw[mi+1][i]][i];
           if( s2 > nlstate){ 
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            lli=log(out[s1][s2] - savm[s1][s2]);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          }else{
   for(i=1; i <=nlstate; i++){            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     for(j=1; j <=nlstate+ndeath-1; j++){          }
       fscanf(ficpar,"%1d%1d",&i1,&j1);          ipmx +=1;
       printf("%1d%1d",i,j);          sw += weight[i];
       fprintf(ficparo,"%1d%1d",i1,j1);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(k=1; k<=ncovmodel;k++){  /*      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]); */
         fscanf(ficpar,"%le",&delti3[i][j][k]);        } /* end of wave */
         printf(" %le",delti3[i][j][k]);      } /* end of individual */
         fprintf(ficparo," %le",delti3[i][j][k]);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       fscanf(ficpar,"\n");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       printf("\n");        for(mi=1; mi<= wav[i]-1; mi++){
       fprintf(ficparo,"\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
     }            for (j=1;j<=nlstate+ndeath;j++){
   }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   delti=delti3[1][1];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
   /* Reads comments: lines beginning with '#' */          for(d=0; d<dh[mi][i]; d++){
   while((c=getc(ficpar))=='#' && c!= EOF){            newm=savm;
     ungetc(c,ficpar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     fgets(line, MAXLINE, ficpar);            for (kk=1; kk<=cptcovage;kk++) {
     puts(line);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     fputs(line,ficparo);            }
   }          
   ungetc(c,ficpar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   matcov=matrix(1,npar,1,npar);            savm=oldm;
   for(i=1; i <=npar; i++){            oldm=newm;
     fscanf(ficpar,"%s",&str);          } /* end mult */
     printf("%s",str);        
     fprintf(ficparo,"%s",str);          s1=s[mw[mi][i]][i];
     for(j=1; j <=i; j++){          s2=s[mw[mi+1][i]][i];
       fscanf(ficpar," %le",&matcov[i][j]);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       printf(" %.5le",matcov[i][j]);          ipmx +=1;
       fprintf(ficparo," %.5le",matcov[i][j]);          sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     fscanf(ficpar,"\n");          /*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]);*/
     printf("\n");        } /* end of wave */
     fprintf(ficparo,"\n");      } /* end of individual */
   }    } /* End of if */
   for(i=1; i <=npar; i++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     for(j=i+1;j<=npar;j++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       matcov[i][j]=matcov[j][i];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
        return -l;
   printf("\n");  }
   
   /*************** log-likelihood *************/
     /*-------- data file ----------*/  double funcone( double *x)
     if((ficres =fopen(fileres,"w"))==NULL) {  {
       printf("Problem with resultfile: %s\n", fileres);goto end;    /* Same as likeli but slower because of a lot of printf and if */
     }    int i, ii, j, k, mi, d, kk;
     fprintf(ficres,"#%s\n",version);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
        double **out;
     if((fic=fopen(datafile,"r"))==NULL)    {    double lli; /* Individual log likelihood */
       printf("Problem with datafile: %s\n", datafile);goto end;    double llt;
     }    int s1, s2;
     double bbh, survp;
     n= lastobs;    /*extern weight */
     severity = vector(1,maxwav);    /* We are differentiating ll according to initial status */
     outcome=imatrix(1,maxwav+1,1,n);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     num=ivector(1,n);    /*for(i=1;i<imx;i++) 
     moisnais=vector(1,n);      printf(" %d\n",s[4][i]);
     annais=vector(1,n);    */
     moisdc=vector(1,n);    cov[1]=1.;
     andc=vector(1,n);  
     agedc=vector(1,n);    for(k=1; k<=nlstate; k++) ll[k]=0.;
     cod=ivector(1,n);  
     weight=vector(1,n);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     mint=matrix(1,maxwav,1,n);      for(mi=1; mi<= wav[i]-1; mi++){
     anint=matrix(1,maxwav,1,n);        for (ii=1;ii<=nlstate+ndeath;ii++)
     s=imatrix(1,maxwav+1,1,n);          for (j=1;j<=nlstate+ndeath;j++){
     adl=imatrix(1,maxwav+1,1,n);                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     tab=ivector(1,NCOVMAX);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
     ncodemax=ivector(1,8);          }
         for(d=0; d<dh[mi][i]; d++){
     i=1;          newm=savm;
     while (fgets(line, MAXLINE, fic) != NULL)    {          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if ((i >= firstobs) && (i <=lastobs)) {          for (kk=1; kk<=cptcovage;kk++) {
                    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for (j=maxwav;j>=1;j--){          }
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
           strcpy(line,stra);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
         }          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
                  savm=oldm;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);          oldm=newm;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        } /* end mult */
         
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        s1=s[mw[mi][i]][i];
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm; 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        /* bias is positive if real duration
         for (j=ncov;j>=1;j--){         * is higher than the multiple of stepm and negative otherwise.
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);         */
         }        if( s2 > nlstate && (mle <5) ){  /* Jackson */
         num[i]=atol(stra);          lli=log(out[s1][s2] - savm[s1][s2]);
                } else if  (s2==-2) {
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          for (j=1,survp=0. ; j<=nlstate; j++) 
           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;}*/            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);
         i=i+1;        }else if (mle==1){
       }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     }        } else if(mle==2){
     /* printf("ii=%d", ij);          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 */
        scanf("%d",i);*/        } else if(mle==3){  /* exponential inter-extrapolation */
   imx=i-1; /* Number of individuals */          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         } else if (mle==4){  /* mle=4 no inter-extrapolation */
   /* for (i=1; i<=imx; i++){          lli=log(out[s1][s2]); /* Original formula */
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;        } else{  /* mle=0 back to 1 */
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          /*lli=log(out[s1][s2]); */ /* Original formula */
     }        } /* End of if */
         ipmx +=1;
     for (i=1; i<=imx; i++)        sw += weight[i];
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/        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]); */
   /* Calculation of the number of parameter from char model*/        if(globpr){
   Tvar=ivector(1,15);          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   Tprod=ivector(1,15);   %11.6f %11.6f %11.6f ", \
   Tvaraff=ivector(1,15);                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   Tvard=imatrix(1,15,1,2);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   Tage=ivector(1,15);                for(k=1,llt=0.,l=0.; k<=nlstate; k++){
                llt +=ll[k]*gipmx/gsw;
   if (strlen(model) >1){            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     j=0, j1=0, k1=1, k2=1;          }
     j=nbocc(model,'+');          fprintf(ficresilk," %10.6f\n", -llt);
     j1=nbocc(model,'*');        }
     cptcovn=j+1;      } /* end of wave */
     cptcovprod=j1;    } /* end of individual */
        for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
        /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     strcpy(modelsav,model);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    if(globpr==0){ /* First time we count the contributions and weights */
       printf("Error. Non available option model=%s ",model);      gipmx=ipmx;
       goto end;      gsw=sw;
     }    }
        return -l;
     for(i=(j+1); i>=1;i--){  }
       cutv(stra,strb,modelsav,'+');  
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  /*************** function likelione ***********/
       /*scanf("%d",i);*/  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
       if (strchr(strb,'*')) {  {
         cutv(strd,strc,strb,'*');    /* This routine should help understanding what is done with 
         if (strcmp(strc,"age")==0) {       the selection of individuals/waves and
           cptcovprod--;       to check the exact contribution to the likelihood.
           cutv(strb,stre,strd,'V');       Plotting could be done.
           Tvar[i]=atoi(stre);     */
           cptcovage++;    int k;
             Tage[cptcovage]=i;  
             /*printf("stre=%s ", stre);*/    if(*globpri !=0){ /* Just counts and sums, no printings */
         }      strcpy(fileresilk,"ilk"); 
         else if (strcmp(strd,"age")==0) {      strcat(fileresilk,fileres);
           cptcovprod--;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
           cutv(strb,stre,strc,'V');        printf("Problem with resultfile: %s\n", fileresilk);
           Tvar[i]=atoi(stre);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
           cptcovage++;      }
           Tage[cptcovage]=i;      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");
         }      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
         else {      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
           cutv(strb,stre,strc,'V');      for(k=1; k<=nlstate; k++) 
           Tvar[i]=ncov+k1;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
           cutv(strb,strc,strd,'V');      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
           Tprod[k1]=i;    }
           Tvard[k1][1]=atoi(strc);  
           Tvard[k1][2]=atoi(stre);    *fretone=(*funcone)(p);
           Tvar[cptcovn+k2]=Tvard[k1][1];    if(*globpri !=0){
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      fclose(ficresilk);
           for (k=1; k<=lastobs;k++)      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      fflush(fichtm); 
           k1++;    } 
           k2=k2+2;    return;
         }  }
       }  
       else {  
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  /*********** Maximum Likelihood Estimation ***************/
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       Tvar[i]=atoi(strc);  {
       }    int i,j, iter=0;
       strcpy(modelsav,stra);      double **xi;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    double fret;
         scanf("%d",i);*/    double fretone; /* Only one call to likelihood */
     }    /*  char filerespow[FILENAMELENGTH];*/
 }  
    #ifdef NLOPT
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    int creturn;
   printf("cptcovprod=%d ", cptcovprod);    nlopt_opt opt;
   scanf("%d ",i);*/    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
     fclose(fic);    double *lb;
     double minf; /* the minimum objective value, upon return */
     /*  if(mle==1){*/    double * p1; /* Shifted parameters from 0 instead of 1 */
     if (weightopt != 1) { /* Maximisation without weights*/    myfunc_data dinst, *d = &dinst;
       for(i=1;i<=n;i++) weight[i]=1.0;  #endif
     }  
     /*-calculation of age at interview from date of interview and age at death -*/  
     agev=matrix(1,maxwav,1,imx);    xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
    for (i=1; i<=imx; i++)      for (j=1;j<=npar;j++)
      for(m=2; (m<= maxwav); m++)        xi[i][j]=(i==j ? 1.0 : 0.0);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    printf("Powell\n");  fprintf(ficlog,"Powell\n");
          anint[m][i]=9999;    strcpy(filerespow,"pow"); 
          s[m][i]=-1;    strcat(filerespow,fileres);
        }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
          printf("Problem with resultfile: %s\n", filerespow);
     for (i=1; i<=imx; i++)  {      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    }
       for(m=1; (m<= maxwav); m++){    fprintf(ficrespow,"# Powell\n# iter -2*LL");
         if(s[m][i] >0){    for (i=1;i<=nlstate;i++)
           if (s[m][i] == nlstate+1) {      for(j=1;j<=nlstate+ndeath;j++)
             if(agedc[i]>0)        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
               if(moisdc[i]!=99 && andc[i]!=9999)    fprintf(ficrespow,"\n");
               agev[m][i]=agedc[i];  #ifdef POWELL
             else {    powell(p,xi,npar,ftol,&iter,&fret,func);
               if (andc[i]!=9999){  #endif
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;  #ifdef NLOPT
               }  #ifdef NEWUOA
             }    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
           }  #else
           else if(s[m][i] !=9){ /* Should no more exist */    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  #endif
             if(mint[m][i]==99 || anint[m][i]==9999)    lb=vector(0,npar-1);
               agev[m][i]=1;    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
             else if(agev[m][i] <agemin){    nlopt_set_lower_bounds(opt, lb);
               agemin=agev[m][i];    nlopt_set_initial_step1(opt, 0.1);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    
             }    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
             else if(agev[m][i] >agemax){    d->function = func;
               agemax=agev[m][i];    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    nlopt_set_min_objective(opt, myfunc, d);
             }    nlopt_set_xtol_rel(opt, ftol);
             /*agev[m][i]=anint[m][i]-annais[i];*/    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
             /*   agev[m][i] = age[i]+2*m;*/      printf("nlopt failed! %d\n",creturn); 
           }    }
           else { /* =9 */    else {
             agev[m][i]=1;      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
             s[m][i]=-1;      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
           }      iter=1; /* not equal */
         }    }
         else /*= 0 Unknown */    nlopt_destroy(opt);
           agev[m][i]=1;  #endif
       }    free_matrix(xi,1,npar,1,npar);
        fclose(ficrespow);
     }    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     for (i=1; i<=imx; i++)  {    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
       for(m=1; (m<= maxwav); m++){    fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
         if (s[m][i] > (nlstate+ndeath)) {  
           printf("Error: Wrong value in nlstate or ndeath\n");    }
           goto end;  
         }  /**** Computes Hessian and covariance matrix ***/
       }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     }  {
     double  **a,**y,*x,pd;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    double **hess;
     int i, j;
     free_vector(severity,1,maxwav);    int *indx;
     free_imatrix(outcome,1,maxwav+1,1,n);  
     free_vector(moisnais,1,n);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     free_vector(annais,1,n);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     /* free_matrix(mint,1,maxwav,1,n);    void lubksb(double **a, int npar, int *indx, double b[]) ;
        free_matrix(anint,1,maxwav,1,n);*/    void ludcmp(double **a, int npar, int *indx, double *d) ;
     free_vector(moisdc,1,n);    double gompertz(double p[]);
     free_vector(andc,1,n);    hess=matrix(1,npar,1,npar);
   
        printf("\nCalculation of the hessian matrix. Wait...\n");
     wav=ivector(1,imx);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    for (i=1;i<=npar;i++){
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      printf("%d",i);fflush(stdout);
          fprintf(ficlog,"%d",i);fflush(ficlog);
     /* Concatenates waves */     
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       
       /*  printf(" %f ",p[i]);
       Tcode=ivector(1,100);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    }
       ncodemax[1]=1;    
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    for (i=1;i<=npar;i++) {
            for (j=1;j<=npar;j++)  {
    codtab=imatrix(1,100,1,10);        if (j>i) { 
    h=0;          printf(".%d%d",i,j);fflush(stdout);
    m=pow(2,cptcoveff);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
            hess[i][j]=hessij(p,delti,i,j,func,npar);
    for(k=1;k<=cptcoveff; k++){          
      for(i=1; i <=(m/pow(2,k));i++){          hess[j][i]=hess[i][j];    
        for(j=1; j <= ncodemax[k]; j++){          /*printf(" %lf ",hess[i][j]);*/
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        }
            h++;      }
            if (h>m) h=1;codtab[h][k]=j;    }
          }    printf("\n");
        }    fprintf(ficlog,"\n");
      }  
    }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
        fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
    /* Calculates basic frequencies. Computes observed prevalence at single age    
        and prints on file fileres'p'. */    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
        x=vector(1,npar);
        indx=ivector(1,npar);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    for (i=1;i<=npar;i++)
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    ludcmp(a,npar,indx,&pd);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    for (j=1;j<=npar;j++) {
            for (i=1;i<=npar;i++) x[i]=0;
     /* For Powell, parameters are in a vector p[] starting at p[1]      x[j]=1;
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */      lubksb(a,npar,indx,x);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
     if(mle==1){      }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    }
     }  
        printf("\n#Hessian matrix#\n");
     /*--------- results files --------------*/    fprintf(ficlog,"\n#Hessian matrix#\n");
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);    for (i=1;i<=npar;i++) { 
        for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
    jk=1;        fprintf(ficlog,"%.3e ",hess[i][j]);
    fprintf(ficres,"# Parameters\n");      }
    printf("# Parameters\n");      printf("\n");
    for(i=1,jk=1; i <=nlstate; i++){      fprintf(ficlog,"\n");
      for(k=1; k <=(nlstate+ndeath); k++){    }
        if (k != i)  
          {    /* Recompute Inverse */
            printf("%d%d ",i,k);    for (i=1;i<=npar;i++)
            fprintf(ficres,"%1d%1d ",i,k);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
            for(j=1; j <=ncovmodel; j++){    ludcmp(a,npar,indx,&pd);
              printf("%f ",p[jk]);  
              fprintf(ficres,"%f ",p[jk]);    /*  printf("\n#Hessian matrix recomputed#\n");
              jk++;  
            }    for (j=1;j<=npar;j++) {
            printf("\n");      for (i=1;i<=npar;i++) x[i]=0;
            fprintf(ficres,"\n");      x[j]=1;
          }      lubksb(a,npar,indx,x);
      }      for (i=1;i<=npar;i++){ 
    }        y[i][j]=x[i];
  if(mle==1){        printf("%.3e ",y[i][j]);
     /* Computing hessian and covariance matrix */        fprintf(ficlog,"%.3e ",y[i][j]);
     ftolhess=ftol; /* Usually correct */      }
     hesscov(matcov, p, npar, delti, ftolhess, func);      printf("\n");
  }      fprintf(ficlog,"\n");
     fprintf(ficres,"# Scales\n");    }
     printf("# Scales\n");    */
      for(i=1,jk=1; i <=nlstate; i++){  
       for(j=1; j <=nlstate+ndeath; j++){    free_matrix(a,1,npar,1,npar);
         if (j!=i) {    free_matrix(y,1,npar,1,npar);
           fprintf(ficres,"%1d%1d",i,j);    free_vector(x,1,npar);
           printf("%1d%1d",i,j);    free_ivector(indx,1,npar);
           for(k=1; k<=ncovmodel;k++){    free_matrix(hess,1,npar,1,npar);
             printf(" %.5e",delti[jk]);  
             fprintf(ficres," %.5e",delti[jk]);  
             jk++;  }
           }  
           printf("\n");  /*************** hessian matrix ****************/
           fprintf(ficres,"\n");  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
         }  {
       }    int i;
      }    int l=1, lmax=20;
        double k1,k2;
     k=1;    double p2[MAXPARM+1]; /* identical to x */
     fprintf(ficres,"# Covariance\n");    double res;
     printf("# Covariance\n");    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     for(i=1;i<=npar;i++){    double fx;
       /*  if (k>nlstate) k=1;    int k=0,kmax=10;
       i1=(i-1)/(ncovmodel*nlstate)+1;    double l1;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);  
       printf("%s%d%d",alph[k],i1,tab[i]);*/    fx=func(x);
       fprintf(ficres,"%3d",i);    for (i=1;i<=npar;i++) p2[i]=x[i];
       printf("%3d",i);    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
       for(j=1; j<=i;j++){      l1=pow(10,l);
         fprintf(ficres," %.5e",matcov[i][j]);      delts=delt;
         printf(" %.5e",matcov[i][j]);      for(k=1 ; k <kmax; k=k+1){
       }        delt = delta*(l1*k);
       fprintf(ficres,"\n");        p2[theta]=x[theta] +delt;
       printf("\n");        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
       k++;        p2[theta]=x[theta]-delt;
     }        k2=func(p2)-fx;
            /*res= (k1-2.0*fx+k2)/delt/delt; */
     while((c=getc(ficpar))=='#' && c!= EOF){        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       ungetc(c,ficpar);        
       fgets(line, MAXLINE, ficpar);  #ifdef DEBUGHESS
       puts(line);        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);
       fputs(line,ficparo);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     }  #endif
     ungetc(c,ficpar);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
          if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);          k=kmax;
            }
     if (fage <= 2) {        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       bage = agemin;          k=kmax; l=lmax*10;
       fage = agemax;        }
     }        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
     fprintf(ficres,"# agemin agemax for life expectancy.\n");        }
       }
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    }
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    delti[theta]=delts;
      return res; 
     while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);  }
     fgets(line, MAXLINE, ficpar);  
     puts(line);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     fputs(line,ficparo);  {
   }    int i;
   ungetc(c,ficpar);    int l=1, lmax=20;
      double k1,k2,k3,k4,res,fx;
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);    double p2[MAXPARM+1];
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);    int k;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);  
          fx=func(x);
   while((c=getc(ficpar))=='#' && c!= EOF){    for (k=1; k<=2; k++) {
     ungetc(c,ficpar);      for (i=1;i<=npar;i++) p2[i]=x[i];
     fgets(line, MAXLINE, ficpar);      p2[thetai]=x[thetai]+delti[thetai]/k;
     puts(line);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     fputs(line,ficparo);      k1=func(p2)-fx;
   }    
   ungetc(c,ficpar);      p2[thetai]=x[thetai]+delti[thetai]/k;
        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   fscanf(ficpar,"pop_based=%d\n",&popbased);      k3=func(p2)-fx;
    fprintf(ficparo,"pop_based=%d\n",popbased);      
    fprintf(ficres,"pop_based=%d\n",popbased);        p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   while((c=getc(ficpar))=='#' && c!= EOF){      k4=func(p2)-fx;
     ungetc(c,ficpar);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     fgets(line, MAXLINE, ficpar);  #ifdef DEBUG
     puts(line);      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);
     fputs(line,ficparo);      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   }  #endif
   ungetc(c,ficpar);    }
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);    return res;
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);  }
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);  
   /************** Inverse of matrix **************/
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);  void ludcmp(double **a, int n, int *indx, double *d) 
   { 
  /*------------ gnuplot -------------*/    int i,imax,j,k; 
 chdir(pathcd);    double big,dum,sum,temp; 
   if((ficgp=fopen("graph.plt","w"))==NULL) {    double *vv; 
     printf("Problem with file graph.gp");goto end;   
   }    vv=vector(1,n); 
 #ifdef windows    *d=1.0; 
   fprintf(ficgp,"cd \"%s\" \n",pathc);    for (i=1;i<=n;i++) { 
 #endif      big=0.0; 
 m=pow(2,cptcoveff);      for (j=1;j<=n;j++) 
          if ((temp=fabs(a[i][j])) > big) big=temp; 
  /* 1eme*/      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   for (cpt=1; cpt<= nlstate ; cpt ++) {      vv[i]=1.0/big; 
    for (k1=1; k1<= m ; k1 ++) {    } 
     for (j=1;j<=n;j++) { 
 #ifdef windows      for (i=1;i<j;i++) { 
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);        sum=a[i][j]; 
 #endif        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
 #ifdef unix        a[i][j]=sum; 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      } 
 #endif      big=0.0; 
       for (i=j;i<=n;i++) { 
 for (i=1; i<= nlstate ; i ++) {        sum=a[i][j]; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for (k=1;k<j;k++) 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          sum -= a[i][k]*a[k][j]; 
 }        a[i][j]=sum; 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     for (i=1; i<= nlstate ; i ++) {          big=dum; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          imax=i; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");        } 
 }      } 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      if (j != imax) { 
      for (i=1; i<= nlstate ; i ++) {        for (k=1;k<=n;k++) { 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          dum=a[imax][k]; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          a[imax][k]=a[j][k]; 
 }            a[j][k]=dum; 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        } 
 #ifdef unix        *d = -(*d); 
 fprintf(ficgp,"\nset ter gif small size 400,300");        vv[imax]=vv[j]; 
 #endif      } 
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      indx[j]=imax; 
    }      if (a[j][j] == 0.0) a[j][j]=TINY; 
   }      if (j != n) { 
   /*2 eme*/        dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   for (k1=1; k1<= m ; k1 ++) {      } 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    } 
        free_vector(vv,1,n);  /* Doesn't work */
     for (i=1; i<= nlstate+1 ; i ++) {  ;
       k=2*i;  } 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {  void lubksb(double **a, int n, int *indx, double b[]) 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  { 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    int i,ii=0,ip,j; 
 }      double sum; 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");   
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    for (i=1;i<=n;i++) { 
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      ip=indx[i]; 
       for (j=1; j<= nlstate+1 ; j ++) {      sum=b[ip]; 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      b[ip]=b[i]; 
         else fprintf(ficgp," \%%*lf (\%%*lf)");      if (ii) 
 }          for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       fprintf(ficgp,"\" t\"\" w l 0,");      else if (sum) ii=i; 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      b[i]=sum; 
       for (j=1; j<= nlstate+1 ; j ++) {    } 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    for (i=n;i>=1;i--) { 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      sum=b[i]; 
 }        for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      b[i]=sum/a[i][i]; 
       else fprintf(ficgp,"\" t\"\" w l 0,");    } 
     }  } 
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);  
   }  void pstamp(FILE *fichier)
    {
   /*3eme*/    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   }
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<= nlstate ; cpt ++) {  /************ Frequencies ********************/
       k=2+nlstate*(cpt-1);  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[])
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);  {  /* Some frequencies */
       for (i=1; i< nlstate ; i ++) {    
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);    int i, m, jk, j1, bool, z1,j;
       }    int first;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    double ***freq; /* Frequencies */
     }    double *pp, **prop;
   }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
      char fileresp[FILENAMELENGTH];
   /* CV preval stat */    
   for (k1=1; k1<= m ; k1 ++) {    pp=vector(1,nlstate);
     for (cpt=1; cpt<nlstate ; cpt ++) {    prop=matrix(1,nlstate,iagemin,iagemax+3);
       k=3;    strcpy(fileresp,"p");
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);    strcat(fileresp,fileres);
       for (i=1; i< nlstate ; i ++)    if((ficresp=fopen(fileresp,"w"))==NULL) {
         fprintf(ficgp,"+$%d",k+i+1);      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
            exit(0);
       l=3+(nlstate+ndeath)*cpt;    }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
       for (i=1; i< nlstate ; i ++) {    j1=0;
         l=3+(nlstate+ndeath)*cpt;    
         fprintf(ficgp,"+$%d",l+i+1);    j=cptcoveff;
       }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    first=1;
     }  
   }      /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
     /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
   /* proba elementaires */    /*    j1++; */
    for(i=1,jk=1; i <=nlstate; i++){    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
     for(k=1; k <=(nlstate+ndeath); k++){        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       if (k != i) {          scanf("%d", i);*/
         for(j=1; j <=ncovmodel; j++){        for (i=-5; i<=nlstate+ndeath; i++)  
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/          for (jk=-5; jk<=nlstate+ndeath; jk++)  
           /*fprintf(ficgp,"%s",alph[1]);*/            for(m=iagemin; m <= iagemax+3; m++)
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);              freq[i][jk][m]=0;
           jk++;        
           fprintf(ficgp,"\n");        for (i=1; i<=nlstate; i++)  
         }          for(m=iagemin; m <= iagemax+3; m++)
       }            prop[i][m]=0;
     }        
     }        dateintsum=0;
         k2cpt=0;
   for(jk=1; jk <=m; jk++) {        for (i=1; i<=imx; i++) {
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);          bool=1;
    i=1;          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
    for(k2=1; k2<=nlstate; k2++) {            for (z1=1; z1<=cptcoveff; z1++)       
      k3=i;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
      for(k=1; k<=(nlstate+ndeath); k++) {                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
        if (k != k2){                bool=0;
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);                /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
 ij=1;                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
         for(j=3; j <=ncovmodel; j++) {                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);              } 
             ij++;          }
           }   
           else          if (bool==1){
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            for(m=firstpass; m<=lastpass; m++){
         }              k2=anint[m][i]+(mint[m][i]/12.);
           fprintf(ficgp,")/(1");              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                        if(agev[m][i]==0) agev[m][i]=iagemax+1;
         for(k1=1; k1 <=nlstate; k1++){                  if(agev[m][i]==1) agev[m][i]=iagemax+2;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
 ij=1;                if (m<lastpass) {
           for(j=3; j <=ncovmodel; j++){                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                }
             ij++;                
           }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
           else                  dateintsum=dateintsum+k2;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                  k2cpt++;
           }                }
           fprintf(ficgp,")");                /*}*/
         }            }
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);          }
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        } /* end i */
         i=i+ncovmodel;         
        }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
      }        pstamp(ficresp);
    }        if  (cptcovn>0) {
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);          fprintf(ficresp, "\n#********** Variable "); 
   }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
              fprintf(ficresp, "**********\n#");
   fclose(ficgp);          fprintf(ficlog, "\n#********** Variable "); 
              for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 chdir(path);          fprintf(ficlog, "**********\n#");
            }
     free_ivector(wav,1,imx);        for(i=1; i<=nlstate;i++) 
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          fprintf(ficresp, "\n");
     free_ivector(num,1,n);        
     free_vector(agedc,1,n);        for(i=iagemin; i <= iagemax+3; i++){
     /*free_matrix(covar,1,NCOVMAX,1,n);*/          if(i==iagemax+3){
     fclose(ficparo);            fprintf(ficlog,"Total");
     fclose(ficres);          }else{
     /*  }*/            if(first==1){
                  first=0;
    /*________fin mle=1_________*/              printf("See log file for details...\n");
                }
             fprintf(ficlog,"Age %d", i);
            }
     /* No more information from the sample is required now */          for(jk=1; jk <=nlstate ; jk++){
   /* Reads comments: lines beginning with '#' */            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   while((c=getc(ficpar))=='#' && c!= EOF){              pp[jk] += freq[jk][m][i]; 
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);          for(jk=1; jk <=nlstate ; jk++){
     puts(line);            for(m=-1, pos=0; m <=0 ; m++)
     fputs(line,ficparo);              pos += freq[jk][m][i];
   }            if(pp[jk]>=1.e-10){
   ungetc(c,ficpar);              if(first==1){
                  printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);              }
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);            }else{
 /*--------- index.htm --------*/              if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   strcpy(optionfilehtm,optionfile);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   strcat(optionfilehtm,".htm");            }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          }
     printf("Problem with %s \n",optionfilehtm);goto end;  
   }          for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">              pp[jk] += freq[jk][m][i];
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>          }       
 Total number of observations=%d <br>          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>            pos += pp[jk];
 <hr  size=\"2\" color=\"#EC5E5E\">            posprop += prop[jk][i];
 <li>Outputs files<br><br>\n          }
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          for(jk=1; jk <=nlstate ; jk++){
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>            if(pos>=1.e-5){
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>              if(first==1)
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>            }else{
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>              if(first==1)
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>            }
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);            if( i <= iagemax){
               if(pos>=1.e-5){
  fprintf(fichtm," <li>Graphs</li><p>");                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
  m=cptcoveff;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}              }
               else
  j1=0;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
  for(k1=1; k1<=m;k1++){            }
    for(i1=1; i1<=ncodemax[k1];i1++){          }
        j1++;          
        if (cptcovn > 0) {          for(jk=-1; jk <=nlstate+ndeath; jk++)
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");            for(m=-1; m <=nlstate+ndeath; m++)
          for (cpt=1; cpt<=cptcoveff;cpt++)              if(freq[jk][m][i] !=0 ) {
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);              if(first==1)
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
        }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>              }
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);              if(i <= iagemax)
        for(cpt=1; cpt<nlstate;cpt++){            fprintf(ficresp,"\n");
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>          if(first==1)
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);            printf("Others in log...\n");
        }          fprintf(ficlog,"\n");
     for(cpt=1; cpt<=nlstate;cpt++) {        }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        /*}*/
 interval) in state (%d): v%s%d%d.gif <br>    }
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      dateintmean=dateintsum/k2cpt; 
      }   
      for(cpt=1; cpt<=nlstate;cpt++) {    fclose(ficresp);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    free_vector(pp,1,nlstate);
      }    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    /* End of Freq */
 health expectancies in states (1) and (2): e%s%d.gif<br>  }
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);  
 fprintf(fichtm,"\n</body>");  /************ Prevalence ********************/
    }  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
  }  {  
 fclose(fichtm);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
   /*--------------- Prevalence limit --------------*/       We still use firstpass and lastpass as another selection.
      */
   strcpy(filerespl,"pl");   
   strcat(filerespl,fileres);    int i, m, jk, j1, bool, z1,j;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    double **prop;
   }    double posprop; 
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    double  y2; /* in fractional years */
   fprintf(ficrespl,"#Prevalence limit\n");    int iagemin, iagemax;
   fprintf(ficrespl,"#Age ");    int first; /** to stop verbosity which is redirected to log file */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  
   fprintf(ficrespl,"\n");    iagemin= (int) agemin;
      iagemax= (int) agemax;
   prlim=matrix(1,nlstate,1,nlstate);    /*pp=vector(1,nlstate);*/
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    j1=0;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    /*j=cptcoveff;*/
   k=0;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   agebase=agemin;    
   agelim=agemax;    first=1;
   ftolpl=1.e-10;    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
   i1=cptcoveff;      /*for(i1=1; i1<=ncodemax[k1];i1++){
   if (cptcovn < 1){i1=1;}        j1++;*/
         
   for(cptcov=1;cptcov<=i1;cptcov++){        for (i=1; i<=nlstate; i++)  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for(m=iagemin; m <= iagemax+3; m++)
         k=k+1;            prop[i][m]=0.0;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/       
         fprintf(ficrespl,"\n#******");        for (i=1; i<=imx; i++) { /* Each individual */
         for(j=1;j<=cptcoveff;j++)          bool=1;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          if  (cptcovn>0) {
         fprintf(ficrespl,"******\n");            for (z1=1; z1<=cptcoveff; z1++) 
                      if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         for (age=agebase; age<=agelim; age++){                bool=0;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          } 
           fprintf(ficrespl,"%.0f",age );          if (bool==1) { 
           for(i=1; i<=nlstate;i++)            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
           fprintf(ficrespl," %.5f", prlim[i][i]);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
           fprintf(ficrespl,"\n");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   fclose(ficrespl);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
   /*------------- h Pij x at various ages ------------*/                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                    prop[s[m][i]][iagemax+3] += weight[i]; 
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);                } 
   if((ficrespij=fopen(filerespij,"w"))==NULL) {              }
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;            } /* end selection of waves */
   }          }
   printf("Computing pij: result on file '%s' \n", filerespij);        }
          for(i=iagemin; i <= iagemax+3; i++){  
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   /*if (stepm<=24) stepsize=2;*/            posprop += prop[jk][i]; 
           } 
   agelim=AGESUP;          
   hstepm=stepsize*YEARM; /* Every year of age */          for(jk=1; jk <=nlstate ; jk++){     
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */            if( i <=  iagemax){ 
                if(posprop>=1.e-5){ 
   k=0;                probs[i][jk][j1]= prop[jk][i]/posprop;
   for(cptcov=1;cptcov<=i1;cptcov++){              } else{
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                if(first==1){
       k=k+1;                  first=0;
         fprintf(ficrespij,"\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]);
         for(j=1;j<=cptcoveff;j++)                }
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              }
         fprintf(ficrespij,"******\n");            } 
                  }/* end jk */ 
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        }/* end i */ 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      /*} *//* end i1 */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    } /* end j1 */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
           oldm=oldms;savm=savms;    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      /*free_vector(pp,1,nlstate);*/
           fprintf(ficrespij,"# Age");    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
           for(i=1; i<=nlstate;i++)  }  /* End of prevalence */
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %1d-%1d",i,j);  /************* Waves Concatenation ***************/
           fprintf(ficrespij,"\n");  
           for (h=0; h<=nhstepm; h++){  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)
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  {
             for(i=1; i<=nlstate;i++)    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
               for(j=1; j<=nlstate+ndeath;j++)       Death is a valid wave (if date is known).
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
             fprintf(ficrespij,"\n");       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
           }       and mw[mi+1][i]. dh depends on stepm.
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       */
           fprintf(ficrespij,"\n");  
         }    int i, mi, m;
     }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   }       double sum=0., jmean=0.;*/
     int first;
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    int j, k=0,jk, ju, jl;
     double sum=0.;
   fclose(ficrespij);    first=0;
     jmin=100000;
   /*---------- Forecasting ------------------*/    jmax=-1;
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    jmean=0.;
     for(i=1; i<=imx; i++){
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      mi=0;
       m=firstpass;
       while(s[m][i] <= nlstate){
   strcpy(fileresf,"f");        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   strcat(fileresf,fileres);          mw[++mi][i]=m;
   if((ficresf=fopen(fileresf,"w"))==NULL) {        if(m >=lastpass)
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;          break;
   }        else
   printf("Computing forecasting: result on file '%s' \n", fileresf);          m++;
       }/* end while */
   free_matrix(mint,1,maxwav,1,n);      if (s[m][i] > nlstate){
   free_matrix(anint,1,maxwav,1,n);        mi++;     /* Death is another wave */
   free_matrix(agev,1,maxwav,1,imx);        /* if(mi==0)  never been interviewed correctly before death */
   /* Mobile average */           /* Only death is a correct wave */
         mw[mi][i]=m;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      }
   
   if (mobilav==1) {      wav[i]=mi;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      if(mi==0){
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)        nbwarn++;
       for (i=1; i<=nlstate;i++)        if(first==0){
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           mobaverage[(int)agedeb][i][cptcod]=0.;          first=1;
            }
     for (agedeb=bage+4; agedeb<=fage; agedeb++){        if(first==1){
       for (i=1; i<=nlstate;i++){          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        }
           for (cpt=0;cpt<=4;cpt++){      } /* end mi==0 */
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    } /* End individuals */
           }  
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    for(i=1; i<=imx; i++){
         }      for(mi=1; mi<wav[i];mi++){
       }        if (stepm <=0)
     }            dh[mi][i]=1;
   }        else{
           if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   stepsize=(int) (stepm+YEARM-1)/YEARM;            if (agedc[i] < 2*AGESUP) {
   if (stepm<=12) stepsize=1;              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               if(j==0) j=1;  /* Survives at least one month after exam */
   agelim=AGESUP;              else if(j<0){
   /*hstepm=stepsize*YEARM; *//* Every year of age */                nberr++;
   hstepm=1;                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]);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */                j=1; /* Temporary Dangerous patch */
   yp1=modf(dateintmean,&yp);                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);
   anprojmean=yp;                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]);
   yp2=modf((yp1*12),&yp);                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);
   mprojmean=yp;              }
   yp1=modf((yp2*30.5),&yp);              k=k+1;
   jprojmean=yp;              if (j >= jmax){
   if(jprojmean==0) jprojmean=1;                jmax=j;
   if(mprojmean==0) jprojmean=1;                ijmax=i;
               }
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);              if (j <= jmin){
                 jmin=j;
   if (popforecast==1) {                ijmin=i;
     if((ficpop=fopen(popfile,"r"))==NULL)    {              }
       printf("Problem with population file : %s\n",popfile);goto end;              sum=sum+j;
     }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     popage=ivector(0,AGESUP);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     popeffectif=vector(0,AGESUP);            }
     popcount=vector(0,AGESUP);          }
           else{
     i=1;              j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)  /*        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]); */
       {  
         i=i+1;            k=k+1;
       }            if (j >= jmax) {
     imx=i;              jmax=j;
                  ijmax=i;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];            }
   }            else if (j <= jmin){
               jmin=j;
   for(cptcov=1;cptcov<=i1;cptcov++){              ijmin=i;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            }
       k=k+1;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       fprintf(ficresf,"\n#******");            /*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]);*/
       for(j=1;j<=cptcoveff;j++) {            if(j<0){
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              nberr++;
       }              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       fprintf(ficresf,"******\n");              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]);
       fprintf(ficresf,"# StartingAge FinalAge");            }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);            sum=sum+j;
       if (popforecast==1)  fprintf(ficresf," [Population]");          }
            jk= j/stepm;
       for (cpt=0; cpt<=5;cpt++) {          jl= j -jk*stepm;
         fprintf(ficresf,"\n");          ju= j -(jk+1)*stepm;
   fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */            if(jl==0){
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              dh[mi][i]=jk;
         nhstepm = nhstepm/hstepm;              bh[mi][i]=0;
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/            }else{ /* We want a negative bias in order to only have interpolation ie
                     * to avoid the price of an extra matrix product in likelihood */
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              dh[mi][i]=jk+1;
         oldm=oldms;savm=savms;              bh[mi][i]=ju;
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              }
                          }else{
         for (h=0; h<=nhstepm; h++){            if(jl <= -ju){
           if (h==(int) (calagedate+YEARM*cpt)) {              dh[mi][i]=jk;
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);              bh[mi][i]=jl;       /* bias is positive if real duration
           }                                   * is higher than the multiple of stepm and negative otherwise.
           for(j=1; j<=nlstate+ndeath;j++) {                                   */
             kk1=0.;kk2=0;            }
             for(i=1; i<=nlstate;i++) {                    else{
               if (mobilav==1)              dh[mi][i]=jk+1;
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];              bh[mi][i]=ju;
               else {            }
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            if(dh[mi][i]==0){
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/              dh[mi][i]=1; /* At least one step */
               }              bh[mi][i]=ju; /* At least one step */
               /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];            }
             }          } /* end if mle */
                  }
             if (h==(int)(calagedate+12*cpt)){      } /* end wave */
               fprintf(ficresf," %.3f", kk1);    }
                  jmean=sum/k;
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);    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);
           }   }
         }  
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*********** Tricode ****************************/
       }  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
       }  {
     }    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   }    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * Boring subroutine which should only output nbcode[Tvar[j]][k]
   if (popforecast==1) {     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
     free_ivector(popage,0,AGESUP);     * nbcode[Tvar[j]][1]= 
     free_vector(popeffectif,0,AGESUP);    */
     free_vector(popcount,0,AGESUP);  
   }    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   free_imatrix(s,1,maxwav+1,1,n);    int modmaxcovj=0; /* Modality max of covariates j */
   free_vector(weight,1,n);    int cptcode=0; /* Modality max of covariates j */
   fclose(ficresf);    int modmincovj=0; /* Modality min of covariates j */
   /*---------- Health expectancies and variances ------------*/  
   
   strcpy(filerest,"t");    cptcoveff=0; 
   strcat(filerest,fileres);   
   if((ficrest=fopen(filerest,"w"))==NULL) {    for (k=-1; k < maxncov; k++) Ndum[k]=0;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    /* Loop on covariates without age and products */
     for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
       for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
   strcpy(filerese,"e");                                 modality of this covariate Vj*/ 
   strcat(filerese,fileres);        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
   if((ficreseij=fopen(filerese,"w"))==NULL) {                                      * If product of Vn*Vm, still boolean *:
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                                      * 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   */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                                         modality of the nth covariate of individual i. */
  strcpy(fileresv,"v");        if (ij > modmaxcovj)
   strcat(fileresv,fileres);          modmaxcovj=ij; 
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        else if (ij < modmincovj) 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);          modmincovj=ij; 
   }        if ((ij < -1) && (ij > NCOVMAX)){
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
           exit(1);
   k=0;        }else
   for(cptcov=1;cptcov<=i1;cptcov++){        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
       k=k+1;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       fprintf(ficrest,"\n#****** ");        /* getting the maximum value of the modality of the covariate
       for(j=1;j<=cptcoveff;j++)           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);           female is 1, then modmaxcovj=1.*/
       fprintf(ficrest,"******\n");      }
       printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
       fprintf(ficreseij,"\n#****** ");      cptcode=modmaxcovj;
       for(j=1;j<=cptcoveff;j++)      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);     /*for (i=0; i<=cptcode; i++) {*/
       fprintf(ficreseij,"******\n");      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
         printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
       fprintf(ficresvij,"\n#****** ");        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
       for(j=1;j<=cptcoveff;j++)          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);        }
       fprintf(ficresvij,"******\n");        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
            historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      } /* Ndum[-1] number of undefined modalities */
       oldm=oldms;savm=savms;  
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);        /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
       oldm=oldms;savm=savms;      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);         modmincovj=3; modmaxcovj = 7;
               There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);         variables V1_1 and V1_2.
       fprintf(ficrest,"\n");         nbcode[Tvar[j]][ij]=k;
                 nbcode[Tvar[j]][1]=0;
       hf=1;         nbcode[Tvar[j]][2]=1;
       if (stepm >= YEARM) hf=stepm/YEARM;         nbcode[Tvar[j]][3]=2;
       epj=vector(1,nlstate+1);      */
       for(age=bage; age <=fage ;age++){      ij=1; /* ij is similar to i but can jumps over null modalities */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
         if (popbased==1) {        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
           for(i=1; i<=nlstate;i++)          /*recode from 0 */
             prlim[i][i]=probs[(int)age][i][k];          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
         }            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
                                               k is a modality. If we have model=V1+V1*sex 
         fprintf(ficrest," %.0f",age);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){            ij++;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          }
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];          if (ij > ncodemax[j]) break; 
           }        }  /* end of loop on */
           epj[nlstate+1] +=epj[j];      } /* end of loop on modality */ 
         }    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
         for(i=1, vepp=0.;i <=nlstate;i++)    
           for(j=1;j <=nlstate;j++)   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
             vepp += vareij[i][j][(int)age];    
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
         for(j=1;j <=nlstate;j++){     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
         }     Ndum[ij]++; 
         fprintf(ficrest,"\n");   } 
       }  
     }   ij=1;
   }   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)){
        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
        Tvaraff[ij]=i; /*For printing (unclear) */
  fclose(ficreseij);       ij++;
  fclose(ficresvij);     }else
   fclose(ficrest);         Tvaraff[ij]=0;
   fclose(ficpar);   }
   free_vector(epj,1,nlstate+1);   ij--;
   /*  scanf("%d ",i); */   cptcoveff=ij; /*Number of total covariates*/
   
   /*------- Variance limit prevalence------*/    }
   
 strcpy(fileresvpl,"vpl");  
   strcat(fileresvpl,fileres);  /*********** Health Expectancies ****************/
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
     exit(0);  
   }  {
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    /* Health expectancies, no variances */
     int i, j, nhstepm, hstepm, h, nstepm;
  k=0;    int nhstepma, nstepma; /* Decreasing with age */
  for(cptcov=1;cptcov<=i1;cptcov++){    double age, agelim, hf;
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double ***p3mat;
      k=k+1;    double eip;
      fprintf(ficresvpl,"\n#****** ");  
      for(j=1;j<=cptcoveff;j++)    pstamp(ficreseij);
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
      fprintf(ficresvpl,"******\n");    fprintf(ficreseij,"# Age");
          for(i=1; i<=nlstate;i++){
      varpl=matrix(1,nlstate,(int) bage, (int) fage);      for(j=1; j<=nlstate;j++){
      oldm=oldms;savm=savms;        fprintf(ficreseij," e%1d%1d ",i,j);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      }
    }      fprintf(ficreseij," e%1d. ",i);
  }    }
     fprintf(ficreseij,"\n");
   fclose(ficresvpl);  
     
   /*---------- End : free ----------------*/    if(estepm < stepm){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      printf ("Problem %d lower than %d\n",estepm, stepm);
      }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    else  hstepm=estepm;   
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    /* 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
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);     * we are calculating an estimate of the Life Expectancy assuming a linear 
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);     * progression in between and thus overestimating or underestimating according
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);     * to the curvature of the survival function. If, for the same date, we 
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);     * 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 
   free_matrix(matcov,1,npar,1,npar);     * hypothesis. A more precise result, taking into account a more precise
   free_vector(delti,1,npar);     * curvature will be obtained if estepm is as small as stepm. */
    
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    /* 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. 
   printf("End of Imach\n");       nhstepm is the number of hstepm from age to agelim 
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */       nstepm is the number of stepm from age to agelin. 
         Look at hpijx to understand the reason of that which relies in memory size
   /* 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);*/       and note for a fixed period like estepm months */
   /*printf("Total time was %d uSec.\n", total_usecs);*/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   /*------ End -----------*/       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 
  end:       results. So we changed our mind and took the option of the best precision.
 #ifdef windows    */
  chdir(pathcd);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 #endif  
      agelim=AGESUP;
  system("..\\gp37mgw\\wgnuplot graph.plt");    /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
 #ifdef windows         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   while (z[0] != 'q') {      
     chdir(pathcd);  /* nhstepm age range expressed in number of stepm */
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     scanf("%s",z);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     if (z[0] == 'c') system("./imach");    /* if (stepm >= YEARM) hstepm=1;*/
     else if (z[0] == 'e') {    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       chdir(path);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       system(optionfilehtm);  
     }    for (age=bage; age<=fage; age ++){ 
     else if (z[0] == 'q') exit(0);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 #endif      /* 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 pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",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]][codtab[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]][codtab[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]][codtab[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]][codtab[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]][codtab[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;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[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<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[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]][codtab[jj1][cpt]]);
          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>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance 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]][codtab[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 */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; 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)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  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]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[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]][codtab[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]][codtab[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]][codtab[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);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);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
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - 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];
   
     /*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;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 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  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%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;
       }
       
       /*   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]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+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 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*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 + */
     } /* end model */
     
     /*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()
    {
      /* #include "syscompilerinfo.h"*/
   
   #if defined __INTEL_COMPILER
      struct utsname sysInfo;
   #elif defined(__GNUC__) 
   #include <gnu/libc-version.h>  /* Only on gnu */
      struct utsname sysInfo;
   #endif
   
   #include <stdint.h>
      int cross = CROSS;
      if (cross){
        printf("Cross-");
        fprintf(ficlog,"Cross-");
      }
      printf("Compiled with:");fprintf(ficlog,"Compiled with:");
   #if defined(__clang__)
      printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
   #endif
   #if defined(__ICC) || defined(__INTEL_COMPILER)
      printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
   #endif
   #if defined(__GNUC__) || defined(__GNUG__)
      printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
   #endif
   #if defined(__HP_cc) || defined(__HP_aCC)
      printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
   #endif
   #if defined(__IBMC__) || defined(__IBMCPP__)
      printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
   #endif
   #if defined(_MSC_VER)
      printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
   #endif
   #if defined(__PGI)
      printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
   #endif
   #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
      printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
   #endif
      printf(" for ");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) ");fprintf(ficlog,"Windows (x64 and x86) ");
   #elif __unix__ // all unices, not all compilers
       // Unix
      printf("Unix ");fprintf(ficlog,"Unix ");
   #elif __linux__
       // linux
      printf("linux ");fprintf(ficlog,"linux ");
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
      printf("Mac OS ");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"); fprintf(ficlog," 32-bit");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
   #else
      printf(" wtf-bit"); 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__);
      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);
        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
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version()); 
   #endif
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              frintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
   
    }
   
   /***********************************************/
   /**************** 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 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;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt;
     int jl;
     int i1, j1, jk, stepsize;
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     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, agebase;
     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;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,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);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       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 --------*/
   
     /* 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,"\n%s\n%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();
   
     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 */
   
     /*---------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;
     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);
   
     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=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       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*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     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 choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose 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) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose 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 != j)){
             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,j);
           fprintf(ficlog,"%1d%1d",i,j);
           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.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         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");
       }
       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 */
   
   
     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 */
   
     /* 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
                         */  
   
     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 > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     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],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     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)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     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     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*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);
   
   
       
     /*------------ 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);*/
     /*--------- 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);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* 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*/
   
     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]));
   
       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 / */
       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 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       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; /* 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 */
         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=%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("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",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);
       }
       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);
       
       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(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 / */
       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);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       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); */
         /*      } */
       }
     
   
       /* 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(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);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       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: ");
       scanf("%s",z);
     }
   }

Removed from v.1.20  
changed lines
  Added in v.1.177


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