Diff for /imach/src/imach.c between versions 1.52 and 1.121

version 1.52, 2002/07/19 18:49:30 version 1.121, 2006/03/16 17:45:01
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.121  2006/03/16 17:45:01  lievre
      * imach.c (Module): Comments concerning covariates added
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    * imach.c (Module): refinements in the computation of lli if
   first survey ("cross") where individuals from different ages are    status=-2 in order to have more reliable computation if stepm is
   interviewed on their health status or degree of disability (in the    not 1 month. Version 0.98f
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.120  2006/03/16 15:10:38  lievre
   (if any) in individual health status.  Health expectancies are    (Module): refinements in the computation of lli if
   computed from the time spent in each health state according to a    status=-2 in order to have more reliable computation if stepm is
   model. More health states you consider, more time is necessary to reach the    not 1 month. Version 0.98f
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.119  2006/03/15 17:42:26  brouard
   probability to be observed in state j at the second wave    (Module): Bug if status = -2, the loglikelihood was
   conditional to be observed in state i at the first wave. Therefore    computed as likelihood omitting the logarithm. Version O.98e
   the model is: 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    Revision 1.118  2006/03/14 18:20:07  brouard
   complex model than "constant and age", you should modify the program    (Module): varevsij Comments added explaining the second
   where the markup *Covariates have to be included here again* invites    table of variances if popbased=1 .
   you to do it.  More covariates you add, slower the    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   convergence.    (Module): Function pstamp added
     (Module): Version 0.98d
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.117  2006/03/14 17:16:22  brouard
   identical for each individual. Also, if a individual missed an    (Module): varevsij Comments added explaining the second
   intermediate interview, the information is lost, but taken into    table of variances if popbased=1 .
   account using an interpolation or extrapolation.      (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
   hPijx is the probability to be observed in state i at age x+h    (Module): Version 0.98d
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Revision 1.116  2006/03/06 10:29:27  brouard
   states. This elementary transition (by month or quarter trimester,    (Module): Variance-covariance wrong links and
   semester or year) is model as a multinomial logistic.  The hPx    varian-covariance of ej. is needed (Saito).
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.115  2006/02/27 12:17:45  brouard
   hPijx.    (Module): One freematrix added in mlikeli! 0.98c
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.114  2006/02/26 12:57:58  brouard
   of the life expectancies. It also computes the prevalence limits.    (Module): Some improvements in processing parameter
      filename with strsep.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.113  2006/02/24 14:20:24  brouard
   This software have been partly granted by Euro-REVES, a concerted action    (Module): Memory leaks checks with valgrind and:
   from the European Union.    datafile was not closed, some imatrix were not freed and on matrix
   It is copyrighted identically to a GNU software product, ie programme and    allocation too.
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Revision 1.112  2006/01/30 09:55:26  brouard
   **********************************************************************/    (Module): Back to gnuplot.exe instead of wgnuplot.exe
    
 #include <math.h>    Revision 1.111  2006/01/25 20:38:18  brouard
 #include <stdio.h>    (Module): Lots of cleaning and bugs added (Gompertz)
 #include <stdlib.h>    (Module): Comments can be added in data file. Missing date values
 #include <unistd.h>    can be a simple dot '.'.
   
 #define MAXLINE 256    Revision 1.110  2006/01/25 00:51:50  brouard
 #define GNUPLOTPROGRAM "gnuplot"    (Module): Lots of cleaning and bugs added (Gompertz)
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    Revision 1.109  2006/01/24 19:37:15  brouard
 /*#define DEBUG*/    (Module): Comments (lines starting with a #) are allowed in data.
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.108  2006/01/19 18:05:42  lievre
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Gnuplot problem appeared...
     To be fixed
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.107  2006/01/19 16:20:37  brouard
     Test existence of gnuplot in imach path
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.106  2006/01/19 13:24:36  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Some cleaning and links added in html output
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.105  2006/01/05 20:23:19  lievre
 #define YEARM 12. /* Number of months per year */    *** empty log message ***
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.104  2005/09/30 16:11:43  lievre
 #ifdef windows    (Module): sump fixed, loop imx fixed, and simplifications.
 #define DIRSEPARATOR '\\'    (Module): If the status is missing at the last wave but we know
 #define ODIRSEPARATOR '/'    that the person is alive, then we can code his/her status as -2
 #else    (instead of missing=-1 in earlier versions) and his/her
 #define DIRSEPARATOR '/'    contributions to the likelihood is 1 - Prob of dying from last
 #define ODIRSEPARATOR '\\'    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 #endif    the healthy state at last known wave). Version is 0.98
   
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";    Revision 1.103  2005/09/30 15:54:49  lievre
 int erreur; /* Error number */    (Module): sump fixed, loop imx fixed, and simplifications.
 int nvar;  
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.102  2004/09/15 17:31:30  brouard
 int npar=NPARMAX;    Add the possibility to read data file including tab characters.
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.101  2004/09/15 10:38:38  brouard
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Fix on curr_time
 int popbased=0;  
     Revision 1.100  2004/07/12 18:29:06  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    Add version for Mac OS X. Just define UNIX in Makefile
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.99  2004/06/05 08:57:40  brouard
 int mle, weightopt;    *** empty log message ***
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.98  2004/05/16 15:05:56  brouard
 double jmean; /* Mean space between 2 waves */    New version 0.97 . First attempt to estimate force of mortality
 double **oldm, **newm, **savm; /* Working pointers to matrices */    directly from the data i.e. without the need of knowing the health
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    state at each age, but using a Gompertz model: log u =a + b*age .
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    This is the basic analysis of mortality and should be done before any
 FILE *ficlog;    other analysis, in order to test if the mortality estimated from the
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    cross-longitudinal survey is different from the mortality estimated
 FILE *ficresprobmorprev;    from other sources like vital statistic data.
 FILE *fichtm; /* Html File */  
 FILE *ficreseij;    The same imach parameter file can be used but the option for mle should be -3.
 char filerese[FILENAMELENGTH];  
 FILE  *ficresvij;    Agnès, who wrote this part of the code, tried to keep most of the
 char fileresv[FILENAMELENGTH];    former routines in order to include the new code within the former code.
 FILE  *ficresvpl;  
 char fileresvpl[FILENAMELENGTH];    The output is very simple: only an estimate of the intercept and of
 char title[MAXLINE];    the slope with 95% confident intervals.
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    Current limitations:
     A) Even if you enter covariates, i.e. with the
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 char filelog[FILENAMELENGTH]; /* Log file */    B) There is no computation of Life Expectancy nor Life Table.
 char filerest[FILENAMELENGTH];  
 char fileregp[FILENAMELENGTH];    Revision 1.97  2004/02/20 13:25:42  lievre
 char popfile[FILENAMELENGTH];    Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  
     Revision 1.96  2003/07/15 15:38:55  brouard
 #define NR_END 1    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #define FREE_ARG char*    rewritten within the same printf. Workaround: many printfs.
 #define FTOL 1.0e-10  
     Revision 1.95  2003/07/08 07:54:34  brouard
 #define NRANSI    * imach.c (Repository):
 #define ITMAX 200    (Repository): Using imachwizard code to output a more meaningful covariance
     matrix (cov(a12,c31) instead of numbers.
 #define TOL 2.0e-4  
     Revision 1.94  2003/06/27 13:00:02  brouard
 #define CGOLD 0.3819660    Just cleaning
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.93  2003/06/25 16:33:55  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 #define GOLD 1.618034    exist so I changed back to asctime which exists.
 #define GLIMIT 100.0    (Module): Version 0.96b
 #define TINY 1.0e-20  
     Revision 1.92  2003/06/25 16:30:45  brouard
 static double maxarg1,maxarg2;    (Module): On windows (cygwin) function asctime_r doesn't
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    exist so I changed back to asctime which exists.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.91  2003/06/25 15:30:29  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    * imach.c (Repository): Duplicated warning errors corrected.
 #define rint(a) floor(a+0.5)    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
 static double sqrarg;    is stamped in powell.  We created a new html file for the graphs
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    concerning matrix of covariance. It has extension -cov.htm.
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.90  2003/06/24 12:34:15  brouard
 int imx;    (Module): Some bugs corrected for windows. Also, when
 int stepm;    mle=-1 a template is output in file "or"mypar.txt with the design
 /* Stepm, step in month: minimum step interpolation*/    of the covariance matrix to be input.
   
 int estepm;    Revision 1.89  2003/06/24 12:30:52  brouard
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 int m,nb;    of the covariance matrix to be input.
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.88  2003/06/23 17:54:56  brouard
 double **pmmij, ***probs, ***mobaverage;    * 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.
 double dateintmean=0;  
     Revision 1.87  2003/06/18 12:26:01  brouard
 double *weight;    Version 0.96
 int **s; /* Status */  
 double *agedc, **covar, idx;    Revision 1.86  2003/06/17 20:04:08  brouard
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    (Module): Change position of html and gnuplot routines and added
     routine fileappend.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
 /**************** split *************************/    current date of interview. It may happen when the death was just
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    prior to the death. In this case, dh was negative and likelihood
 {    was wrong (infinity). We still send an "Error" but patch by
    char *s;                             /* pointer */    assuming that the date of death was just one stepm after the
    int  l1, l2;                         /* length counters */    interview.
     (Repository): Because some people have very long ID (first column)
    l1 = strlen( path );                 /* length of path */    we changed int to long in num[] and we added a new lvector for
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    memory allocation. But we also truncated to 8 characters (left
    s= strrchr( path, DIRSEPARATOR );            /* find last / */    truncation)
    if ( s == NULL ) {                   /* no directory, so use current */    (Repository): No more line truncation errors.
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)  
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/    Revision 1.84  2003/06/13 21:44:43  brouard
 #if     defined(__bsd__)                /* get current working directory */    * imach.c (Repository): Replace "freqsummary" at a correct
       extern char       *getwd( );    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
       if ( getwd( dirc ) == NULL ) {    parcimony.
 #else    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
       extern char       *getcwd( );  
     Revision 1.83  2003/06/10 13:39:11  lievre
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    *** empty log message ***
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.82  2003/06/05 15:57:20  brouard
       }    Add log in  imach.c and  fullversion number is now printed.
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  */
       s++;                              /* after this, the filename */  /*
       l2 = strlen( s );                 /* length of filename */     Interpolated Markov Chain
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Short summary of the programme:
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    
       dirc[l1-l2] = 0;                  /* add zero */    This program computes Healthy Life Expectancies from
    }    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
    l1 = strlen( dirc );                 /* length of directory */    first survey ("cross") where individuals from different ages are
 #ifdef windows    interviewed on their health status or degree of disability (in the
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    case of a health survey which is our main interest) -2- at least a
 #else    second wave of interviews ("longitudinal") which measure each change
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    (if any) in individual health status.  Health expectancies are
 #endif    computed from the time spent in each health state according to a
    s = strrchr( name, '.' );            /* find last / */    model. More health states you consider, more time is necessary to reach the
    s++;    Maximum Likelihood of the parameters involved in the model.  The
    strcpy(ext,s);                       /* save extension */    simplest model is the multinomial logistic model where pij is the
    l1= strlen( name);    probability to be observed in state j at the second wave
    l2= strlen( s)+1;    conditional to be observed in state i at the first wave. Therefore
    strncpy( finame, name, l1-l2);    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
    finame[l1-l2]= 0;    'age' is age and 'sex' is a covariate. If you want to have a more
    return( 0 );                         /* we're done */    complex model than "constant and age", you should modify the program
 }    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
     convergence.
 /******************************************/  
     The advantage of this computer programme, compared to a simple
 void replace(char *s, char*t)    multinomial logistic model, is clear when the delay between waves is not
 {    identical for each individual. Also, if a individual missed an
   int i;    intermediate interview, the information is lost, but taken into
   int lg=20;    account using an interpolation or extrapolation.  
   i=0;  
   lg=strlen(t);    hPijx is the probability to be observed in state i at age x+h
   for(i=0; i<= lg; i++) {    conditional to the observed state i at age x. The delay 'h' can be
     (s[i] = t[i]);    split into an exact number (nh*stepm) of unobserved intermediate
     if (t[i]== '\\') s[i]='/';    states. This elementary transition (by month, quarter,
   }    semester or year) is modelled as a multinomial logistic.  The hPx
 }    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
 int nbocc(char *s, char occ)    hPijx.
 {  
   int i,j=0;    Also this programme outputs the covariance matrix of the parameters but also
   int lg=20;    of the life expectancies. It also computes the period (stable) prevalence. 
   i=0;    
   lg=strlen(s);    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   for(i=0; i<= lg; i++) {             Institut national d'études démographiques, Paris.
   if  (s[i] == occ ) j++;    This software have been partly granted by Euro-REVES, a concerted action
   }    from the European Union.
   return j;    It is copyrighted identically to a GNU software product, ie programme and
 }    software can be distributed freely for non commercial use. Latest version
     can be accessed at http://euroreves.ined.fr/imach .
 void cutv(char *u,char *v, char*t, char occ)  
 {    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   /* cuts string t into u and v where u is ended by char occ excluding it    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)    
      gives u="abcedf" and v="ghi2j" */    **********************************************************************/
   int i,lg,j,p=0;  /*
   i=0;    main
   for(j=0; j<=strlen(t)-1; j++) {    read parameterfile
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    read datafile
   }    concatwav
     freqsummary
   lg=strlen(t);    if (mle >= 1)
   for(j=0; j<p; j++) {      mlikeli
     (u[j] = t[j]);    print results files
   }    if mle==1 
      u[p]='\0';       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
    for(j=0; j<= lg; j++) {        begin-prev-date,...
     if (j>=(p+1))(v[j-p-1] = t[j]);    open gnuplot file
   }    open html file
 }    period (stable) prevalence
      for age prevalim()
 /********************** nrerror ********************/    h Pij x
     variance of p varprob
 void nrerror(char error_text[])    forecasting if prevfcast==1 prevforecast call prevalence()
 {    health expectancies
   fprintf(stderr,"ERREUR ...\n");    Variance-covariance of DFLE
   fprintf(stderr,"%s\n",error_text);    prevalence()
   exit(1);     movingaverage()
 }    varevsij() 
 /*********************** vector *******************/    if popbased==1 varevsij(,popbased)
 double *vector(int nl, int nh)    total life expectancies
 {    Variance of period (stable) prevalence
   double *v;   end
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  */
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;  
 }  
    
 /************************ free vector ******************/  #include <math.h>
 void free_vector(double*v, int nl, int nh)  #include <stdio.h>
 {  #include <stdlib.h>
   free((FREE_ARG)(v+nl-NR_END));  #include <string.h>
 }  #include <unistd.h>
   
 /************************ivector *******************************/  #include <limits.h>
 int *ivector(long nl,long nh)  #include <sys/types.h>
 {  #include <sys/stat.h>
   int *v;  #include <errno.h>
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  extern int errno;
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;  /* #include <sys/time.h> */
 }  #include <time.h>
   #include "timeval.h"
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)  /* #include <libintl.h> */
 {  /* #define _(String) gettext (String) */
   free((FREE_ARG)(v+nl-NR_END));  
 }  #define MAXLINE 256
   
 /******************* imatrix *******************************/  #define GNUPLOTPROGRAM "gnuplot"
 int **imatrix(long nrl, long nrh, long ncl, long nch)  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  #define FILENAMELENGTH 132
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   int **m;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
    
   /* allocate pointers to rows */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  #define NINTERVMAX 8
   m -= nrl;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
    #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
    #define NCOVMAX 8 /* Maximum number of covariates */
   /* allocate rows and set pointers to them */  #define MAXN 20000
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #define YEARM 12. /* Number of months per year */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define AGESUP 130
   m[nrl] += NR_END;  #define AGEBASE 40
   m[nrl] -= ncl;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
    #ifdef UNIX
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  #define DIRSEPARATOR '/'
    #define CHARSEPARATOR "/"
   /* return pointer to array of pointers to rows */  #define ODIRSEPARATOR '\\'
   return m;  #else
 }  #define DIRSEPARATOR '\\'
   #define CHARSEPARATOR "\\"
 /****************** free_imatrix *************************/  #define ODIRSEPARATOR '/'
 void free_imatrix(m,nrl,nrh,ncl,nch)  #endif
       int **m;  
       long nch,ncl,nrh,nrl;  /* $Id$ */
      /* free an int matrix allocated by imatrix() */  /* $State$ */
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  char version[]="Imach version 0.98f, March 2006, INED-EUROREVES-Institut de longevite ";
   free((FREE_ARG) (m+nrl-NR_END));  char fullversion[]="$Revision$ $Date$"; 
 }  char strstart[80];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 /******************* matrix *******************************/  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 double **matrix(long nrl, long nrh, long ncl, long nch)  int nvar;
 {  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  int npar=NPARMAX;
   double **m;  int nlstate=2; /* Number of live states */
   int ndeath=1; /* Number of dead states */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   if (!m) nrerror("allocation failure 1 in matrix()");  int popbased=0;
   m += NR_END;  
   m -= nrl;  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav; /* Maxim number of waves */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int jmin, jmax; /* min, max spacing between 2 waves */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   m[nrl] += NR_END;  int gipmx, gsw; /* Global variables on the number of contributions 
   m[nrl] -= ncl;                     to the likelihood and the sum of weights (done by funcone)*/
   int mle, weightopt;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   return m;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 }  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
              * wave mi and wave mi+1 is not an exact multiple of stepm. */
 /*************************free matrix ************************/  double jmean; /* Mean space between 2 waves */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  double **oldm, **newm, **savm; /* Working pointers to matrices */
 {  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   free((FREE_ARG)(m+nrl-NR_END));  FILE *ficlog, *ficrespow;
 }  int globpr; /* Global variable for printing or not */
   double fretone; /* Only one call to likelihood */
 /******************* ma3x *******************************/  long ipmx; /* Number of contributions */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  double sw; /* Sum of weights */
 {  char filerespow[FILENAMELENGTH];
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   double ***m;  FILE *ficresilk;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  FILE *ficresprobmorprev;
   if (!m) nrerror("allocation failure 1 in matrix()");  FILE *fichtm, *fichtmcov; /* Html File */
   m += NR_END;  FILE *ficreseij;
   m -= nrl;  char filerese[FILENAMELENGTH];
   FILE *ficresstdeij;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  char fileresstde[FILENAMELENGTH];
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  FILE *ficrescveij;
   m[nrl] += NR_END;  char filerescve[FILENAMELENGTH];
   m[nrl] -= ncl;  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  char title[MAXLINE];
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   m[nrl][ncl] += NR_END;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   m[nrl][ncl] -= nll;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   for (j=ncl+1; j<=nch; j++)  char command[FILENAMELENGTH];
     m[nrl][j]=m[nrl][j-1]+nlay;  int  outcmd=0;
    
   for (i=nrl+1; i<=nrh; i++) {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  char filelog[FILENAMELENGTH]; /* Log file */
       m[i][j]=m[i][j-1]+nlay;  char filerest[FILENAMELENGTH];
   }  char fileregp[FILENAMELENGTH];
   return m;  char popfile[FILENAMELENGTH];
 }  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 {  struct timezone tzp;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  extern int gettimeofday();
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   free((FREE_ARG)(m+nrl-NR_END));  long time_value;
 }  extern long time();
   char strcurr[80], strfor[80];
 /***************** f1dim *************************/  
 extern int ncom;  char *endptr;
 extern double *pcom,*xicom;  long lval;
 extern double (*nrfunc)(double []);  
    #define NR_END 1
 double f1dim(double x)  #define FREE_ARG char*
 {  #define FTOL 1.0e-10
   int j;  
   double f;  #define NRANSI 
   double *xt;  #define ITMAX 200 
    
   xt=vector(1,ncom);  #define TOL 2.0e-4 
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);  #define CGOLD 0.3819660 
   free_vector(xt,1,ncom);  #define ZEPS 1.0e-10 
   return f;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 }  
   #define GOLD 1.618034 
 /*****************brent *************************/  #define GLIMIT 100.0 
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  #define TINY 1.0e-20 
 {  
   int iter;  static double maxarg1,maxarg2;
   double a,b,d,etemp;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   double fu,fv,fw,fx;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   double ftemp;    
   double p,q,r,tol1,tol2,u,v,w,x,xm;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   double e=0.0;  #define rint(a) floor(a+0.5)
    
   a=(ax < cx ? ax : cx);  static double sqrarg;
   b=(ax > cx ? ax : cx);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   x=w=v=bx;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   fw=fv=fx=(*f)(x);  int agegomp= AGEGOMP;
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);  int imx; 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  int stepm=1;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  /* Stepm, step in month: minimum step interpolation*/
     printf(".");fflush(stdout);  
     fprintf(ficlog,".");fflush(ficlog);  int estepm;
 #ifdef DEBUG  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  
     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  int m,nb;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  long *num;
 #endif  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       *xmin=x;  double **pmmij, ***probs;
       return fx;  double *ageexmed,*agecens;
     }  double dateintmean=0;
     ftemp=fu;  
     if (fabs(e) > tol1) {  double *weight;
       r=(x-w)*(fx-fv);  int **s; /* Status */
       q=(x-v)*(fx-fw);  double *agedc, **covar, idx;
       p=(x-v)*q-(x-w)*r;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
       q=2.0*(q-r);  double *lsurv, *lpop, *tpop;
       if (q > 0.0) p = -p;  
       q=fabs(q);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
       etemp=e;  double ftolhess; /* Tolerance for computing hessian */
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  /**************** split *************************/
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       else {  {
         d=p/q;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
         u=x+d;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
         if (u-a < tol2 || b-u < tol2)    */ 
           d=SIGN(tol1,xm-x);    char  *ss;                            /* pointer */
       }    int   l1, l2;                         /* length counters */
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    l1 = strlen(path );                   /* length of path */
     }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     fu=(*f)(u);    if ( ss == NULL ) {                   /* no directory, so determine current directory */
     if (fu <= fx) {      strcpy( name, path );               /* we got the fullname name because no directory */
       if (u >= x) a=x; else b=x;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       SHFT(v,w,x,u)        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
         SHFT(fv,fw,fx,fu)      /* get current working directory */
         } else {      /*    extern  char* getcwd ( char *buf , int len);*/
           if (u < x) a=u; else b=u;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
           if (fu <= fw || w == x) {        return( GLOCK_ERROR_GETCWD );
             v=w;      }
             w=u;      /* got dirc from getcwd*/
             fv=fw;      printf(" DIRC = %s \n",dirc);
             fw=fu;    } else {                              /* strip direcotry from path */
           } else if (fu <= fv || v == x || v == w) {      ss++;                               /* after this, the filename */
             v=u;      l2 = strlen( ss );                  /* length of filename */
             fv=fu;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
           }      strcpy( name, ss );         /* save file name */
         }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   }      dirc[l1-l2] = 0;                    /* add zero */
   nrerror("Too many iterations in brent");      printf(" DIRC2 = %s \n",dirc);
   *xmin=x;    }
   return fx;    /* We add a separator at the end of dirc if not exists */
 }    l1 = strlen( dirc );                  /* length of directory */
     if( dirc[l1-1] != DIRSEPARATOR ){
 /****************** mnbrak ***********************/      dirc[l1] =  DIRSEPARATOR;
       dirc[l1+1] = 0; 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      printf(" DIRC3 = %s \n",dirc);
             double (*func)(double))    }
 {    ss = strrchr( name, '.' );            /* find last / */
   double ulim,u,r,q, dum;    if (ss >0){
   double fu;      ss++;
        strcpy(ext,ss);                     /* save extension */
   *fa=(*func)(*ax);      l1= strlen( name);
   *fb=(*func)(*bx);      l2= strlen(ss)+1;
   if (*fb > *fa) {      strncpy( finame, name, l1-l2);
     SHFT(dum,*ax,*bx,dum)      finame[l1-l2]= 0;
       SHFT(dum,*fb,*fa,dum)    }
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);    return( 0 );                          /* we're done */
   *fc=(*func)(*cx);  }
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);  /******************************************/
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  void replace_back_to_slash(char *s, char*t)
     ulim=(*bx)+GLIMIT*(*cx-*bx);  {
     if ((*bx-u)*(u-*cx) > 0.0) {    int i;
       fu=(*func)(u);    int lg=0;
     } else if ((*cx-u)*(u-ulim) > 0.0) {    i=0;
       fu=(*func)(u);    lg=strlen(t);
       if (fu < *fc) {    for(i=0; i<= lg; i++) {
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))      (s[i] = t[i]);
           SHFT(*fb,*fc,fu,(*func)(u))      if (t[i]== '\\') s[i]='/';
           }    }
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  }
       u=ulim;  
       fu=(*func)(u);  int nbocc(char *s, char occ)
     } else {  {
       u=(*cx)+GOLD*(*cx-*bx);    int i,j=0;
       fu=(*func)(u);    int lg=20;
     }    i=0;
     SHFT(*ax,*bx,*cx,u)    lg=strlen(s);
       SHFT(*fa,*fb,*fc,fu)    for(i=0; i<= lg; i++) {
       }    if  (s[i] == occ ) j++;
 }    }
     return j;
 /*************** linmin ************************/  }
   
 int ncom;  void cutv(char *u,char *v, char*t, char occ)
 double *pcom,*xicom;  {
 double (*nrfunc)(double []);    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
         and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))       gives u="abcedf" and v="ghi2j" */
 {    int i,lg,j,p=0;
   double brent(double ax, double bx, double cx,    i=0;
                double (*f)(double), double tol, double *xmin);    for(j=0; j<=strlen(t)-1; j++) {
   double f1dim(double x);      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    }
               double *fc, double (*func)(double));  
   int j;    lg=strlen(t);
   double xx,xmin,bx,ax;    for(j=0; j<p; j++) {
   double fx,fb,fa;      (u[j] = t[j]);
      }
   ncom=n;       u[p]='\0';
   pcom=vector(1,n);  
   xicom=vector(1,n);     for(j=0; j<= lg; j++) {
   nrfunc=func;      if (j>=(p+1))(v[j-p-1] = t[j]);
   for (j=1;j<=n;j++) {    }
     pcom[j]=p[j];  }
     xicom[j]=xi[j];  
   }  /********************** nrerror ********************/
   ax=0.0;  
   xx=1.0;  void nrerror(char error_text[])
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  {
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    fprintf(stderr,"ERREUR ...\n");
 #ifdef DEBUG    fprintf(stderr,"%s\n",error_text);
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    exit(EXIT_FAILURE);
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  }
 #endif  /*********************** vector *******************/
   for (j=1;j<=n;j++) {  double *vector(int nl, int nh)
     xi[j] *= xmin;  {
     p[j] += xi[j];    double *v;
   }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   free_vector(xicom,1,n);    if (!v) nrerror("allocation failure in vector");
   free_vector(pcom,1,n);    return v-nl+NR_END;
 }  }
   
 /*************** powell ************************/  /************************ free vector ******************/
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  void free_vector(double*v, int nl, int nh)
             double (*func)(double []))  {
 {    free((FREE_ARG)(v+nl-NR_END));
   void linmin(double p[], double xi[], int n, double *fret,  }
               double (*func)(double []));  
   int i,ibig,j;  /************************ivector *******************************/
   double del,t,*pt,*ptt,*xit;  int *ivector(long nl,long nh)
   double fp,fptt;  {
   double *xits;    int *v;
   pt=vector(1,n);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   ptt=vector(1,n);    if (!v) nrerror("allocation failure in ivector");
   xit=vector(1,n);    return v-nl+NR_END;
   xits=vector(1,n);  }
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];  /******************free ivector **************************/
   for (*iter=1;;++(*iter)) {  void free_ivector(int *v, long nl, long nh)
     fp=(*fret);  {
     ibig=0;    free((FREE_ARG)(v+nl-NR_END));
     del=0.0;  }
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  /************************lvector *******************************/
     for (i=1;i<=n;i++)  long *lvector(long nl,long nh)
       printf(" %d %.12f",i, p[i]);  {
     fprintf(ficlog," %d %.12f",i, p[i]);    long *v;
     printf("\n");    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     fprintf(ficlog,"\n");    if (!v) nrerror("allocation failure in ivector");
     for (i=1;i<=n;i++) {    return v-nl+NR_END;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  }
       fptt=(*fret);  
 #ifdef DEBUG  /******************free lvector **************************/
       printf("fret=%lf \n",*fret);  void free_lvector(long *v, long nl, long nh)
       fprintf(ficlog,"fret=%lf \n",*fret);  {
 #endif    free((FREE_ARG)(v+nl-NR_END));
       printf("%d",i);fflush(stdout);  }
       fprintf(ficlog,"%d",i);fflush(ficlog);  
       linmin(p,xit,n,fret,func);  /******************* imatrix *******************************/
       if (fabs(fptt-(*fret)) > del) {  int **imatrix(long nrl, long nrh, long ncl, long nch) 
         del=fabs(fptt-(*fret));       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
         ibig=i;  { 
       }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 #ifdef DEBUG    int **m; 
       printf("%d %.12e",i,(*fret));    
       fprintf(ficlog,"%d %.12e",i,(*fret));    /* allocate pointers to rows */ 
       for (j=1;j<=n;j++) {    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    if (!m) nrerror("allocation failure 1 in matrix()"); 
         printf(" x(%d)=%.12e",j,xit[j]);    m += NR_END; 
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);    m -= nrl; 
       }    
       for(j=1;j<=n;j++) {    
         printf(" p=%.12e",p[j]);    /* allocate rows and set pointers to them */ 
         fprintf(ficlog," p=%.12e",p[j]);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       printf("\n");    m[nrl] += NR_END; 
       fprintf(ficlog,"\n");    m[nrl] -= ncl; 
 #endif    
     }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    
 #ifdef DEBUG    /* return pointer to array of pointers to rows */ 
       int k[2],l;    return m; 
       k[0]=1;  } 
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  /****************** free_imatrix *************************/
       fprintf(ficlog,"Max: %.12e",(*func)(p));  void free_imatrix(m,nrl,nrh,ncl,nch)
       for (j=1;j<=n;j++) {        int **m;
         printf(" %.12e",p[j]);        long nch,ncl,nrh,nrl; 
         fprintf(ficlog," %.12e",p[j]);       /* free an int matrix allocated by imatrix() */ 
       }  { 
       printf("\n");    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       fprintf(ficlog,"\n");    free((FREE_ARG) (m+nrl-NR_END)); 
       for(l=0;l<=1;l++) {  } 
         for (j=1;j<=n;j++) {  
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  /******************* matrix *******************************/
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  double **matrix(long nrl, long nrh, long ncl, long nch)
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  {
         }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    double **m;
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 #endif    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
     m -= nrl;
       free_vector(xit,1,n);  
       free_vector(xits,1,n);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       free_vector(ptt,1,n);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       free_vector(pt,1,n);    m[nrl] += NR_END;
       return;    m[nrl] -= ncl;
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     for (j=1;j<=n;j++) {    return m;
       ptt[j]=2.0*p[j]-pt[j];    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       xit[j]=p[j]-pt[j];     */
       pt[j]=p[j];  }
     }  
     fptt=(*func)(ptt);  /*************************free matrix ************************/
     if (fptt < fp) {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  {
       if (t < 0.0) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         linmin(p,xit,n,fret,func);    free((FREE_ARG)(m+nrl-NR_END));
         for (j=1;j<=n;j++) {  }
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];  /******************* ma3x *******************************/
         }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 #ifdef DEBUG  {
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    double ***m;
         for(j=1;j<=n;j++){  
           printf(" %.12e",xit[j]);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
           fprintf(ficlog," %.12e",xit[j]);    if (!m) nrerror("allocation failure 1 in matrix()");
         }    m += NR_END;
         printf("\n");    m -= nrl;
         fprintf(ficlog,"\n");  
 #endif    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     }    m[nrl] += NR_END;
   }    m[nrl] -= ncl;
 }  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 /**** Prevalence limit ****************/  
     m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 {    m[nrl][ncl] += NR_END;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    m[nrl][ncl] -= nll;
      matrix by transitions matrix until convergence is reached */    for (j=ncl+1; j<=nch; j++) 
       m[nrl][j]=m[nrl][j-1]+nlay;
   int i, ii,j,k;    
   double min, max, maxmin, maxmax,sumnew=0.;    for (i=nrl+1; i<=nrh; i++) {
   double **matprod2();      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   double **out, cov[NCOVMAX], **pmij();      for (j=ncl+1; j<=nch; j++) 
   double **newm;        m[i][j]=m[i][j-1]+nlay;
   double agefin, delaymax=50 ; /* Max number of years to converge */    }
     return m; 
   for (ii=1;ii<=nlstate+ndeath;ii++)    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     for (j=1;j<=nlstate+ndeath;j++){             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    */
     }  }
   
    cov[1]=1.;  /*************************free ma3x ************************/
    void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  {
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     newm=savm;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     /* Covariates have to be included here again */    free((FREE_ARG)(m+nrl-NR_END));
      cov[2]=agefin;  }
    
       for (k=1; k<=cptcovn;k++) {  /*************** function subdirf ***********/
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  char *subdirf(char fileres[])
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  {
       }    /* Caution optionfilefiname is hidden */
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    strcpy(tmpout,optionfilefiname);
       for (k=1; k<=cptcovprod;k++)    strcat(tmpout,"/"); /* Add to the right */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    strcat(tmpout,fileres);
     return tmpout;
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  }
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  /*************** function subdirf2 ***********/
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  char *subdirf2(char fileres[], char *preop)
   {
     savm=oldm;    
     oldm=newm;    /* Caution optionfilefiname is hidden */
     maxmax=0.;    strcpy(tmpout,optionfilefiname);
     for(j=1;j<=nlstate;j++){    strcat(tmpout,"/");
       min=1.;    strcat(tmpout,preop);
       max=0.;    strcat(tmpout,fileres);
       for(i=1; i<=nlstate; i++) {    return tmpout;
         sumnew=0;  }
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  /*************** function subdirf3 ***********/
         max=FMAX(max,prlim[i][j]);  char *subdirf3(char fileres[], char *preop, char *preop2)
         min=FMIN(min,prlim[i][j]);  {
       }    
       maxmin=max-min;    /* Caution optionfilefiname is hidden */
       maxmax=FMAX(maxmax,maxmin);    strcpy(tmpout,optionfilefiname);
     }    strcat(tmpout,"/");
     if(maxmax < ftolpl){    strcat(tmpout,preop);
       return prlim;    strcat(tmpout,preop2);
     }    strcat(tmpout,fileres);
   }    return tmpout;
 }  }
   
 /*************** transition probabilities ***************/  /***************** f1dim *************************/
   extern int ncom; 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  extern double *pcom,*xicom;
 {  extern double (*nrfunc)(double []); 
   double s1, s2;   
   /*double t34;*/  double f1dim(double x) 
   int i,j,j1, nc, ii, jj;  { 
     int j; 
     for(i=1; i<= nlstate; i++){    double f;
     for(j=1; j<i;j++){    double *xt; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){   
         /*s2 += param[i][j][nc]*cov[nc];*/    xt=vector(1,ncom); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    f=(*nrfunc)(xt); 
       }    free_vector(xt,1,ncom); 
       ps[i][j]=s2;    return f; 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  } 
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){  /*****************brent *************************/
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  { 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    int iter; 
       }    double a,b,d,etemp;
       ps[i][j]=s2;    double fu,fv,fw,fx;
     }    double ftemp;
   }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     /*ps[3][2]=1;*/    double e=0.0; 
    
   for(i=1; i<= nlstate; i++){    a=(ax < cx ? ax : cx); 
      s1=0;    b=(ax > cx ? ax : cx); 
     for(j=1; j<i; j++)    x=w=v=bx; 
       s1+=exp(ps[i][j]);    fw=fv=fx=(*f)(x); 
     for(j=i+1; j<=nlstate+ndeath; j++)    for (iter=1;iter<=ITMAX;iter++) { 
       s1+=exp(ps[i][j]);      xm=0.5*(a+b); 
     ps[i][i]=1./(s1+1.);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     for(j=1; j<i; j++)      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       ps[i][j]= exp(ps[i][j])*ps[i][i];      printf(".");fflush(stdout);
     for(j=i+1; j<=nlstate+ndeath; j++)      fprintf(ficlog,".");fflush(ficlog);
       ps[i][j]= exp(ps[i][j])*ps[i][i];  #ifdef DEBUG
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      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);
   } /* end 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 ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  #endif
     for(jj=1; jj<= nlstate+ndeath; jj++){      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       ps[ii][jj]=0;        *xmin=x; 
       ps[ii][ii]=1;        return fx; 
     }      } 
   }      ftemp=fu;
       if (fabs(e) > tol1) { 
         r=(x-w)*(fx-fv); 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        q=(x-v)*(fx-fw); 
     for(jj=1; jj<= nlstate+ndeath; jj++){        p=(x-v)*q-(x-w)*r; 
      printf("%lf ",ps[ii][jj]);        q=2.0*(q-r); 
    }        if (q > 0.0) p = -p; 
     printf("\n ");        q=fabs(q); 
     }        etemp=e; 
     printf("\n ");printf("%lf ",cov[2]);*/        e=d; 
 /*        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   goto end;*/        else { 
     return ps;          d=p/q; 
 }          u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
 /**************** Product of 2 matrices ******************/            d=SIGN(tol1,xm-x); 
         } 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      } else { 
 {        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      } 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   /* in, b, out are matrice of pointers which should have been initialized      fu=(*f)(u); 
      before: only the contents of out is modified. The function returns      if (fu <= fx) { 
      a pointer to pointers identical to out */        if (u >= x) a=x; else b=x; 
   long i, j, k;        SHFT(v,w,x,u) 
   for(i=nrl; i<= nrh; i++)          SHFT(fv,fw,fx,fu) 
     for(k=ncolol; k<=ncoloh; k++)          } else { 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)            if (u < x) a=u; else b=u; 
         out[i][k] +=in[i][j]*b[j][k];            if (fu <= fw || w == x) { 
               v=w; 
   return out;              w=u; 
 }              fv=fw; 
               fw=fu; 
             } else if (fu <= fv || v == x || v == w) { 
 /************* Higher Matrix Product ***************/              v=u; 
               fv=fu; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )            } 
 {          } 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    } 
      duration (i.e. until    nrerror("Too many iterations in brent"); 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    *xmin=x; 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    return fx; 
      (typically every 2 years instead of every month which is too big).  } 
      Model is determined by parameters x and covariates have to be  
      included manually here.  /****************** mnbrak ***********************/
   
      */  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               double (*func)(double)) 
   int i, j, d, h, k;  { 
   double **out, cov[NCOVMAX];    double ulim,u,r,q, dum;
   double **newm;    double fu; 
    
   /* Hstepm could be zero and should return the unit matrix */    *fa=(*func)(*ax); 
   for (i=1;i<=nlstate+ndeath;i++)    *fb=(*func)(*bx); 
     for (j=1;j<=nlstate+ndeath;j++){    if (*fb > *fa) { 
       oldm[i][j]=(i==j ? 1.0 : 0.0);      SHFT(dum,*ax,*bx,dum) 
       po[i][j][0]=(i==j ? 1.0 : 0.0);        SHFT(dum,*fb,*fa,dum) 
     }        } 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    *cx=(*bx)+GOLD*(*bx-*ax); 
   for(h=1; h <=nhstepm; h++){    *fc=(*func)(*cx); 
     for(d=1; d <=hstepm; d++){    while (*fb > *fc) { 
       newm=savm;      r=(*bx-*ax)*(*fb-*fc); 
       /* Covariates have to be included here again */      q=(*bx-*cx)*(*fb-*fa); 
       cov[1]=1.;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       for (k=1; k<=cptcovage;k++)      if ((*bx-u)*(u-*cx) > 0.0) { 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        fu=(*func)(u); 
       for (k=1; k<=cptcovprod;k++)      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        fu=(*func)(u); 
         if (fu < *fc) { 
           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/            SHFT(*fb,*fc,fu,(*func)(u)) 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/            } 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        u=ulim; 
       savm=oldm;        fu=(*func)(u); 
       oldm=newm;      } else { 
     }        u=(*cx)+GOLD*(*cx-*bx); 
     for(i=1; i<=nlstate+ndeath; i++)        fu=(*func)(u); 
       for(j=1;j<=nlstate+ndeath;j++) {      } 
         po[i][j][h]=newm[i][j];      SHFT(*ax,*bx,*cx,u) 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        SHFT(*fa,*fb,*fc,fu) 
          */        } 
       }  } 
   } /* end h */  
   return po;  /*************** linmin ************************/
 }  
   int ncom; 
   double *pcom,*xicom;
 /*************** log-likelihood *************/  double (*nrfunc)(double []); 
 double func( double *x)   
 {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   int i, ii, j, k, mi, d, kk;  { 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    double brent(double ax, double bx, double cx, 
   double **out;                 double (*f)(double), double tol, double *xmin); 
   double sw; /* Sum of weights */    double f1dim(double x); 
   double lli; /* Individual log likelihood */    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   long ipmx;                double *fc, double (*func)(double)); 
   /*extern weight */    int j; 
   /* We are differentiating ll according to initial status */    double xx,xmin,bx,ax; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    double fx,fb,fa;
   /*for(i=1;i<imx;i++)   
     printf(" %d\n",s[4][i]);    ncom=n; 
   */    pcom=vector(1,n); 
   cov[1]=1.;    xicom=vector(1,n); 
     nrfunc=func; 
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for (j=1;j<=n;j++) { 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      pcom[j]=p[j]; 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      xicom[j]=xi[j]; 
     for(mi=1; mi<= wav[i]-1; mi++){    } 
       for (ii=1;ii<=nlstate+ndeath;ii++)    ax=0.0; 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    xx=1.0; 
       for(d=0; d<dh[mi][i]; d++){    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         newm=savm;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  #ifdef DEBUG
         for (kk=1; kk<=cptcovage;kk++) {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         }  #endif
            for (j=1;j<=n;j++) { 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      xi[j] *= xmin; 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      p[j] += xi[j]; 
         savm=oldm;    } 
         oldm=newm;    free_vector(xicom,1,n); 
            free_vector(pcom,1,n); 
          } 
       } /* end mult */  
        char *asc_diff_time(long time_sec, char ascdiff[])
       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]]);*/    long sec_left, days, hours, minutes;
       ipmx +=1;    days = (time_sec) / (60*60*24);
       sw += weight[i];    sec_left = (time_sec) % (60*60*24);
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    hours = (sec_left) / (60*60) ;
     } /* end of wave */    sec_left = (sec_left) %(60*60);
   } /* end of individual */    minutes = (sec_left) /60;
     sec_left = (sec_left) % (60);
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    return ascdiff;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  }
   return -l;  
 }  /*************** powell ************************/
   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               double (*func)(double [])) 
 /*********** Maximum Likelihood Estimation ***************/  { 
     void linmin(double p[], double xi[], int n, double *fret, 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))                double (*func)(double [])); 
 {    int i,ibig,j; 
   int i,j, iter;    double del,t,*pt,*ptt,*xit;
   double **xi,*delti;    double fp,fptt;
   double fret;    double *xits;
   xi=matrix(1,npar,1,npar);    int niterf, itmp;
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)    pt=vector(1,n); 
       xi[i][j]=(i==j ? 1.0 : 0.0);    ptt=vector(1,n); 
   printf("Powell\n");  fprintf(ficlog,"Powell\n");    xit=vector(1,n); 
   powell(p,xi,npar,ftol,&iter,&fret,func);    xits=vector(1,n); 
     *fret=(*func)(p); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    for (j=1;j<=n;j++) pt[j]=p[j]; 
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    for (*iter=1;;++(*iter)) { 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      fp=(*fret); 
       ibig=0; 
 }      del=0.0; 
       last_time=curr_time;
 /**** Computes Hessian and covariance matrix ***/      (void) gettimeofday(&curr_time,&tzp);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
 {      /*    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
   double  **a,**y,*x,pd;      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   double **hess;      */
   int i, j,jk;     for (i=1;i<=n;i++) {
   int *indx;        printf(" %d %.12f",i, p[i]);
         fprintf(ficlog," %d %.12lf",i, p[i]);
   double hessii(double p[], double delta, int theta, double delti[]);        fprintf(ficrespow," %.12lf", p[i]);
   double hessij(double p[], double delti[], int i, int j);      }
   void lubksb(double **a, int npar, int *indx, double b[]) ;      printf("\n");
   void ludcmp(double **a, int npar, int *indx, double *d) ;      fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");fflush(ficrespow);
   hess=matrix(1,npar,1,npar);      if(*iter <=3){
         tm = *localtime(&curr_time.tv_sec);
   printf("\nCalculation of the hessian matrix. Wait...\n");        strcpy(strcurr,asctime(&tm));
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");  /*       asctime_r(&tm,strcurr); */
   for (i=1;i<=npar;i++){        forecast_time=curr_time; 
     printf("%d",i);fflush(stdout);        itmp = strlen(strcurr);
     fprintf(ficlog,"%d",i);fflush(ficlog);        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     hess[i][i]=hessii(p,ftolhess,i,delti);          strcurr[itmp-1]='\0';
     /*printf(" %f ",p[i]);*/        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     /*printf(" %lf ",hess[i][i]);*/        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   }        for(niterf=10;niterf<=30;niterf+=10){
            forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   for (i=1;i<=npar;i++) {          tmf = *localtime(&forecast_time.tv_sec);
     for (j=1;j<=npar;j++)  {  /*      asctime_r(&tmf,strfor); */
       if (j>i) {          strcpy(strfor,asctime(&tmf));
         printf(".%d%d",i,j);fflush(stdout);          itmp = strlen(strfor);
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);          if(strfor[itmp-1]=='\n')
         hess[i][j]=hessij(p,delti,i,j);          strfor[itmp-1]='\0';
         hess[j][i]=hess[i][j];              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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
         /*printf(" %lf ",hess[i][j]);*/          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       }        }
     }      }
   }      for (i=1;i<=n;i++) { 
   printf("\n");        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   fprintf(ficlog,"\n");        fptt=(*fret); 
   #ifdef DEBUG
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        printf("fret=%lf \n",*fret);
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");        fprintf(ficlog,"fret=%lf \n",*fret);
    #endif
   a=matrix(1,npar,1,npar);        printf("%d",i);fflush(stdout);
   y=matrix(1,npar,1,npar);        fprintf(ficlog,"%d",i);fflush(ficlog);
   x=vector(1,npar);        linmin(p,xit,n,fret,func); 
   indx=ivector(1,npar);        if (fabs(fptt-(*fret)) > del) { 
   for (i=1;i<=npar;i++)          del=fabs(fptt-(*fret)); 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          ibig=i; 
   ludcmp(a,npar,indx,&pd);        } 
   #ifdef DEBUG
   for (j=1;j<=npar;j++) {        printf("%d %.12e",i,(*fret));
     for (i=1;i<=npar;i++) x[i]=0;        fprintf(ficlog,"%d %.12e",i,(*fret));
     x[j]=1;        for (j=1;j<=n;j++) {
     lubksb(a,npar,indx,x);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     for (i=1;i<=npar;i++){          printf(" x(%d)=%.12e",j,xit[j]);
       matcov[i][j]=x[i];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     }        }
   }        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
   printf("\n#Hessian matrix#\n");          fprintf(ficlog," p=%.12e",p[j]);
   fprintf(ficlog,"\n#Hessian matrix#\n");        }
   for (i=1;i<=npar;i++) {        printf("\n");
     for (j=1;j<=npar;j++) {        fprintf(ficlog,"\n");
       printf("%.3e ",hess[i][j]);  #endif
       fprintf(ficlog,"%.3e ",hess[i][j]);      } 
     }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     printf("\n");  #ifdef DEBUG
     fprintf(ficlog,"\n");        int k[2],l;
   }        k[0]=1;
         k[1]=-1;
   /* Recompute Inverse */        printf("Max: %.12e",(*func)(p));
   for (i=1;i<=npar;i++)        fprintf(ficlog,"Max: %.12e",(*func)(p));
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        for (j=1;j<=n;j++) {
   ludcmp(a,npar,indx,&pd);          printf(" %.12e",p[j]);
           fprintf(ficlog," %.12e",p[j]);
   /*  printf("\n#Hessian matrix recomputed#\n");        }
         printf("\n");
   for (j=1;j<=npar;j++) {        fprintf(ficlog,"\n");
     for (i=1;i<=npar;i++) x[i]=0;        for(l=0;l<=1;l++) {
     x[j]=1;          for (j=1;j<=n;j++) {
     lubksb(a,npar,indx,x);            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     for (i=1;i<=npar;i++){            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       y[i][j]=x[i];            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("%.3e ",y[i][j]);          }
       fprintf(ficlog,"%.3e ",y[i][j]);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     printf("\n");        }
     fprintf(ficlog,"\n");  #endif
   }  
   */  
         free_vector(xit,1,n); 
   free_matrix(a,1,npar,1,npar);        free_vector(xits,1,n); 
   free_matrix(y,1,npar,1,npar);        free_vector(ptt,1,n); 
   free_vector(x,1,npar);        free_vector(pt,1,n); 
   free_ivector(indx,1,npar);        return; 
   free_matrix(hess,1,npar,1,npar);      } 
       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
 }        ptt[j]=2.0*p[j]-pt[j]; 
         xit[j]=p[j]-pt[j]; 
 /*************** hessian matrix ****************/        pt[j]=p[j]; 
 double hessii( double x[], double delta, int theta, double delti[])      } 
 {      fptt=(*func)(ptt); 
   int i;      if (fptt < fp) { 
   int l=1, lmax=20;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   double k1,k2;        if (t < 0.0) { 
   double p2[NPARMAX+1];          linmin(p,xit,n,fret,func); 
   double res;          for (j=1;j<=n;j++) { 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;            xi[j][ibig]=xi[j][n]; 
   double fx;            xi[j][n]=xit[j]; 
   int k=0,kmax=10;          }
   double l1;  #ifdef DEBUG
           printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   fx=func(x);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   for (i=1;i<=npar;i++) p2[i]=x[i];          for(j=1;j<=n;j++){
   for(l=0 ; l <=lmax; l++){            printf(" %.12e",xit[j]);
     l1=pow(10,l);            fprintf(ficlog," %.12e",xit[j]);
     delts=delt;          }
     for(k=1 ; k <kmax; k=k+1){          printf("\n");
       delt = delta*(l1*k);          fprintf(ficlog,"\n");
       p2[theta]=x[theta] +delt;  #endif
       k1=func(p2)-fx;        }
       p2[theta]=x[theta]-delt;      } 
       k2=func(p2)-fx;    } 
       /*res= (k1-2.0*fx+k2)/delt/delt; */  } 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  
        /**** Prevalence limit (stable or period prevalence)  ****************/
 #ifdef DEBUG  
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       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    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */       matrix by transitions matrix until convergence is reached */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  
         k=kmax;    int i, ii,j,k;
       }    double min, max, maxmin, maxmax,sumnew=0.;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    double **matprod2();
         k=kmax; l=lmax*10.;    double **out, cov[NCOVMAX], **pmij();
       }    double **newm;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    double agefin, delaymax=50 ; /* Max number of years to converge */
         delts=delt;  
       }    for (ii=1;ii<=nlstate+ndeath;ii++)
     }      for (j=1;j<=nlstate+ndeath;j++){
   }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   delti[theta]=delts;      }
   return res;  
       cov[1]=1.;
 }   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 double hessij( double x[], double delti[], int thetai,int thetaj)    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 {      newm=savm;
   int i;      /* Covariates have to be included here again */
   int l=1, l1, lmax=20;       cov[2]=agefin;
   double k1,k2,k3,k4,res,fx;    
   double p2[NPARMAX+1];        for (k=1; k<=cptcovn;k++) {
   int k;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
   fx=func(x);        }
   for (k=1; k<=2; k++) {        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for (i=1;i<=npar;i++) p2[i]=x[i];        for (k=1; k<=cptcovprod;k++)
     p2[thetai]=x[thetai]+delti[thetai]/k;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k1=func(p2)-fx;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
          /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     p2[thetai]=x[thetai]+delti[thetai]/k;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     k2=func(p2)-fx;  
        savm=oldm;
     p2[thetai]=x[thetai]-delti[thetai]/k;      oldm=newm;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      maxmax=0.;
     k3=func(p2)-fx;      for(j=1;j<=nlstate;j++){
          min=1.;
     p2[thetai]=x[thetai]-delti[thetai]/k;        max=0.;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        for(i=1; i<=nlstate; i++) {
     k4=func(p2)-fx;          sumnew=0;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
 #ifdef DEBUG          prlim[i][j]= newm[i][j]/(1-sumnew);
     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);          max=FMAX(max,prlim[i][j]);
     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);          min=FMIN(min,prlim[i][j]);
 #endif        }
   }        maxmin=max-min;
   return res;        maxmax=FMAX(maxmax,maxmin);
 }      }
       if(maxmax < ftolpl){
 /************** Inverse of matrix **************/        return prlim;
 void ludcmp(double **a, int n, int *indx, double *d)      }
 {    }
   int i,imax,j,k;  }
   double big,dum,sum,temp;  
   double *vv;  /*************** transition probabilities ***************/ 
    
   vv=vector(1,n);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   *d=1.0;  {
   for (i=1;i<=n;i++) {    double s1, s2;
     big=0.0;    /*double t34;*/
     for (j=1;j<=n;j++)    int i,j,j1, nc, ii, jj;
       if ((temp=fabs(a[i][j])) > big) big=temp;  
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      for(i=1; i<= nlstate; i++){
     vv[i]=1.0/big;        for(j=1; j<i;j++){
   }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   for (j=1;j<=n;j++) {            /*s2 += param[i][j][nc]*cov[nc];*/
     for (i=1;i<j;i++) {            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       sum=a[i][j];  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          }
       a[i][j]=sum;          ps[i][j]=s2;
     }  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
     big=0.0;        }
     for (i=j;i<=n;i++) {        for(j=i+1; j<=nlstate+ndeath;j++){
       sum=a[i][j];          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       for (k=1;k<j;k++)            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         sum -= a[i][k]*a[k][j];  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
       a[i][j]=sum;          }
       if ( (dum=vv[i]*fabs(sum)) >= big) {          ps[i][j]=s2;
         big=dum;        }
         imax=i;      }
       }      /*ps[3][2]=1;*/
     }      
     if (j != imax) {      for(i=1; i<= nlstate; i++){
       for (k=1;k<=n;k++) {        s1=0;
         dum=a[imax][k];        for(j=1; j<i; j++)
         a[imax][k]=a[j][k];          s1+=exp(ps[i][j]);
         a[j][k]=dum;        for(j=i+1; j<=nlstate+ndeath; j++)
       }          s1+=exp(ps[i][j]);
       *d = -(*d);        ps[i][i]=1./(s1+1.);
       vv[imax]=vv[j];        for(j=1; j<i; j++)
     }          ps[i][j]= exp(ps[i][j])*ps[i][i];
     indx[j]=imax;        for(j=i+1; j<=nlstate+ndeath; j++)
     if (a[j][j] == 0.0) a[j][j]=TINY;          ps[i][j]= exp(ps[i][j])*ps[i][i];
     if (j != n) {        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       dum=1.0/(a[j][j]);      } /* end i */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      
     }      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   }        for(jj=1; jj<= nlstate+ndeath; jj++){
   free_vector(vv,1,n);  /* Doesn't work */          ps[ii][jj]=0;
 ;          ps[ii][ii]=1;
 }        }
       }
 void lubksb(double **a, int n, int *indx, double b[])      
 {  
   int i,ii=0,ip,j;  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   double sum;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
    /*         printf("ddd %lf ",ps[ii][jj]); */
   for (i=1;i<=n;i++) {  /*       } */
     ip=indx[i];  /*       printf("\n "); */
     sum=b[ip];  /*        } */
     b[ip]=b[i];  /*        printf("\n ");printf("%lf ",cov[2]); */
     if (ii)         /*
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        for(i=1; i<= npar; i++) printf("%f ",x[i]);
     else if (sum) ii=i;        goto end;*/
     b[i]=sum;      return ps;
   }  }
   for (i=n;i>=1;i--) {  
     sum=b[i];  /**************** Product of 2 matrices ******************/
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  
     b[i]=sum/a[i][i];  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   }  {
 }    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
        b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
 /************ Frequencies ********************/    /* in, b, out are matrice of pointers which should have been initialized 
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)       before: only the contents of out is modified. The function returns
 {  /* Some frequencies */       a pointer to pointers identical to out */
      long i, j, k;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    for(i=nrl; i<= nrh; i++)
   int first;      for(k=ncolol; k<=ncoloh; k++)
   double ***freq; /* Frequencies */        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   double *pp;          out[i][k] +=in[i][j]*b[j][k];
   double pos, k2, dateintsum=0,k2cpt=0;  
   FILE *ficresp;    return out;
   char fileresp[FILENAMELENGTH];  }
    
   pp=vector(1,nlstate);  
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  /************* Higher Matrix Product ***************/
   strcpy(fileresp,"p");  
   strcat(fileresp,fileres);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   if((ficresp=fopen(fileresp,"w"))==NULL) {  {
     printf("Problem with prevalence resultfile: %s\n", fileresp);    /* Computes the transition matrix starting at age 'age' over 
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);       'nhstepm*hstepm*stepm' months (i.e. until
     exit(0);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   }       nhstepm*hstepm matrices. 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   j1=0;       (typically every 2 years instead of every month which is too big 
         for the memory).
   j=cptcoveff;       Model is determined by parameters x and covariates have to be 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}       included manually here. 
   
   first=1;       */
   
   for(k1=1; k1<=j;k1++){    int i, j, d, h, k;
     for(i1=1; i1<=ncodemax[k1];i1++){    double **out, cov[NCOVMAX];
       j1++;    double **newm;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  
         scanf("%d", i);*/    /* Hstepm could be zero and should return the unit matrix */
       for (i=-1; i<=nlstate+ndeath; i++)      for (i=1;i<=nlstate+ndeath;i++)
         for (jk=-1; jk<=nlstate+ndeath; jk++)        for (j=1;j<=nlstate+ndeath;j++){
           for(m=agemin; m <= agemax+3; m++)        oldm[i][j]=(i==j ? 1.0 : 0.0);
             freq[i][jk][m]=0;        po[i][j][0]=(i==j ? 1.0 : 0.0);
            }
       dateintsum=0;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       k2cpt=0;    for(h=1; h <=nhstepm; h++){
       for (i=1; i<=imx; i++) {      for(d=1; d <=hstepm; d++){
         bool=1;        newm=savm;
         if  (cptcovn>0) {        /* Covariates have to be included here again */
           for (z1=1; z1<=cptcoveff; z1++)        cov[1]=1.;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
               bool=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         }        for (k=1; k<=cptcovage;k++)
         if (bool==1) {          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for(m=firstpass; m<=lastpass; m++){        for (k=1; k<=cptcovprod;k++)
             k2=anint[m][i]+(mint[m][i]/12.);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  
               if(agev[m][i]==0) agev[m][i]=agemax+1;  
               if(agev[m][i]==1) agev[m][i]=agemax+2;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
               if (m<lastpass) {        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];                     pmij(pmmij,cov,ncovmodel,x,nlstate));
               }        savm=oldm;
                      oldm=newm;
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      }
                 dateintsum=dateintsum+k2;      for(i=1; i<=nlstate+ndeath; i++)
                 k2cpt++;        for(j=1;j<=nlstate+ndeath;j++) {
               }          po[i][j][h]=newm[i][j];
             }          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
           }           */
         }        }
       }    } /* end h */
            return po;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  }
   
       if  (cptcovn>0) {  
         fprintf(ficresp, "\n#********** Variable ");  /*************** log-likelihood *************/
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  double func( double *x)
         fprintf(ficresp, "**********\n#");  {
       }    int i, ii, j, k, mi, d, kk;
       for(i=1; i<=nlstate;i++)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    double **out;
       fprintf(ficresp, "\n");    double sw; /* Sum of weights */
          double lli; /* Individual log likelihood */
       for(i=(int)agemin; i <= (int)agemax+3; i++){    int s1, s2;
         if(i==(int)agemax+3){    double bbh, survp;
           fprintf(ficlog,"Total");    long ipmx;
         }else{    /*extern weight */
           if(first==1){    /* We are differentiating ll according to initial status */
             first=0;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
             printf("See log file for details...\n");    /*for(i=1;i<imx;i++) 
           }      printf(" %d\n",s[4][i]);
           fprintf(ficlog,"Age %d", i);    */
         }    cov[1]=1.;
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
             pp[jk] += freq[jk][m][i];  
         }    if(mle==1){
         for(jk=1; jk <=nlstate ; jk++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           for(m=-1, pos=0; m <=0 ; m++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             pos += freq[jk][m][i];        for(mi=1; mi<= wav[i]-1; mi++){
           if(pp[jk]>=1.e-10){          for (ii=1;ii<=nlstate+ndeath;ii++)
             if(first==1){            for (j=1;j<=nlstate+ndeath;j++){
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            }
           }else{          for(d=0; d<dh[mi][i]; d++){
             if(first==1)            newm=savm;
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            for (kk=1; kk<=cptcovage;kk++) {
           }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for(jk=1; jk <=nlstate ; jk++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            savm=oldm;
             pp[jk] += freq[jk][m][i];            oldm=newm;
         }          } /* end mult */
         
         for(jk=1,pos=0; jk <=nlstate ; jk++)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           pos += pp[jk];          /* But now since version 0.9 we anticipate for bias at large stepm.
         for(jk=1; jk <=nlstate ; jk++){           * If stepm is larger than one month (smallest stepm) and if the exact delay 
           if(pos>=1.e-5){           * (in months) between two waves is not a multiple of stepm, we rounded to 
             if(first==1)           * the nearest (and in case of equal distance, to the lowest) interval but now
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
           }else{           * probability in order to take into account the bias as a fraction of the way
             if(first==1)           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);           * -stepm/2 to stepm/2 .
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);           * For stepm=1 the results are the same as for previous versions of Imach.
           }           * For stepm > 1 the results are less biased than in previous versions. 
           if( i <= (int) agemax){           */
             if(pos>=1.e-5){          s1=s[mw[mi][i]][i];
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          s2=s[mw[mi+1][i]][i];
               probs[i][jk][j1]= pp[jk]/pos;          bbh=(double)bh[mi][i]/(double)stepm; 
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          /* bias bh is positive if real duration
             }           * is higher than the multiple of stepm and negative otherwise.
             else           */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           }          if( s2 > nlstate){ 
         }            /* i.e. if s2 is a death state and if the date of death is known 
                       then the contribution to the likelihood is the probability to 
         for(jk=-1; jk <=nlstate+ndeath; jk++)               die between last step unit time and current  step unit time, 
           for(m=-1; m <=nlstate+ndeath; m++)               which is also equal to probability to die before dh 
             if(freq[jk][m][i] !=0 ) {               minus probability to die before dh-stepm . 
             if(first==1)               In version up to 0.92 likelihood was computed
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          as if date of death was unknown. Death was treated as any other
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);          health state: the date of the interview describes the actual state
             }          and not the date of a change in health state. The former idea was
         if(i <= (int) agemax)          to consider that at each interview the state was recorded
           fprintf(ficresp,"\n");          (healthy, disable or death) and IMaCh was corrected; but when we
         if(first==1)          introduced the exact date of death then we should have modified
           printf("Others in log...\n");          the contribution of an exact death to the likelihood. This new
         fprintf(ficlog,"\n");          contribution is smaller and very dependent of the step unit
       }          stepm. It is no more the probability to die between last interview
     }          and month of death but the probability to survive from last
   }          interview up to one month before death multiplied by the
   dateintmean=dateintsum/k2cpt;          probability to die within a month. Thanks to Chris
            Jackson for correcting this bug.  Former versions increased
   fclose(ficresp);          mortality artificially. The bad side is that we add another loop
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          which slows down the processing. The difference can be up to 10%
   free_vector(pp,1,nlstate);          lower mortality.
              */
   /* End of Freq */            lli=log(out[s1][s2] - savm[s1][s2]);
 }  
   
 /************ Prevalence ********************/          } else if  (s2==-2) {
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)            for (j=1,survp=0. ; j<=nlstate; j++) 
 {  /* Some frequencies */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
              /*survp += out[s1][j]; */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;            lli= log(survp);
   double ***freq; /* Frequencies */          }
   double *pp;          
   double pos, k2;          else if  (s2==-4) { 
             for (j=3,survp=0. ; j<=nlstate; j++)  
   pp=vector(1,nlstate);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            lli= log(survp); 
            } 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;          else if  (s2==-5) { 
              for (j=1,survp=0. ; j<=2; j++)  
   j=cptcoveff;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            lli= log(survp); 
            } 
   for(k1=1; k1<=j;k1++){          
     for(i1=1; i1<=ncodemax[k1];i1++){          else{
       j1++;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                  /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
       for (i=-1; i<=nlstate+ndeath; i++)            } 
         for (jk=-1; jk<=nlstate+ndeath; jk++)            /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           for(m=agemin; m <= agemax+3; m++)          /*if(lli ==000.0)*/
             freq[i][jk][m]=0;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
                ipmx +=1;
       for (i=1; i<=imx; i++) {          sw += weight[i];
         bool=1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         if  (cptcovn>0) {        } /* end of wave */
           for (z1=1; z1<=cptcoveff; z1++)      } /* end of individual */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    }  else if(mle==2){
               bool=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         if (bool==1) {        for(mi=1; mi<= wav[i]-1; mi++){
           for(m=firstpass; m<=lastpass; m++){          for (ii=1;ii<=nlstate+ndeath;ii++)
             k2=anint[m][i]+(mint[m][i]/12.);            for (j=1;j<=nlstate+ndeath;j++){
             if ((k2>=dateprev1) && (k2<=dateprev2)) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               if(agev[m][i]==0) agev[m][i]=agemax+1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
               if(agev[m][i]==1) agev[m][i]=agemax+2;            }
               if (m<lastpass) {          for(d=0; d<=dh[mi][i]; d++){
                 if (calagedate>0)            newm=savm;
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                 else            for (kk=1; kk<=cptcovage;kk++) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];            }
               }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           }            savm=oldm;
         }            oldm=newm;
       }          } /* end mult */
       for(i=(int)agemin; i <= (int)agemax+3; i++){        
         for(jk=1; jk <=nlstate ; jk++){          s1=s[mw[mi][i]][i];
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          s2=s[mw[mi+1][i]][i];
             pp[jk] += freq[jk][m][i];          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 */
         for(jk=1; jk <=nlstate ; jk++){          ipmx +=1;
           for(m=-1, pos=0; m <=0 ; m++)          sw += weight[i];
             pos += freq[jk][m][i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         }        } /* end of wave */
              } /* end of individual */
         for(jk=1; jk <=nlstate ; jk++){    }  else if(mle==3){  /* exponential inter-extrapolation */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             pp[jk] += freq[jk][m][i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
                  for (ii=1;ii<=nlstate+ndeath;ii++)
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];            for (j=1;j<=nlstate+ndeath;j++){
                      oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(jk=1; jk <=nlstate ; jk++){                  savm[ii][j]=(ii==j ? 1.0 : 0.0);
           if( i <= (int) agemax){            }
             if(pos>=1.e-5){          for(d=0; d<dh[mi][i]; d++){
               probs[i][jk][j1]= pp[jk]/pos;            newm=savm;
             }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           }            for (kk=1; kk<=cptcovage;kk++) {
         }/* end jk */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }/* end i */            }
     } /* end i1 */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   } /* end k1 */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
              oldm=newm;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          } /* end mult */
   free_vector(pp,1,nlstate);        
            s1=s[mw[mi][i]][i];
 }  /* End of Freq */          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
 /************* Waves Concatenation ***************/          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;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          sw += weight[i];
 {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        } /* end of wave */
      Death is a valid wave (if date is known).      } /* end of individual */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    }else if (mle==4){  /* ml=4 no inter-extrapolation */
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      and mw[mi+1][i]. dh depends on stepm.        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      */        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   int i, mi, m;            for (j=1;j<=nlstate+ndeath;j++){
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      double sum=0., jmean=0.;*/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int first;            }
   int j, k=0,jk, ju, jl;          for(d=0; d<dh[mi][i]; d++){
   double sum=0.;            newm=savm;
   first=0;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   jmin=1e+5;            for (kk=1; kk<=cptcovage;kk++) {
   jmax=-1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   jmean=0.;            }
   for(i=1; i<=imx; i++){          
     mi=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     m=firstpass;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     while(s[m][i] <= nlstate){            savm=oldm;
       if(s[m][i]>=1)            oldm=newm;
         mw[++mi][i]=m;          } /* end mult */
       if(m >=lastpass)        
         break;          s1=s[mw[mi][i]][i];
       else          s2=s[mw[mi+1][i]][i];
         m++;          if( s2 > nlstate){ 
     }/* end while */            lli=log(out[s1][s2] - savm[s1][s2]);
     if (s[m][i] > nlstate){          }else{
       mi++;     /* Death is another wave */            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       /* if(mi==0)  never been interviewed correctly before death */          }
          /* Only death is a correct wave */          ipmx +=1;
       mw[mi][i]=m;          sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     wav[i]=mi;        } /* end of wave */
     if(mi==0){      } /* end of individual */
       if(first==0){    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         first=1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       }        for(mi=1; mi<= wav[i]-1; mi++){
       if(first==1){          for (ii=1;ii<=nlstate+ndeath;ii++)
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);            for (j=1;j<=nlstate+ndeath;j++){
       }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     } /* end mi==0 */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            }
           for(d=0; d<dh[mi][i]; d++){
   for(i=1; i<=imx; i++){            newm=savm;
     for(mi=1; mi<wav[i];mi++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if (stepm <=0)            for (kk=1; kk<=cptcovage;kk++) {
         dh[mi][i]=1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       else{            }
         if (s[mw[mi+1][i]][i] > nlstate) {          
           if (agedc[i] < 2*AGESUP) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           if(j==0) j=1;  /* Survives at least one month after exam */            savm=oldm;
           k=k+1;            oldm=newm;
           if (j >= jmax) jmax=j;          } /* end mult */
           if (j <= jmin) jmin=j;        
           sum=sum+j;          s1=s[mw[mi][i]][i];
           /*if (j<0) printf("j=%d num=%d \n",j,i); */          s2=s[mw[mi+1][i]][i];
           }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         }          ipmx +=1;
         else{          sw += weight[i];
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           k=k+1;          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
           if (j >= jmax) jmax=j;        } /* end of wave */
           else if (j <= jmin)jmin=j;      } /* end of individual */
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    } /* End of if */
           sum=sum+j;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         jk= j/stepm;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         jl= j -jk*stepm;    return -l;
         ju= j -(jk+1)*stepm;  }
         if(jl <= -ju)  
           dh[mi][i]=jk;  /*************** log-likelihood *************/
         else  double funcone( double *x)
           dh[mi][i]=jk+1;  {
         if(dh[mi][i]==0)    /* Same as likeli but slower because of a lot of printf and if */
           dh[mi][i]=1; /* At least one step */    int i, ii, j, k, mi, d, kk;
       }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     }    double **out;
   }    double lli; /* Individual log likelihood */
   jmean=sum/k;    double llt;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    int s1, s2;
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    double bbh, survp;
  }    /*extern weight */
     /* We are differentiating ll according to initial status */
 /*********** Tricode ****************************/    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 void tricode(int *Tvar, int **nbcode, int imx)    /*for(i=1;i<imx;i++) 
 {      printf(" %d\n",s[4][i]);
   int Ndum[20],ij=1, k, j, i;    */
   int cptcode=0;    cov[1]=1.;
   cptcoveff=0;  
      for(k=1; k<=nlstate; k++) ll[k]=0.;
   for (k=0; k<19; k++) Ndum[k]=0;  
   for (k=1; k<=7; k++) ncodemax[k]=0;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      for(mi=1; mi<= wav[i]-1; mi++){
     for (i=1; i<=imx; i++) {        for (ii=1;ii<=nlstate+ndeath;ii++)
       ij=(int)(covar[Tvar[j]][i]);          for (j=1;j<=nlstate+ndeath;j++){
       Ndum[ij]++;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            savm[ii][j]=(ii==j ? 1.0 : 0.0);
       if (ij > cptcode) cptcode=ij;          }
     }        for(d=0; d<dh[mi][i]; d++){
           newm=savm;
     for (i=0; i<=cptcode; i++) {          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if(Ndum[i]!=0) ncodemax[j]++;          for (kk=1; kk<=cptcovage;kk++) {
     }            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     ij=1;          }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for (i=1; i<=ncodemax[j]; i++) {          savm=oldm;
       for (k=0; k<=19; k++) {          oldm=newm;
         if (Ndum[k] != 0) {        } /* end mult */
           nbcode[Tvar[j]][ij]=k;        
                  s1=s[mw[mi][i]][i];
           ij++;        s2=s[mw[mi+1][i]][i];
         }        bbh=(double)bh[mi][i]/(double)stepm; 
         if (ij > ncodemax[j]) break;        /* bias is positive if real duration
       }           * is higher than the multiple of stepm and negative otherwise.
     }         */
   }          if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
  for (k=0; k<19; k++) Ndum[k]=0;        } else if  (s2==-2) {
           for (j=1,survp=0. ; j<=nlstate; j++) 
  for (i=1; i<=ncovmodel-2; i++) {            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
    ij=Tvar[i];          lli= log(survp);
    Ndum[ij]++;        }else if (mle==1){
  }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
  ij=1;          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 */
  for (i=1; i<=10; i++) {        } else if(mle==3){  /* exponential inter-extrapolation */
    if((Ndum[i]!=0) && (i<=ncovcol)){          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 */
      Tvaraff[ij]=i;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
      ij++;          lli=log(out[s1][s2]); /* Original formula */
    }        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
  }          lli=log(out[s1][s2]); /* Original formula */
          } /* End of if */
  cptcoveff=ij-1;        ipmx +=1;
 }        sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 /*********** Health Expectancies ****************/  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         if(globpr){
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
    %11.6f %11.6f %11.6f ", \
 {                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   /* Health expectancies */                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   double age, agelim, hf;            llt +=ll[k]*gipmx/gsw;
   double ***p3mat,***varhe;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   double **dnewm,**doldm;          }
   double *xp;          fprintf(ficresilk," %10.6f\n", -llt);
   double **gp, **gm;        }
   double ***gradg, ***trgradg;      } /* end of wave */
   int theta;    } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   xp=vector(1,npar);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   dnewm=matrix(1,nlstate*2,1,npar);    if(globpr==0){ /* First time we count the contributions and weights */
   doldm=matrix(1,nlstate*2,1,nlstate*2);      gipmx=ipmx;
        gsw=sw;
   fprintf(ficreseij,"# Health expectancies\n");    }
   fprintf(ficreseij,"# Age");    return -l;
   for(i=1; i<=nlstate;i++)  }
     for(j=1; j<=nlstate;j++)  
       fprintf(ficreseij," %1d-%1d (SE)",i,j);  
   fprintf(ficreseij,"\n");  /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   if(estepm < stepm){  {
     printf ("Problem %d lower than %d\n",estepm, stepm);    /* This routine should help understanding what is done with 
   }       the selection of individuals/waves and
   else  hstepm=estepm;         to check the exact contribution to the likelihood.
   /* We compute the life expectancy from trapezoids spaced every estepm months       Plotting could be done.
    * 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    int k;
    * we are calculating an estimate of the Life Expectancy assuming a linear  
    * progression inbetween and thus overestimating or underestimating according    if(*globpri !=0){ /* Just counts and sums, no printings */
    * to the curvature of the survival function. If, for the same date, we      strcpy(fileresilk,"ilk"); 
    * estimate the model with stepm=1 month, we can keep estepm to 24 months      strcat(fileresilk,fileres);
    * to compare the new estimate of Life expectancy with the same linear      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
    * hypothesis. A more precise result, taking into account a more precise        printf("Problem with resultfile: %s\n", fileresilk);
    * curvature will be obtained if estepm is as small as stepm. */        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
   /* For example we decided to compute the life expectancy with the smallest unit */      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");
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
      nhstepm is the number of hstepm from age to agelim      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
      nstepm is the number of stepm from age to agelin.      for(k=1; k<=nlstate; k++) 
      Look at hpijx to understand the reason of that which relies in memory size        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
      and note for a fixed period like estepm months */      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   /* 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    *fretone=(*funcone)(p);
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    if(*globpri !=0){
      results. So we changed our mind and took the option of the best precision.      fclose(ficresilk);
   */      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      fflush(fichtm); 
     } 
   agelim=AGESUP;    return;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  }
     /* nhstepm age range expressed in number of stepm */  
     nstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */  /*********** Maximum Likelihood Estimation ***************/
     /* if (stepm >= YEARM) hstepm=1;*/  
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  {
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    int i,j, iter;
     gp=matrix(0,nhstepm,1,nlstate*2);    double **xi;
     gm=matrix(0,nhstepm,1,nlstate*2);    double fret;
     double fretone; /* Only one call to likelihood */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    /*  char filerespow[FILENAMELENGTH];*/
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    xi=matrix(1,npar,1,npar);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
     /* Computing Variances of health expectancies */    strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
      for(theta=1; theta <=npar; theta++){      printf("Problem with resultfile: %s\n", filerespow);
       for(i=1; i<=npar; i++){      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    }
       }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      for (i=1;i<=nlstate;i++)
        for(j=1;j<=nlstate+ndeath;j++)
       cptj=0;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       for(j=1; j<= nlstate; j++){    fprintf(ficrespow,"\n");
         for(i=1; i<=nlstate; i++){  
           cptj=cptj+1;    powell(p,xi,npar,ftol,&iter,&fret,func);
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){  
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    free_matrix(xi,1,npar,1,npar);
           }    fclose(ficrespow);
         }    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       }    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
          fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
        
       for(i=1; i<=npar; i++)  }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    /**** Computes Hessian and covariance matrix ***/
        void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       cptj=0;  {
       for(j=1; j<= nlstate; j++){    double  **a,**y,*x,pd;
         for(i=1;i<=nlstate;i++){    double **hess;
           cptj=cptj+1;    int i, j,jk;
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    int *indx;
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
         }    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
       }    void lubksb(double **a, int npar, int *indx, double b[]) ;
       for(j=1; j<= nlstate*2; j++)    void ludcmp(double **a, int npar, int *indx, double *d) ;
         for(h=0; h<=nhstepm-1; h++){    double gompertz(double p[]);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    hess=matrix(1,npar,1,npar);
         }  
      }    printf("\nCalculation of the hessian matrix. Wait...\n");
        fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
 /* End theta */    for (i=1;i<=npar;i++){
       printf("%d",i);fflush(stdout);
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);      fprintf(ficlog,"%d",i);fflush(ficlog);
      
      for(h=0; h<=nhstepm-1; h++)       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       for(j=1; j<=nlstate*2;j++)      
         for(theta=1; theta <=npar; theta++)      /*  printf(" %f ",p[i]);
           trgradg[h][j][theta]=gradg[h][theta][j];          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
          }
     
      for(i=1;i<=nlstate*2;i++)    for (i=1;i<=npar;i++) {
       for(j=1;j<=nlstate*2;j++)      for (j=1;j<=npar;j++)  {
         varhe[i][j][(int)age] =0.;        if (j>i) { 
           printf(".%d%d",i,j);fflush(stdout);
      printf("%d|",(int)age);fflush(stdout);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);          hess[i][j]=hessij(p,delti,i,j,func,npar);
      for(h=0;h<=nhstepm-1;h++){          
       for(k=0;k<=nhstepm-1;k++){          hess[j][i]=hess[i][j];    
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);          /*printf(" %lf ",hess[i][j]);*/
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);        }
         for(i=1;i<=nlstate*2;i++)      }
           for(j=1;j<=nlstate*2;j++)    }
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    printf("\n");
       }    fprintf(ficlog,"\n");
     }  
     /* Computing expectancies */    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     for(i=1; i<=nlstate;i++)    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       for(j=1; j<=nlstate;j++)    
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    a=matrix(1,npar,1,npar);
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    y=matrix(1,npar,1,npar);
              x=vector(1,npar);
 /* 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]);*/    indx=ivector(1,npar);
     for (i=1;i<=npar;i++)
         }      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     ludcmp(a,npar,indx,&pd);
     fprintf(ficreseij,"%3.0f",age );  
     cptj=0;    for (j=1;j<=npar;j++) {
     for(i=1; i<=nlstate;i++)      for (i=1;i<=npar;i++) x[i]=0;
       for(j=1; j<=nlstate;j++){      x[j]=1;
         cptj++;      lubksb(a,npar,indx,x);
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      for (i=1;i<=npar;i++){ 
       }        matcov[i][j]=x[i];
     fprintf(ficreseij,"\n");      }
        }
     free_matrix(gm,0,nhstepm,1,nlstate*2);  
     free_matrix(gp,0,nhstepm,1,nlstate*2);    printf("\n#Hessian matrix#\n");
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    fprintf(ficlog,"\n#Hessian matrix#\n");
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);    for (i=1;i<=npar;i++) { 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (j=1;j<=npar;j++) { 
   }        printf("%.3e ",hess[i][j]);
   printf("\n");        fprintf(ficlog,"%.3e ",hess[i][j]);
   fprintf(ficlog,"\n");      }
       printf("\n");
   free_vector(xp,1,npar);      fprintf(ficlog,"\n");
   free_matrix(dnewm,1,nlstate*2,1,npar);    }
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);  
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);    /* Recompute Inverse */
 }    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
 /************ Variance ******************/    ludcmp(a,npar,indx,&pd);
 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)  
 {    /*  printf("\n#Hessian matrix recomputed#\n");
   /* Variance of health expectancies */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    for (j=1;j<=npar;j++) {
   /* double **newm;*/      for (i=1;i<=npar;i++) x[i]=0;
   double **dnewm,**doldm;      x[j]=1;
   double **dnewmp,**doldmp;      lubksb(a,npar,indx,x);
   int i, j, nhstepm, hstepm, h, nstepm ;      for (i=1;i<=npar;i++){ 
   int k, cptcode;        y[i][j]=x[i];
   double *xp;        printf("%.3e ",y[i][j]);
   double **gp, **gm;  /* for var eij */        fprintf(ficlog,"%.3e ",y[i][j]);
   double ***gradg, ***trgradg; /*for var eij */      }
   double **gradgp, **trgradgp; /* for var p point j */      printf("\n");
   double *gpp, *gmp; /* for var p point j */      fprintf(ficlog,"\n");
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */    }
   double ***p3mat;    */
   double age,agelim, hf;  
   int theta;    free_matrix(a,1,npar,1,npar);
   char digit[4];    free_matrix(y,1,npar,1,npar);
   char digitp[16];    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
   char fileresprobmorprev[FILENAMELENGTH];    free_matrix(hess,1,npar,1,npar);
   
   if(popbased==1)  
     strcpy(digitp,"-populbased-");  }
   else  
     strcpy(digitp,"-stablbased-");  /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   strcpy(fileresprobmorprev,"prmorprev");  {
   sprintf(digit,"%-d",ij);    int i;
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/    int l=1, lmax=20;
   strcat(fileresprobmorprev,digit); /* Tvar to be done */    double k1,k2;
   strcat(fileresprobmorprev,digitp); /* Popbased or not */    double p2[NPARMAX+1];
   strcat(fileresprobmorprev,fileres);    double res;
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     printf("Problem with resultfile: %s\n", fileresprobmorprev);    double fx;
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);    int k=0,kmax=10;
   }    double l1;
   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);    fx=func(x);
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");    for (i=1;i<=npar;i++) p2[i]=x[i];
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);    for(l=0 ; l <=lmax; l++){
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){      l1=pow(10,l);
     fprintf(ficresprobmorprev," p.%-d SE",j);      delts=delt;
     for(i=1; i<=nlstate;i++)      for(k=1 ; k <kmax; k=k+1){
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);        delt = delta*(l1*k);
   }          p2[theta]=x[theta] +delt;
   fprintf(ficresprobmorprev,"\n");        k1=func(p2)-fx;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {        p2[theta]=x[theta]-delt;
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);        k2=func(p2)-fx;
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);        /*res= (k1-2.0*fx+k2)/delt/delt; */
     exit(0);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   }        
   else{  #ifdef DEBUG
     fprintf(ficgp,"\n# Routine varevsij");        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {  #endif
     printf("Problem with html file: %s\n", optionfilehtm);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     exit(0);          k=kmax;
   }        }
   else{        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");          k=kmax; l=lmax*10.;
   }        }
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");        }
   fprintf(ficresvij,"# Age");      }
   for(i=1; i<=nlstate;i++)    }
     for(j=1; j<=nlstate;j++)    delti[theta]=delts;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    return res; 
   fprintf(ficresvij,"\n");    
   }
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   doldm=matrix(1,nlstate,1,nlstate);  {
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);    int i;
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);    double p2[NPARMAX+1];
   gpp=vector(nlstate+1,nlstate+ndeath);    int k;
   gmp=vector(nlstate+1,nlstate+ndeath);  
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/    fx=func(x);
      for (k=1; k<=2; k++) {
   if(estepm < stepm){      for (i=1;i<=npar;i++) p2[i]=x[i];
     printf ("Problem %d lower than %d\n",estepm, stepm);      p2[thetai]=x[thetai]+delti[thetai]/k;
   }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   else  hstepm=estepm;        k1=func(p2)-fx;
   /* 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.      p2[thetai]=x[thetai]+delti[thetai]/k;
      nhstepm is the number of hstepm from age to agelim      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
      nstepm is the number of stepm from age to agelin.      k2=func(p2)-fx;
      Look at hpijx to understand the reason of that which relies in memory size    
      and note for a fixed period like k years */      p2[thetai]=x[thetai]-delti[thetai]/k;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
      survival function given by stepm (the optimization length). Unfortunately it      k3=func(p2)-fx;
      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      p2[thetai]=x[thetai]-delti[thetai]/k;
      results. So we changed our mind and took the option of the best precision.      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   */      k4=func(p2)-fx;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   agelim = AGESUP;  #ifdef DEBUG
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      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);
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      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);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  #endif
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    return res;
     gp=matrix(0,nhstepm,1,nlstate);  }
     gm=matrix(0,nhstepm,1,nlstate);  
   /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
     for(theta=1; theta <=npar; theta++){  { 
       for(i=1; i<=npar; i++){ /* Computes gradient */    int i,imax,j,k; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double big,dum,sum,temp; 
       }    double *vv; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);     
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    vv=vector(1,n); 
     *d=1.0; 
       if (popbased==1) {    for (i=1;i<=n;i++) { 
         for(i=1; i<=nlstate;i++)      big=0.0; 
           prlim[i][i]=probs[(int)age][i][ij];      for (j=1;j<=n;j++) 
       }        if ((temp=fabs(a[i][j])) > big) big=temp; 
        if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       for(j=1; j<= nlstate; j++){      vv[i]=1.0/big; 
         for(h=0; h<=nhstepm; h++){    } 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    for (j=1;j<=n;j++) { 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      for (i=1;i<j;i++) { 
         }        sum=a[i][j]; 
       }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       /* This for computing forces of mortality (h=1)as a weighted average */        a[i][j]=sum; 
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){      } 
         for(i=1; i<= nlstate; i++)      big=0.0; 
           gpp[j] += prlim[i][i]*p3mat[i][j][1];      for (i=j;i<=n;i++) { 
       }            sum=a[i][j]; 
       /* end force of mortality */        for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
       for(i=1; i<=npar; i++) /* Computes gradient */        a[i][j]=sum; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            big=dum; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          imax=i; 
          } 
       if (popbased==1) {      } 
         for(i=1; i<=nlstate;i++)      if (j != imax) { 
           prlim[i][i]=probs[(int)age][i][ij];        for (k=1;k<=n;k++) { 
       }          dum=a[imax][k]; 
           a[imax][k]=a[j][k]; 
       for(j=1; j<= nlstate; j++){          a[j][k]=dum; 
         for(h=0; h<=nhstepm; h++){        } 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        *d = -(*d); 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        vv[imax]=vv[j]; 
         }      } 
       }      indx[j]=imax; 
       /* This for computing force of mortality (h=1)as a weighted average */      if (a[j][j] == 0.0) a[j][j]=TINY; 
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){      if (j != n) { 
         for(i=1; i<= nlstate; i++)        dum=1.0/(a[j][j]); 
           gmp[j] += prlim[i][i]*p3mat[i][j][1];        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       }          } 
       /* end force of mortality */    } 
     free_vector(vv,1,n);  /* Doesn't work */
       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];  
         }  void lubksb(double **a, int n, int *indx, double b[]) 
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */  { 
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];    int i,ii=0,ip,j; 
       }    double sum; 
    
     } /* End theta */    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */      sum=b[ip]; 
       b[ip]=b[i]; 
     for(h=0; h<=nhstepm; h++) /* veij */      if (ii) 
       for(j=1; j<=nlstate;j++)        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
         for(theta=1; theta <=npar; theta++)      else if (sum) ii=i; 
           trgradg[h][j][theta]=gradg[h][theta][j];      b[i]=sum; 
     } 
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */    for (i=n;i>=1;i--) { 
       for(theta=1; theta <=npar; theta++)      sum=b[i]; 
         trgradgp[j][theta]=gradgp[theta][j];      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       b[i]=sum/a[i][i]; 
     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.;  void pstamp(FILE *fichier)
   {
     for(h=0;h<=nhstepm;h++){    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
       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]);  /************ Frequencies ********************/
         for(i=1;i<=nlstate;i++)  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[])
           for(j=1;j<=nlstate;j++)  {  /* Some frequencies */
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    
       }    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     }    int first;
     double ***freq; /* Frequencies */
     /* pptj */    double *pp, **prop;
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);    char fileresp[FILENAMELENGTH];
     for(j=nlstate+1;j<=nlstate+ndeath;j++)    
       for(i=nlstate+1;i<=nlstate+ndeath;i++)    pp=vector(1,nlstate);
         varppt[j][i]=doldmp[j][i];    prop=matrix(1,nlstate,iagemin,iagemax+3);
     /* end ppptj */    strcpy(fileresp,"p");
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);      strcat(fileresp,fileres);
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);    if((ficresp=fopen(fileresp,"w"))==NULL) {
        printf("Problem with prevalence resultfile: %s\n", fileresp);
     if (popbased==1) {      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       for(i=1; i<=nlstate;i++)      exit(0);
         prlim[i][i]=probs[(int)age][i][ij];    }
     }    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
        j1=0;
     /* This for computing force of mortality (h=1)as a weighted average */    
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){    j=cptcoveff;
       for(i=1; i<= nlstate; i++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         gmp[j] += prlim[i][i]*p3mat[i][j][1];  
     }        first=1;
     /* end force of mortality */  
     for(k1=1; k1<=j;k1++){
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);      for(i1=1; i1<=ncodemax[k1];i1++){
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){        j1++;
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       for(i=1; i<=nlstate;i++){          scanf("%d", i);*/
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);        for (i=-5; i<=nlstate+ndeath; i++)  
       }          for (jk=-5; jk<=nlstate+ndeath; jk++)  
     }            for(m=iagemin; m <= iagemax+3; m++)
     fprintf(ficresprobmorprev,"\n");              freq[i][jk][m]=0;
   
     fprintf(ficresvij,"%.0f ",age );      for (i=1; i<=nlstate; i++)  
     for(i=1; i<=nlstate;i++)        for(m=iagemin; m <= iagemax+3; m++)
       for(j=1; j<=nlstate;j++){          prop[i][m]=0;
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);        
       }        dateintsum=0;
     fprintf(ficresvij,"\n");        k2cpt=0;
     free_matrix(gp,0,nhstepm,1,nlstate);        for (i=1; i<=imx; i++) {
     free_matrix(gm,0,nhstepm,1,nlstate);          bool=1;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          if  (cptcovn>0) {
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);            for (z1=1; z1<=cptcoveff; z1++) 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   } /* End age */                bool=0;
   free_vector(gpp,nlstate+1,nlstate+ndeath);          }
   free_vector(gmp,nlstate+1,nlstate+ndeath);          if (bool==1){
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);            for(m=firstpass; m<=lastpass; m++){
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/              k2=anint[m][i]+(mint[m][i]/12.);
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);                if (m<lastpass) {
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,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);                
 */                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);                  dateintsum=dateintsum+k2;
                   k2cpt++;
   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);         
   fclose(ficresprobmorprev);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   fclose(ficgp);        pstamp(ficresp);
   fclose(fichtm);        if  (cptcovn>0) {
           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#");
 /************ 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++) 
 {          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   /* Variance of prevalence limit */        fprintf(ficresp, "\n");
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        
   double **newm;        for(i=iagemin; i <= iagemax+3; i++){
   double **dnewm,**doldm;          if(i==iagemax+3){
   int i, j, nhstepm, hstepm;            fprintf(ficlog,"Total");
   int k, cptcode;          }else{
   double *xp;            if(first==1){
   double *gp, *gm;              first=0;
   double **gradg, **trgradg;              printf("See log file for details...\n");
   double age,agelim;            }
   int theta;            fprintf(ficlog,"Age %d", i);
              }
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");          for(jk=1; jk <=nlstate ; jk++){
   fprintf(ficresvpl,"# Age");            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   for(i=1; i<=nlstate;i++)              pp[jk] += freq[jk][m][i]; 
       fprintf(ficresvpl," %1d-%1d",i,i);          }
   fprintf(ficresvpl,"\n");          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
   xp=vector(1,npar);              pos += freq[jk][m][i];
   dnewm=matrix(1,nlstate,1,npar);            if(pp[jk]>=1.e-10){
   doldm=matrix(1,nlstate,1,nlstate);              if(first==1){
                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   hstepm=1*YEARM; /* Every year of age */              }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   agelim = AGESUP;            }else{
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              if(first==1)
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     if (stepm >= YEARM) hstepm=1;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            }
     gradg=matrix(1,npar,1,nlstate);          }
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);          for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     for(theta=1; theta <=npar; theta++){              pp[jk] += freq[jk][m][i];
       for(i=1; i<=npar; i++){ /* Computes gradient */          }       
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       }            pos += pp[jk];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            posprop += prop[jk][i];
       for(i=1;i<=nlstate;i++)          }
         gp[i] = prlim[i][i];          for(jk=1; jk <=nlstate ; jk++){
                if(pos>=1.e-5){
       for(i=1; i<=npar; i++) /* Computes gradient */              if(first==1)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       for(i=1;i<=nlstate;i++)            }else{
         gm[i] = prlim[i][i];              if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       for(i=1;i<=nlstate;i++)              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];            }
     } /* End theta */            if( i <= iagemax){
               if(pos>=1.e-5){
     trgradg =matrix(1,nlstate,1,npar);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
     for(j=1; j<=nlstate;j++)                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       for(theta=1; theta <=npar; theta++)              }
         trgradg[j][theta]=gradg[theta][j];              else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     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(jk=-1; jk <=nlstate+ndeath; jk++)
     for(i=1;i<=nlstate;i++)            for(m=-1; m <=nlstate+ndeath; m++)
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */              if(freq[jk][m][i] !=0 ) {
               if(first==1)
     fprintf(ficresvpl,"%.0f ",age );                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     for(i=1; i<=nlstate;i++)                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));              }
     fprintf(ficresvpl,"\n");          if(i <= iagemax)
     free_vector(gp,1,nlstate);            fprintf(ficresp,"\n");
     free_vector(gm,1,nlstate);          if(first==1)
     free_matrix(gradg,1,npar,1,nlstate);            printf("Others in log...\n");
     free_matrix(trgradg,1,nlstate,1,npar);          fprintf(ficlog,"\n");
   } /* End age */        }
       }
   free_vector(xp,1,npar);    }
   free_matrix(doldm,1,nlstate,1,npar);    dateintmean=dateintsum/k2cpt; 
   free_matrix(dnewm,1,nlstate,1,nlstate);   
     fclose(ficresp);
 }    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
 /************ Variance of one-step probabilities  ******************/    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)    /* End of Freq */
 {  }
   int i, j=0,  i1, k1, l1, t, tj;  
   int k2, l2, j1,  z1;  /************ Prevalence ********************/
   int k=0,l, cptcode;  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)
   int first=1, first1;  {  
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   double **dnewm,**doldm;       in each health status at the date of interview (if between dateprev1 and dateprev2).
   double *xp;       We still use firstpass and lastpass as another selection.
   double *gp, *gm;    */
   double **gradg, **trgradg;   
   double **mu;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   double age,agelim, cov[NCOVMAX];    double ***freq; /* Frequencies */
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */    double *pp, **prop;
   int theta;    double pos,posprop; 
   char fileresprob[FILENAMELENGTH];    double  y2; /* in fractional years */
   char fileresprobcov[FILENAMELENGTH];    int iagemin, iagemax;
   char fileresprobcor[FILENAMELENGTH];  
     iagemin= (int) agemin;
   double ***varpij;    iagemax= (int) agemax;
     /*pp=vector(1,nlstate);*/
   strcpy(fileresprob,"prob");    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   strcat(fileresprob,fileres);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    j1=0;
     printf("Problem with resultfile: %s\n", fileresprob);    
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);    j=cptcoveff;
   }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   strcpy(fileresprobcov,"probcov");    
   strcat(fileresprobcov,fileres);    for(k1=1; k1<=j;k1++){
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {      for(i1=1; i1<=ncodemax[k1];i1++){
     printf("Problem with resultfile: %s\n", fileresprobcov);        j1++;
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);        
   }        for (i=1; i<=nlstate; i++)  
   strcpy(fileresprobcor,"probcor");          for(m=iagemin; m <= iagemax+3; m++)
   strcat(fileresprobcor,fileres);            prop[i][m]=0.0;
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {       
     printf("Problem with resultfile: %s\n", fileresprobcor);        for (i=1; i<=imx; i++) { /* Each individual */
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);          bool=1;
   }          if  (cptcovn>0) {
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);            for (z1=1; z1<=cptcoveff; z1++) 
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);                bool=0;
   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);          if (bool==1) { 
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
                y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   fprintf(ficresprob,"# Age");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   fprintf(ficresprobcov,"# Age");                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); 
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   fprintf(ficresprobcov,"# Age");                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
   for(i=1; i<=nlstate;i++)                } 
     for(j=1; j<=(nlstate+ndeath);j++){              }
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);            } /* end selection of waves */
       fprintf(ficresprobcov," p%1d-%1d ",i,j);          }
       fprintf(ficresprobcor," p%1d-%1d ",i,j);        }
     }          for(i=iagemin; i <= iagemax+3; i++){  
   fprintf(ficresprob,"\n");          
   fprintf(ficresprobcov,"\n");          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   fprintf(ficresprobcor,"\n");            posprop += prop[jk][i]; 
   xp=vector(1,npar);          } 
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));          for(jk=1; jk <=nlstate ; jk++){     
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);            if( i <=  iagemax){ 
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);              if(posprop>=1.e-5){ 
   first=1;                probs[i][jk][j1]= prop[jk][i]/posprop;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {              } 
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);            } 
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);          }/* end jk */ 
     exit(0);        }/* end i */ 
   }      } /* end i1 */
   else{    } /* end k1 */
     fprintf(ficgp,"\n# Routine varprob");    
   }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {    /*free_vector(pp,1,nlstate);*/
     printf("Problem with html file: %s\n", optionfilehtm);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);  }  /* End of prevalence */
     exit(0);  
   }  /************* Waves Concatenation ***************/
   else{  
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");  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(fichtm,"\n");  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");       Death is a valid wave (if date is known).
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix 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> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \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.
   }       */
   
      int i, mi, m;
   cov[1]=1;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   tj=cptcoveff;       double sum=0., jmean=0.;*/
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}    int first;
   j1=0;    int j, k=0,jk, ju, jl;
   for(t=1; t<=tj;t++){    double sum=0.;
     for(i1=1; i1<=ncodemax[t];i1++){    first=0;
       j1++;    jmin=1e+5;
          jmax=-1;
       if  (cptcovn>0) {    jmean=0.;
         fprintf(ficresprob, "\n#********** Variable ");    for(i=1; i<=imx; i++){
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      mi=0;
         fprintf(ficresprob, "**********\n#");      m=firstpass;
         fprintf(ficresprobcov, "\n#********** Variable ");      while(s[m][i] <= nlstate){
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
         fprintf(ficresprobcov, "**********\n#");          mw[++mi][i]=m;
                if(m >=lastpass)
         fprintf(ficgp, "\n#********** Variable ");          break;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        else
         fprintf(ficgp, "**********\n#");          m++;
              }/* end while */
              if (s[m][i] > nlstate){
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");        mi++;     /* Death is another wave */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        /* if(mi==0)  never been interviewed correctly before death */
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");           /* Only death is a correct wave */
                mw[mi][i]=m;
         fprintf(ficresprobcor, "\n#********** Variable ");          }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficgp, "**********\n#");          wav[i]=mi;
       }      if(mi==0){
              nbwarn++;
       for (age=bage; age<=fage; age ++){        if(first==0){
         cov[2]=age;          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
         for (k=1; k<=cptcovn;k++) {          first=1;
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];        }
         }        if(first==1){
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         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]]];      } /* end mi==0 */
            } /* End individuals */
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));  
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    for(i=1; i<=imx; i++){
         gp=vector(1,(nlstate)*(nlstate+ndeath));      for(mi=1; mi<wav[i];mi++){
         gm=vector(1,(nlstate)*(nlstate+ndeath));        if (stepm <=0)
              dh[mi][i]=1;
         for(theta=1; theta <=npar; theta++){        else{
           for(i=1; i<=npar; i++)          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             xp[i] = x[i] + (i==theta ?delti[theta]:0);            if (agedc[i] < 2*AGESUP) {
                        j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
           pmij(pmmij,cov,ncovmodel,xp,nlstate);              if(j==0) j=1;  /* Survives at least one month after exam */
                        else if(j<0){
           k=0;                nberr++;
           for(i=1; i<= (nlstate); i++){                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             for(j=1; j<=(nlstate+ndeath);j++){                j=1; /* Temporary Dangerous patch */
               k=k+1;                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);
               gp[k]=pmmij[i][j];                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             }                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
           }              }
                        k=k+1;
           for(i=1; i<=npar; i++)              if (j >= jmax){
             xp[i] = x[i] - (i==theta ?delti[theta]:0);                jmax=j;
                    ijmax=i;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);              }
           k=0;              if (j <= jmin){
           for(i=1; i<=(nlstate); i++){                jmin=j;
             for(j=1; j<=(nlstate+ndeath);j++){                ijmin=i;
               k=k+1;              }
               gm[k]=pmmij[i][j];              sum=sum+j;
             }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
           }              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                  }
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)          }
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            else{
         }            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)  
           for(theta=1; theta <=npar; theta++)            k=k+1;
             trgradg[j][theta]=gradg[theta][j];            if (j >= jmax) {
                      jmax=j;
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);              ijmax=i;
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);            }
                    else if (j <= jmin){
         pmij(pmmij,cov,ncovmodel,x,nlstate);              jmin=j;
                      ijmin=i;
         k=0;            }
         for(i=1; i<=(nlstate); i++){            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           for(j=1; j<=(nlstate+ndeath);j++){            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
             k=k+1;            if(j<0){
             mu[k][(int) age]=pmmij[i][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(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]);
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)            }
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)            sum=sum+j;
             varpij[i][j][(int)age] = doldm[i][j];          }
           jk= j/stepm;
         /*printf("\n%d ",(int)age);          jl= j -jk*stepm;
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){          ju= j -(jk+1)*stepm;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            if(jl==0){
      }*/              dh[mi][i]=jk;
               bh[mi][i]=0;
         fprintf(ficresprob,"\n%d ",(int)age);            }else{ /* We want a negative bias in order to only have interpolation ie
         fprintf(ficresprobcov,"\n%d ",(int)age);                    * at the price of an extra matrix product in likelihood */
         fprintf(ficresprobcor,"\n%d ",(int)age);              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)            }
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));          }else{
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){            if(jl <= -ju){
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);              dh[mi][i]=jk;
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);              bh[mi][i]=jl;       /* bias is positive if real duration
         }                                   * is higher than the multiple of stepm and negative otherwise.
         i=0;                                   */
         for (k=1; k<=(nlstate);k++){            }
           for (l=1; l<=(nlstate+ndeath);l++){            else{
             i=i++;              dh[mi][i]=jk+1;
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);              bh[mi][i]=ju;
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);            }
             for (j=1; j<=i;j++){            if(dh[mi][i]==0){
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);              dh[mi][i]=1; /* At least one step */
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));              bh[mi][i]=ju; /* At least one step */
             }              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
           }            }
         }/* end of loop for state */          } /* end if mle */
       } /* end of loop for age */        }
       } /* end wave */
       /* Confidence intervalle of pij  */    }
       /*    jmean=sum/k;
       fprintf(ficgp,"\nset noparametric;unset label");    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(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
       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);  /*********** Tricode ****************************/
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);  void tricode(int *Tvar, int **nbcode, int imx)
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);  {
       */    
     int Ndum[20],ij=1, k, j, i, maxncov=19;
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/    int cptcode=0;
       first1=1;    cptcoveff=0; 
       for (k2=1; k2<=(nlstate);k2++){   
         for (l2=1; l2<=(nlstate+ndeath);l2++){    for (k=0; k<maxncov; k++) Ndum[k]=0;
           if(l2==k2) continue;    for (k=1; k<=7; k++) ncodemax[k]=0;
           j=(k2-1)*(nlstate+ndeath)+l2;  
           for (k1=1; k1<=(nlstate);k1++){    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
             for (l1=1; l1<=(nlstate+ndeath);l1++){      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
               if(l1==k1) continue;                                 modality*/ 
               i=(k1-1)*(nlstate+ndeath)+l1;        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
               if(i<=j) continue;        Ndum[ij]++; /*store the modality */
               for (age=bage; age<=fage; age ++){        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
                 if ((int)age %5==0){        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;                                         Tvar[j]. If V=sex and male is 0 and 
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;                                         female is 1, then  cptcode=1.*/
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;      }
                   mu1=mu[i][(int) age]/stepm*YEARM ;  
                   mu2=mu[j][(int) age]/stepm*YEARM;      for (i=0; i<=cptcode; i++) {
                   c12=cv12/sqrt(v1*v2);        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
                   /* 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.;      ij=1; 
                   /* Eigen vectors */      for (i=1; i<=ncodemax[j]; i++) {
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));        for (k=0; k<= maxncov; k++) {
                   /*v21=sqrt(1.-v11*v11); *//* error */          if (Ndum[k] != 0) {
                   v21=(lc1-v1)/cv12*v11;            nbcode[Tvar[j]][ij]=k; 
                   v12=-v21;            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
                   v22=v11;            
                   tnalp=v21/v11;            ij++;
                   if(first1==1){          }
                     first1=0;          if (ij > ncodemax[j]) break; 
                     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) */   for (k=0; k< maxncov; k++) Ndum[k]=0;
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */  
                   if(first==1){   for (i=1; i<=ncovmodel-2; i++) { 
                     first=0;     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
                     fprintf(ficgp,"\nset parametric;unset label");     ij=Tvar[i];
                     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);     Ndum[ij]++;
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");   }
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);  
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);   ij=1;
                     fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);   for (i=1; i<= maxncov; i++) {
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);     if((Ndum[i]!=0) && (i<=ncovcol)){
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);       Tvaraff[ij]=i; /*For printing */
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);       ij++;
                     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{   cptcoveff=ij-1; /*Number of simple covariates*/
                     first=0;  }
                     fprintf(fichtm," %d (%.3f),",(int) age, c12);  
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);  /*********** Health Expectancies ****************/
                     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",\  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\  
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));  {
                   }/* if first */    /* Health expectancies, no variances */
                 } /* age mod 5 */    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
               } /* end loop age */    double age, agelim, hf;
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);    double ***p3mat;
               first=1;    double eip;
             } /*l12 */  
           } /* k12 */    pstamp(ficreseij);
         } /*l1 */    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
       }/* k1 */    fprintf(ficreseij,"# Age");
     } /* loop covariates */    for(i=1; i<=nlstate;i++){
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);      for(j=1; j<=nlstate;j++){
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        fprintf(ficreseij," e%1d%1d ",i,j);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      }
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);      fprintf(ficreseij," e%1d. ",i);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    }
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    fprintf(ficreseij,"\n");
   }  
   free_vector(xp,1,npar);    
   fclose(ficresprob);    if(estepm < stepm){
   fclose(ficresprobcov);      printf ("Problem %d lower than %d\n",estepm, stepm);
   fclose(ficresprobcor);    }
   fclose(ficgp);    else  hstepm=estepm;   
   fclose(fichtm);    /* 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 
 /******************* Printing html file ***********/     * progression in between and thus overestimating or underestimating according
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \     * to the curvature of the survival function. If, for the same date, we 
                   int lastpass, int stepm, int weightopt, char model[],\     * estimate the model with stepm=1 month, we can keep estepm to 24 months
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\     * to compare the new estimate of Life expectancy with the same linear 
                   int popforecast, int estepm ,\     * hypothesis. A more precise result, taking into account a more precise
                   double jprev1, double mprev1,double anprev1, \     * curvature will be obtained if estepm is as small as stepm. */
                   double jprev2, double mprev2,double anprev2){  
   int jj1, k1, i1, cpt;    /* For example we decided to compute the life expectancy with the smallest unit */
   /*char optionfilehtm[FILENAMELENGTH];*/    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {       nhstepm is the number of hstepm from age to agelim 
     printf("Problem with %s \n",optionfilehtm), exit(0);       nstepm is the number of stepm from age to agelin. 
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);       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
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n       survival function given by stepm (the optimization length). Unfortunately it
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n       means that if the survival funtion is printed only each two years of age and if
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n       results. So we changed our mind and took the option of the best precision.
  - Life expectancies by age and initial health status (estepm=%2d months):    */
    <a href=\"e%s\">e%s</a> <br>\n</li>", \    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);  
     agelim=AGESUP;
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");    /* nhstepm age range expressed in number of stepm */
     nstepm=(int) rint((agelim-age)*YEARM/stepm); 
  m=cptcoveff;    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
  jj1=0;    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
      jj1++;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
      if (cptcovn > 0) {         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      
        for (cpt=1; cpt<=cptcoveff;cpt++)      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      }      
      /* Pij */      printf("%d|",(int)age);fflush(stdout);
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          
      /* Quasi-incidences */      /* Computing expectancies */
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>      for(i=1; i<=nlstate;i++)
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        for(j=1; j<=nlstate;j++)
        /* Stable prevalence in each health state */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
        for(cpt=1; cpt<nlstate;cpt++){            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>            
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
        }  
      for(cpt=1; cpt<=nlstate;cpt++) {          }
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>  
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      fprintf(ficreseij,"%3.0f",age );
      }      for(i=1; i<=nlstate;i++){
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        eip=0;
 health expectancies in states (1) and (2): e%s%d.png<br>        for(j=1; j<=nlstate;j++){
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          eip +=eij[i][j][(int)age];
    } /* end i1 */          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
  }/* End k1 */        }
  fprintf(fichtm,"</ul>");        fprintf(ficreseij,"%9.4f", eip );
       }
       fprintf(ficreseij,"\n");
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n      
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n    }
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    printf("\n");
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n    fprintf(ficlog,"\n");
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n  }
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);  
   void cvevsij(char fileres[], 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[] )
  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    /* Covariances of health expectancies eij and of total life expectancies according
         <br>",fileres,fileres,fileres,fileres);     to initial status i, ei. .
  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);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");    double age, agelim, hf;
     double ***p3matp, ***p3matm, ***varhe;
  m=cptcoveff;    double **dnewm,**doldm;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    double *xp, *xm;
     double **gp, **gm;
  jj1=0;    double ***gradg, ***trgradg;
  for(k1=1; k1<=m;k1++){    int theta;
    for(i1=1; i1<=ncodemax[k1];i1++){  
      jj1++;    double eip, vip;
      if (cptcovn > 0) {  
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
        for (cpt=1; cpt<=cptcoveff;cpt++)    xp=vector(1,npar);
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    xm=vector(1,npar);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    dnewm=matrix(1,nlstate*nlstate,1,npar);
      }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
      for(cpt=1; cpt<=nlstate;cpt++) {    
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    pstamp(ficresstdeij);
 interval) in state (%d): v%s%d%d.png <br>    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      fprintf(ficresstdeij,"# Age");
      }    for(i=1; i<=nlstate;i++){
    } /* end i1 */      for(j=1; j<=nlstate;j++)
  }/* End k1 */        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
  fprintf(fichtm,"</ul>");      fprintf(ficresstdeij," e%1d. ",i);
 fclose(fichtm);    }
 }    fprintf(ficresstdeij,"\n");
   
 /******************* Gnuplot file **************/    pstamp(ficrescveij);
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    for(i=1; i<=nlstate;i++)
   int ng;      for(j=1; j<=nlstate;j++){
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {        cptj= (j-1)*nlstate+i;
     printf("Problem with file %s",optionfilegnuplot);        for(i2=1; i2<=nlstate;i2++)
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);          for(j2=1; j2<=nlstate;j2++){
   }            cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
 #ifdef windows              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
     fprintf(ficgp,"cd \"%s\" \n",pathc);          }
 #endif      }
 m=pow(2,cptcoveff);    fprintf(ficrescveij,"\n");
      
  /* 1eme*/    if(estepm < stepm){
   for (cpt=1; cpt<= nlstate ; cpt ++) {      printf ("Problem %d lower than %d\n",estepm, stepm);
    for (k1=1; k1<= m ; k1 ++) {    }
     else  hstepm=estepm;   
 #ifdef windows    /* We compute the life expectancy from trapezoids spaced every estepm months
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);     * This is mainly to measure the difference between two models: for example
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);     * if stepm=24 months pijx are given only every 2 years and by summing them
 #endif     * we are calculating an estimate of the Life Expectancy assuming a linear 
 #ifdef unix     * progression in between and thus overestimating or underestimating according
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);     * to the curvature of the survival function. If, for the same date, we 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
 #endif     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
 for (i=1; i<= nlstate ; i ++) {     * curvature will be obtained if estepm is as small as stepm. */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /* 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. 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);       nhstepm is the number of hstepm from age to agelim 
     for (i=1; i<= nlstate ; i ++) {       nstepm is the number of stepm from age to agelin. 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");       Look at hpijx to understand the reason of that which relies in memory size
   else fprintf(ficgp," \%%*lf (\%%*lf)");       and note for a fixed period like estepm months */
 }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);       survival function given by stepm (the optimization length). Unfortunately it
      for (i=1; i<= nlstate ; i ++) {       means that if the survival funtion is printed only each two years of age and if
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   else fprintf(ficgp," \%%*lf (\%%*lf)");       results. So we changed our mind and took the option of the best precision.
 }      */
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 #ifdef unix  
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");    /* If stepm=6 months */
 #endif    /* nhstepm age range expressed in number of stepm */
    }    agelim=AGESUP;
   }    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   /*2 eme*/    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
   for (k1=1; k1<= m ; k1 ++) {    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);    
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     for (i=1; i<= nlstate+1 ; i ++) {    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       k=2*i;    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    gp=matrix(0,nhstepm,1,nlstate*nlstate);
       for (j=1; j<= nlstate+1 ; j ++) {    gm=matrix(0,nhstepm,1,nlstate*nlstate);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for (age=bage; age<=fage; age ++){ 
 }    
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);   
       for (j=1; j<= nlstate+1 ; j ++) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
         else fprintf(ficgp," \%%*lf (\%%*lf)");      /* Computing  Variances of health expectancies */
 }        /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
       fprintf(ficgp,"\" t\"\" w l 0,");         decrease memory allocation */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      for(theta=1; theta <=npar; theta++){
       for (j=1; j<= nlstate+1 ; j ++) {        for(i=1; i<=npar; i++){ 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   else fprintf(ficgp," \%%*lf (\%%*lf)");          xm[i] = x[i] - (i==theta ?delti[theta]:0);
 }          }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       else fprintf(ficgp,"\" t\"\" w l 0,");        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     }    
   }        for(j=1; j<= nlstate; j++){
            for(i=1; i<=nlstate; i++){
   /*3eme*/            for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
   for (k1=1; k1<= m ; k1 ++) {              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
     for (cpt=1; cpt<= nlstate ; cpt ++) {            }
       k=2+nlstate*(2*cpt-2);          }
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        }
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);       
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        for(ij=1; ij<= nlstate*nlstate; ij++)
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          for(h=0; h<=nhstepm-1; h++){
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          }
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      }/* End theta */
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      
       
 */      for(h=0; h<=nhstepm-1; h++)
       for (i=1; i< nlstate ; i ++) {        for(j=1; j<=nlstate*nlstate;j++)
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);          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++)
   /* CV preval stat */          varhe[ij][ji][(int)age] =0.;
     for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<nlstate ; cpt ++) {       printf("%d|",(int)age);fflush(stdout);
       k=3;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);       for(h=0;h<=nhstepm-1;h++){
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);        for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       for (i=1; i< nlstate ; i ++)          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
         fprintf(ficgp,"+$%d",k+i+1);          for(ij=1;ij<=nlstate*nlstate;ij++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            for(ji=1;ji<=nlstate*nlstate;ji++)
                    varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
       l=3+(nlstate+ndeath)*cpt;        }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      }
       for (i=1; i< nlstate ; i ++) {      /* Computing expectancies */
         l=3+(nlstate+ndeath)*cpt;      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
         fprintf(ficgp,"+$%d",l+i+1);      for(i=1; i<=nlstate;i++)
       }        for(j=1; j<=nlstate;j++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            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]);*/
   /* proba elementaires */  
    for(i=1,jk=1; i <=nlstate; i++){          }
     for(k=1; k <=(nlstate+ndeath); k++){  
       if (k != i) {      fprintf(ficresstdeij,"%3.0f",age );
         for(j=1; j <=ncovmodel; j++){      for(i=1; i<=nlstate;i++){
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        eip=0.;
           jk++;        vip=0.;
           fprintf(ficgp,"\n");        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]) );
         }
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
      for(jk=1; jk <=m; jk++) {      }
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);      fprintf(ficresstdeij,"\n");
        if (ng==2)  
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");      fprintf(ficrescveij,"%3.0f",age );
        else      for(i=1; i<=nlstate;i++)
          fprintf(ficgp,"\nset title \"Probability\"\n");        for(j=1; j<=nlstate;j++){
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          cptj= (j-1)*nlstate+i;
        i=1;          for(i2=1; i2<=nlstate;i2++)
        for(k2=1; k2<=nlstate; k2++) {            for(j2=1; j2<=nlstate;j2++){
          k3=i;              cptj2= (j2-1)*nlstate+i2;
          for(k=1; k<=(nlstate+ndeath); k++) {              if(cptj2 <= cptj)
            if (k != k2){                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
              if(ng==2)            }
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);        }
              else      fprintf(ficrescveij,"\n");
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);     
              ij=1;    }
              for(j=3; j <=ncovmodel; j++) {    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
                  ij++;    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
                }    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                else    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    printf("\n");
              }    fprintf(ficlog,"\n");
              fprintf(ficgp,")/(1");  
                  free_vector(xm,1,npar);
              for(k1=1; k1 <=nlstate; k1++){      free_vector(xp,1,npar);
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
                ij=1;    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
                for(j=3; j <=ncovmodel; j++){    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
                  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++;  /************ 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[])
                  else  {
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /* Variance of health expectancies */
                }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
                fprintf(ficgp,")");    /* double **newm;*/
              }    double **dnewm,**doldm;
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);    double **dnewmp,**doldmp;
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    int i, j, nhstepm, hstepm, h, nstepm ;
              i=i+ncovmodel;    int k, cptcode;
            }    double *xp;
          } /* end k */    double **gp, **gm;  /* for var eij */
        } /* end k2 */    double ***gradg, ***trgradg; /*for var eij */
      } /* end jk */    double **gradgp, **trgradgp; /* for var p point j */
    } /* end ng */    double *gpp, *gmp; /* for var p point j */
    fclose(ficgp);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
 }  /* end gnuplot */    double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
 /*************** Moving average **************/    int theta;
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    char digit[4];
     char digitp[25];
   int i, cpt, cptcod;  
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    char fileresprobmorprev[FILENAMELENGTH];
       for (i=1; i<=nlstate;i++)  
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    if(popbased==1){
           mobaverage[(int)agedeb][i][cptcod]=0.;      if(mobilav!=0)
            strcpy(digitp,"-populbased-mobilav-");
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){      else strcpy(digitp,"-populbased-nomobil-");
       for (i=1; i<=nlstate;i++){    }
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    else 
           for (cpt=0;cpt<=4;cpt++){      strcpy(digitp,"-stablbased-");
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  
           }    if (mobilav!=0) {
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      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"); 
 /************** Forecasting ******************/    sprintf(digit,"%-d",ij);
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
      strcat(fileresprobmorprev,digit); /* Tvar to be done */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   int *popage;    strcat(fileresprobmorprev,fileres);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   double *popeffectif,*popcount;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   double ***p3mat;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   char fileresf[FILENAMELENGTH];    }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
  agelim=AGESUP;   
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    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++){
   strcpy(fileresf,"f");      fprintf(ficresprobmorprev," p.%-d SE",j);
   strcat(fileresf,fileres);      for(i=1; i<=nlstate;i++)
   if((ficresf=fopen(fileresf,"w"))==NULL) {        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     printf("Problem with forecast resultfile: %s\n", fileresf);    }  
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);    fprintf(ficresprobmorprev,"\n");
   }    fprintf(ficgp,"\n# Routine varevsij");
   printf("Computing forecasting: result on file '%s' \n", fileresf);    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);    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);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if (mobilav==1) {    pstamp(ficresvij);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     movingaverage(agedeb, fage, ageminpar, mobaverage);    if(popbased==1)
   }      fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
     else
   stepsize=(int) (stepm+YEARM-1)/YEARM;      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
   if (stepm<=12) stepsize=1;    fprintf(ficresvij,"# Age");
      for(i=1; i<=nlstate;i++)
   agelim=AGESUP;      for(j=1; j<=nlstate;j++)
          fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
   hstepm=1;    fprintf(ficresvij,"\n");
   hstepm=hstepm/stepm;  
   yp1=modf(dateintmean,&yp);    xp=vector(1,npar);
   anprojmean=yp;    dnewm=matrix(1,nlstate,1,npar);
   yp2=modf((yp1*12),&yp);    doldm=matrix(1,nlstate,1,nlstate);
   mprojmean=yp;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   yp1=modf((yp2*30.5),&yp);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   jprojmean=yp;  
   if(jprojmean==0) jprojmean=1;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   if(mprojmean==0) jprojmean=1;    gpp=vector(nlstate+1,nlstate+ndeath);
      gmp=vector(nlstate+1,nlstate+ndeath);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      
   for(cptcov=1;cptcov<=i2;cptcov++){    if(estepm < stepm){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      printf ("Problem %d lower than %d\n",estepm, stepm);
       k=k+1;    }
       fprintf(ficresf,"\n#******");    else  hstepm=estepm;   
       for(j=1;j<=cptcoveff;j++) {    /* For example we decided to compute the life expectancy with the smallest unit */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* 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 
       fprintf(ficresf,"******\n");       nstepm is the number of stepm from age to agelin. 
       fprintf(ficresf,"# StartingAge FinalAge");       Look at hpijx to understand the reason of that which relies in memory size
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);       and note for a fixed period like k years */
          /* 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
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {       means that if the survival funtion is printed every two years of age and if
         fprintf(ficresf,"\n");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);         results. So we changed our mind and took the option of the best precision.
     */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    agelim = AGESUP;
           nhstepm = nhstepm/hstepm;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           oldm=oldms;savm=savms;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
              gp=matrix(0,nhstepm,1,nlstate);
           for (h=0; h<=nhstepm; h++){      gm=matrix(0,nhstepm,1,nlstate);
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);  
             }      for(theta=1; theta <=npar; theta++){
             for(j=1; j<=nlstate+ndeath;j++) {        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
               kk1=0.;kk2=0;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
               for(i=1; i<=nlstate;i++) {                      }
                 if (mobilav==1)        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        if (popbased==1) {
                 }          if(mobilav ==0){
                            for(i=1; i<=nlstate;i++)
               }              prlim[i][i]=probs[(int)age][i][ij];
               if (h==(int)(calagedate+12*cpt)){          }else{ /* mobilav */ 
                 fprintf(ficresf," %.3f", kk1);            for(i=1; i<=nlstate;i++)
                                      prlim[i][i]=mobaverage[(int)age][i][ij];
               }          }
             }        }
           }    
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        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];
   }          }
                }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
   fclose(ficresf);           as a weighted average of prlim.
 }        */
 /************** Forecasting ******************/        for(j=nlstate+1;j<=nlstate+ndeath;j++){
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){          for(i=1,gpp[j]=0.; i<= nlstate; i++)
              gpp[j] += prlim[i][i]*p3mat[i][j][1];
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        }    
   int *popage;        /* end probability of death */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  
   double *popeffectif,*popcount;        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   double ***p3mat,***tabpop,***tabpopprev;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   char filerespop[FILENAMELENGTH];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        if (popbased==1) {
   agelim=AGESUP;          if(mobilav ==0){
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;            for(i=1; i<=nlstate;i++)
                prlim[i][i]=probs[(int)age][i][ij];
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
   strcpy(filerespop,"pop");          }
   strcat(filerespop,fileres);        }
   if((ficrespop=fopen(filerespop,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", filerespop);        for(j=1; j<= nlstate; j++){
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);          for(h=0; h<=nhstepm; h++){
   }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   printf("Computing forecasting: result on file '%s' \n", filerespop);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);          }
         }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
   if (mobilav==1) {           as a weighted average of prlim.
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        */
     movingaverage(agedeb, fage, ageminpar, mobaverage);        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];
   stepsize=(int) (stepm+YEARM-1)/YEARM;        }    
   if (stepm<=12) stepsize=1;        /* end probability of death */
    
   agelim=AGESUP;        for(j=1; j<= nlstate; j++) /* vareij */
            for(h=0; h<=nhstepm; h++){
   hstepm=1;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   hstepm=hstepm/stepm;          }
    
   if (popforecast==1) {        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     if((ficpop=fopen(popfile,"r"))==NULL) {          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       printf("Problem with population file : %s\n",popfile);exit(0);        }
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);  
     }      } /* End theta */
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     popcount=vector(0,AGESUP);  
          for(h=0; h<=nhstepm; h++) /* veij */
     i=1;          for(j=1; j<=nlstate;j++)
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;          for(theta=1; theta <=npar; theta++)
                trgradg[h][j][theta]=gradg[h][theta][j];
     imx=i;  
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   }        for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
   for(cptcov=1;cptcov<=i2;cptcov++){    
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       fprintf(ficrespop,"\n#******");      for(i=1;i<=nlstate;i++)
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=nlstate;j++)
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          vareij[i][j][(int)age] =0.;
       }  
       fprintf(ficrespop,"******\n");      for(h=0;h<=nhstepm;h++){
       fprintf(ficrespop,"# Age");        for(k=0;k<=nhstepm;k++){
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       if (popforecast==1)  fprintf(ficrespop," [Population]");          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
                for(i=1;i<=nlstate;i++)
       for (cpt=0; cpt<=0;cpt++) {            for(j=1;j<=nlstate;j++)
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
                }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    
           nhstepm = nhstepm/hstepm;      /* pptj */
                matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
           oldm=oldms;savm=savms;      for(j=nlstate+1;j<=nlstate+ndeath;j++)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for(i=nlstate+1;i<=nlstate+ndeath;i++)
                  varppt[j][i]=doldmp[j][i];
           for (h=0; h<=nhstepm; h++){      /* end ppptj */
             if (h==(int) (calagedate+YEARM*cpt)) {      /*  x centered again */
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
             }      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
             for(j=1; j<=nlstate+ndeath;j++) {   
               kk1=0.;kk2=0;      if (popbased==1) {
               for(i=1; i<=nlstate;i++) {                      if(mobilav ==0){
                 if (mobilav==1)          for(i=1; i<=nlstate;i++)
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            prlim[i][i]=probs[(int)age][i][ij];
                 else {        }else{ /* mobilav */ 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          for(i=1; i<=nlstate;i++)
                 }            prlim[i][i]=mobaverage[(int)age][i][ij];
               }        }
               if (h==(int)(calagedate+12*cpt)){      }
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;               
                   /*fprintf(ficrespop," %.3f", kk1);      /* This for computing probability of death (h=1 means
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
               }         as a weighted average of prlim.
             }      */
             for(i=1; i<=nlstate;i++){      for(j=nlstate+1;j<=nlstate+ndeath;j++){
               kk1=0.;        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
                 for(j=1; j<=nlstate;j++){          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];      }    
                 }      /* end probability of death */
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];  
             }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        for(i=1; i<=nlstate;i++){
           }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
         }      } 
       }      fprintf(ficresprobmorprev,"\n");
    
   /******/      fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {        for(j=1; j<=nlstate;j++){
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      fprintf(ficresvij,"\n");
           nhstepm = nhstepm/hstepm;      free_matrix(gp,0,nhstepm,1,nlstate);
                free_matrix(gm,0,nhstepm,1,nlstate);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
           oldm=oldms;savm=savms;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           for (h=0; h<=nhstepm; h++){    } /* End age */
             if (h==(int) (calagedate+YEARM*cpt)) {    free_vector(gpp,nlstate+1,nlstate+ndeath);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    free_vector(gmp,nlstate+1,nlstate+ndeath);
             }    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
             for(j=1; j<=nlstate+ndeath;j++) {    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
               kk1=0.;kk2=0;    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
               for(i=1; i<=nlstate;i++) {                  /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        fprintf(ficgp,"\n set log y; set nolog 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); */
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  /*   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 1 ",subdirf(fileresprobmorprev));
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
         }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 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);
    */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*   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);
   if (popforecast==1) {  
     free_ivector(popage,0,AGESUP);    free_vector(xp,1,npar);
     free_vector(popeffectif,0,AGESUP);    free_matrix(doldm,1,nlstate,1,nlstate);
     free_vector(popcount,0,AGESUP);    free_matrix(dnewm,1,nlstate,1,npar);
   }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   fclose(ficrespop);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 }    fclose(ficresprobmorprev);
     fflush(ficgp);
 /***********************************************/    fflush(fichtm); 
 /**************** Main Program *****************/  }  /* end varevsij */
 /***********************************************/  
   /************ Variance of prevlim ******************/
 int main(int argc, char *argv[])  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 */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   double agedeb, agefin,hf;    double **newm;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
   double fret;    int k, cptcode;
   double **xi,tmp,delta;    double *xp;
     double *gp, *gm;
   double dum; /* Dummy variable */    double **gradg, **trgradg;
   double ***p3mat;    double age,agelim;
   int *indx;    int theta;
   char line[MAXLINE], linepar[MAXLINE];    
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];    pstamp(ficresvpl);
   int firstobs=1, lastobs=10;    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
   int sdeb, sfin; /* Status at beginning and end */    fprintf(ficresvpl,"# Age");
   int c,  h , cpt,l;    for(i=1; i<=nlstate;i++)
   int ju,jl, mi;        fprintf(ficresvpl," %1d-%1d",i,i);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    fprintf(ficresvpl,"\n");
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  
   int mobilav=0,popforecast=0;    xp=vector(1,npar);
   int hstepm, nhstepm;    dnewm=matrix(1,nlstate,1,npar);
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    doldm=matrix(1,nlstate,1,nlstate);
     
   double bage, fage, age, agelim, agebase;    hstepm=1*YEARM; /* Every year of age */
   double ftolpl=FTOL;    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   double **prlim;    agelim = AGESUP;
   double *severity;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   double ***param; /* Matrix of parameters */      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   double  *p;      if (stepm >= YEARM) hstepm=1;
   double **matcov; /* Matrix of covariance */      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   double ***delti3; /* Scale */      gradg=matrix(1,npar,1,nlstate);
   double *delti; /* Scale */      gp=vector(1,nlstate);
   double ***eij, ***vareij;      gm=vector(1,nlstate);
   double **varpl; /* Variances of prevalence limits by age */  
   double *epj, vepp;      for(theta=1; theta <=npar; theta++){
   double kk1, kk2;        for(i=1; i<=npar; i++){ /* Computes gradient */
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   char *alph[]={"a","a","b","c","d","e"}, str[4];        for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
   char z[1]="c", occ;        for(i=1; i<=npar; i++) /* Computes gradient */
 #include <sys/time.h>          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 #include <time.h>        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        for(i=1;i<=nlstate;i++)
            gm[i] = prlim[i][i];
   /* long total_usecs;  
   struct timeval start_time, end_time;        for(i=1;i<=nlstate;i++)
            gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      } /* End theta */
   getcwd(pathcd, size);  
       trgradg =matrix(1,nlstate,1,npar);
   printf("\n%s",version);  
   if(argc <=1){      for(j=1; j<=nlstate;j++)
     printf("\nEnter the parameter file name: ");        for(theta=1; theta <=npar; theta++)
     scanf("%s",pathtot);          trgradg[j][theta]=gradg[theta][j];
   }  
   else{      for(i=1;i<=nlstate;i++)
     strcpy(pathtot,argv[1]);        varpl[i][(int)age] =0.;
   }      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   /*cygwin_split_path(pathtot,path,optionfile);      for(i=1;i<=nlstate;i++)
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   /* cutv(path,optionfile,pathtot,'\\');*/  
       fprintf(ficresvpl,"%.0f ",age );
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);      for(i=1; i<=nlstate;i++)
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   chdir(path);      fprintf(ficresvpl,"\n");
   replace(pathc,path);      free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
 /*-------- arguments in the command line --------*/      free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
   /* Log file */    } /* End age */
   strcat(filelog, optionfilefiname);  
   strcat(filelog,".log");    /* */    free_vector(xp,1,npar);
   if((ficlog=fopen(filelog,"w"))==NULL)    {    free_matrix(doldm,1,nlstate,1,npar);
     printf("Problem with logfile %s\n",filelog);    free_matrix(dnewm,1,nlstate,1,nlstate);
     goto end;  
   }  }
   fprintf(ficlog,"Log filename:%s\n",filelog);  
   fprintf(ficlog,"\n%s",version);  /************ Variance of one-step probabilities  ******************/
   fprintf(ficlog,"\nEnter the parameter file name: ");  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[])
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  {
   fflush(ficlog);    int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
   /* */    int k=0,l, cptcode;
   strcpy(fileres,"r");    int first=1, first1;
   strcat(fileres, optionfilefiname);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   strcat(fileres,".txt");    /* Other files have txt extension */    double **dnewm,**doldm;
     double *xp;
   /*---------arguments file --------*/    double *gp, *gm;
     double **gradg, **trgradg;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    double **mu;
     printf("Problem with optionfile %s\n",optionfile);    double age,agelim, cov[NCOVMAX];
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     goto end;    int theta;
   }    char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
   strcpy(filereso,"o");    char fileresprobcor[FILENAMELENGTH];
   strcat(filereso,fileres);  
   if((ficparo=fopen(filereso,"w"))==NULL) {    double ***varpij;
     printf("Problem with Output resultfile: %s\n", filereso);  
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);    strcpy(fileresprob,"prob"); 
     goto end;    strcat(fileresprob,fileres);
   }    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
   /* Reads comments: lines beginning with '#' */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    strcpy(fileresprobcov,"probcov"); 
     fgets(line, MAXLINE, ficpar);    strcat(fileresprobcov,fileres);
     puts(line);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     fputs(line,ficparo);      printf("Problem with resultfile: %s\n", fileresprobcov);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   ungetc(c,ficpar);    }
     strcpy(fileresprobcor,"probcor"); 
   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);    strcat(fileresprobcor,fileres);
   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);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   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);      printf("Problem with resultfile: %s\n", fileresprobcor);
 while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     puts(line);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fputs(line,ficparo);    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);
   ungetc(c,ficpar);    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);
   covar=matrix(0,NCOVMAX,1,n);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   cptcovn=0;    fprintf(ficresprob,"# Age");
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   ncovmodel=2+cptcovn;    fprintf(ficresprobcov,"# Age");
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    pstamp(ficresprobcor);
      fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   /* Read guess parameters */    fprintf(ficresprobcor,"# Age");
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);      for(j=1; j<=(nlstate+ndeath);j++){
     puts(line);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
     fputs(line,ficparo);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   ungetc(c,ficpar);      }  
     /* fprintf(ficresprob,"\n");
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    fprintf(ficresprobcov,"\n");
     for(i=1; i <=nlstate; i++)    fprintf(ficresprobcor,"\n");
     for(j=1; j <=nlstate+ndeath-1; j++){   */
       fscanf(ficpar,"%1d%1d",&i1,&j1);   xp=vector(1,npar);
       fprintf(ficparo,"%1d%1d",i1,j1);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       if(mle==1)    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
         printf("%1d%1d",i,j);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
       fprintf(ficlog,"%1d%1d",i,j);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
       for(k=1; k<=ncovmodel;k++){    first=1;
         fscanf(ficpar," %lf",&param[i][j][k]);    fprintf(ficgp,"\n# Routine varprob");
         if(mle==1){    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
           printf(" %lf",param[i][j][k]);    fprintf(fichtm,"\n");
           fprintf(ficlog," %lf",param[i][j][k]);  
         }    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
         else    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
           fprintf(ficlog," %lf",param[i][j][k]);    file %s<br>\n",optionfilehtmcov);
         fprintf(ficparo," %lf",param[i][j][k]);    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.\
       fscanf(ficpar,"\n");   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
       if(mle==1)    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. \
         printf("\n");  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
       fprintf(ficlog,"\n");  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
       fprintf(ficparo,"\n");  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>\
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
   p=param[1][1];    cov[1]=1;
      tj=cptcoveff;
   /* Reads comments: lines beginning with '#' */    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   while((c=getc(ficpar))=='#' && c!= EOF){    j1=0;
     ungetc(c,ficpar);    for(t=1; t<=tj;t++){
     fgets(line, MAXLINE, ficpar);      for(i1=1; i1<=ncodemax[t];i1++){ 
     puts(line);        j1++;
     fputs(line,ficparo);        if  (cptcovn>0) {
   }          fprintf(ficresprob, "\n#********** Variable "); 
   ungetc(c,ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          fprintf(ficresprobcov, "\n#********** Variable "); 
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   for(i=1; i <=nlstate; i++){          fprintf(ficresprobcov, "**********\n#\n");
     for(j=1; j <=nlstate+ndeath-1; j++){          
       fscanf(ficpar,"%1d%1d",&i1,&j1);          fprintf(ficgp, "\n#********** Variable "); 
       printf("%1d%1d",i,j);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fprintf(ficparo,"%1d%1d",i1,j1);          fprintf(ficgp, "**********\n#\n");
       for(k=1; k<=ncovmodel;k++){          
         fscanf(ficpar,"%le",&delti3[i][j][k]);          
         printf(" %le",delti3[i][j][k]);          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
         fprintf(ficparo," %le",delti3[i][j][k]);          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\">");
       fscanf(ficpar,"\n");          
       printf("\n");          fprintf(ficresprobcor, "\n#********** Variable ");    
       fprintf(ficparo,"\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     }          fprintf(ficresprobcor, "**********\n#");    
   }        }
   delti=delti3[1][1];        
          for (age=bage; age<=fage; age ++){ 
   /* Reads comments: lines beginning with '#' */          cov[2]=age;
   while((c=getc(ficpar))=='#' && c!= EOF){          for (k=1; k<=cptcovn;k++) {
     ungetc(c,ficpar);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     fgets(line, MAXLINE, ficpar);          }
     puts(line);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     fputs(line,ficparo);          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]]];
   ungetc(c,ficpar);          
            gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   matcov=matrix(1,npar,1,npar);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   for(i=1; i <=npar; i++){          gp=vector(1,(nlstate)*(nlstate+ndeath));
     fscanf(ficpar,"%s",&str);          gm=vector(1,(nlstate)*(nlstate+ndeath));
     if(mle==1)      
       printf("%s",str);          for(theta=1; theta <=npar; theta++){
     fprintf(ficlog,"%s",str);            for(i=1; i<=npar; i++)
     fprintf(ficparo,"%s",str);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
     for(j=1; j <=i; j++){            
       fscanf(ficpar," %le",&matcov[i][j]);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       if(mle==1){            
         printf(" %.5le",matcov[i][j]);            k=0;
         fprintf(ficlog," %.5le",matcov[i][j]);            for(i=1; i<= (nlstate); i++){
       }              for(j=1; j<=(nlstate+ndeath);j++){
       else                k=k+1;
         fprintf(ficlog," %.5le",matcov[i][j]);                gp[k]=pmmij[i][j];
       fprintf(ficparo," %.5le",matcov[i][j]);              }
     }            }
     fscanf(ficpar,"\n");            
     if(mle==1)            for(i=1; i<=npar; i++)
       printf("\n");              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     fprintf(ficlog,"\n");      
     fprintf(ficparo,"\n");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   }            k=0;
   for(i=1; i <=npar; i++)            for(i=1; i<=(nlstate); i++){
     for(j=i+1;j<=npar;j++)              for(j=1; j<=(nlstate+ndeath);j++){
       matcov[i][j]=matcov[j][i];                k=k+1;
                    gm[k]=pmmij[i][j];
   if(mle==1)              }
     printf("\n");            }
   fprintf(ficlog,"\n");       
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     /*-------- Rewriting paramater file ----------*/          }
      strcpy(rfileres,"r");    /* "Rparameterfile */  
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
      strcat(rfileres,".");    /* */            for(theta=1; theta <=npar; theta++)
      strcat(rfileres,optionfilext);    /* Other files have txt extension */              trgradg[j][theta]=gradg[theta][j];
     if((ficres =fopen(rfileres,"w"))==NULL) {          
       printf("Problem writing new parameter file: %s\n", fileres);goto end;          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     }          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     fprintf(ficres,"#%s\n",version);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
              free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     /*-------- data file ----------*/          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     if((fic=fopen(datafile,"r"))==NULL)    {  
       printf("Problem with datafile: %s\n", datafile);goto end;          pmij(pmmij,cov,ncovmodel,x,nlstate);
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;          
     }          k=0;
           for(i=1; i<=(nlstate); i++){
     n= lastobs;            for(j=1; j<=(nlstate+ndeath);j++){
     severity = vector(1,maxwav);              k=k+1;
     outcome=imatrix(1,maxwav+1,1,n);              mu[k][(int) age]=pmmij[i][j];
     num=ivector(1,n);            }
     moisnais=vector(1,n);          }
     annais=vector(1,n);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     moisdc=vector(1,n);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
     andc=vector(1,n);              varpij[i][j][(int)age] = doldm[i][j];
     agedc=vector(1,n);  
     cod=ivector(1,n);          /*printf("\n%d ",(int)age);
     weight=vector(1,n);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     mint=matrix(1,maxwav,1,n);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     anint=matrix(1,maxwav,1,n);            }*/
     s=imatrix(1,maxwav+1,1,n);  
     adl=imatrix(1,maxwav+1,1,n);              fprintf(ficresprob,"\n%d ",(int)age);
     tab=ivector(1,NCOVMAX);          fprintf(ficresprobcov,"\n%d ",(int)age);
     ncodemax=ivector(1,8);          fprintf(ficresprobcor,"\n%d ",(int)age);
   
     i=1;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     while (fgets(line, MAXLINE, fic) != NULL)    {            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       if ((i >= firstobs) && (i <=lastobs)) {          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                    fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
         for (j=maxwav;j>=1;j--){            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          }
           strcpy(line,stra);          i=0;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          for (k=1; k<=(nlstate);k++){
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            for (l=1; l<=(nlstate+ndeath);l++){ 
         }              i=i++;
                      fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);              for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);              }
             }
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          }/* end of loop for state */
         for (j=ncovcol;j>=1;j--){        } /* end of loop for age */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }        /* Confidence intervalle of pij  */
         num[i]=atol(stra);        /*
                  fprintf(ficgp,"\nset noparametric;unset label");
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           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;}*/          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);
         i=i+1;          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);
     /* printf("ii=%d", ij);        */
        scanf("%d",i);*/  
   imx=i-1; /* Number of individuals */        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
   /* for (i=1; i<=imx; i++){        for (k2=1; k2<=(nlstate);k2++){
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;            if(l2==k2) continue;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;            j=(k2-1)*(nlstate+ndeath)+l2;
     }*/            for (k1=1; k1<=(nlstate);k1++){
    /*  for (i=1; i<=imx; i++){              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
      if (s[4][i]==9)  s[4][i]=-1;                if(l1==k1) continue;
      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]));}*/                i=(k1-1)*(nlstate+ndeath)+l1;
                  if(i<=j) continue;
                  for (age=bage; age<=fage; age ++){ 
   /* Calculation of the number of parameter from char model*/                  if ((int)age %5==0){
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   Tprod=ivector(1,15);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   Tvaraff=ivector(1,15);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   Tvard=imatrix(1,15,1,2);                    mu1=mu[i][(int) age]/stepm*YEARM ;
   Tage=ivector(1,15);                          mu2=mu[j][(int) age]/stepm*YEARM;
                        c12=cv12/sqrt(v1*v2);
   if (strlen(model) >1){                    /* Computing eigen value of matrix of covariance */
     j=0, j1=0, k1=1, k2=1;                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     j=nbocc(model,'+');                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     j1=nbocc(model,'*');                    /* Eigen vectors */
     cptcovn=j+1;                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     cptcovprod=j1;                    /*v21=sqrt(1.-v11*v11); *//* error */
                        v21=(lc1-v1)/cv12*v11;
     strcpy(modelsav,model);                    v12=-v21;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){                    v22=v11;
       printf("Error. Non available option model=%s ",model);                    tnalp=v21/v11;
       fprintf(ficlog,"Error. Non available option model=%s ",model);                    if(first1==1){
       goto end;                      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);
                        }
     for(i=(j+1); i>=1;i--){                    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);
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */                    /*printf(fignu*/
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
       /*scanf("%d",i);*/                    if(first==1){
       if (strchr(strb,'*')) {  /* Model includes a product */                      first=0;
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/                      fprintf(ficgp,"\nset parametric;unset label");
         if (strcmp(strc,"age")==0) { /* Vn*age */                      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);
           cptcovprod--;                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           cutv(strb,stre,strd,'V');                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
           cptcovage++;  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
             Tage[cptcovage]=i;                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
             /*printf("stre=%s ", stre);*/                              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);
         else if (strcmp(strd,"age")==0) { /* or age*Vn */                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
           cptcovprod--;                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           cutv(strb,stre,strc,'V');                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
           Tvar[i]=atoi(stre);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
           cptcovage++;                      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",\
           Tage[cptcovage]=i;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
         }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
         else {  /* Age is not in the model */                    }else{
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/                      first=0;
           Tvar[i]=ncovcol+k1;                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
           Tprod[k1]=i;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
           Tvard[k1][1]=atoi(strc); /* m*/                      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",\
           Tvard[k1][2]=atoi(stre); /* n */                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
           Tvar[cptcovn+k2]=Tvard[k1][1];                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                    }/* if first */
           for (k=1; k<=lastobs;k++)                  } /* age mod 5 */
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                } /* end loop age */
           k1++;                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           k2=k2+2;                first=1;
         }              } /*l12 */
       }            } /* k12 */
       else { /* no more sum */          } /*l1 */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        }/* k1 */
        /*  scanf("%d",i);*/      } /* loop covariates */
       cutv(strd,strc,strb,'V');    }
       Tvar[i]=atoi(strc);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
       }    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
       strcpy(modelsav,stra);      free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
         scanf("%d",i);*/    free_vector(xp,1,npar);
     } /* end of loop + */    fclose(ficresprob);
   } /* end model */    fclose(ficresprobcov);
      fclose(ficresprobcor);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    fflush(ficgp);
   printf("cptcovprod=%d ", cptcovprod);    fflush(fichtmcov);
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);  }
   scanf("%d ",i);*/  
     fclose(fic);  
   /******************* Printing html file ***********/
     /*  if(mle==1){*/  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     if (weightopt != 1) { /* Maximisation without weights*/                    int lastpass, int stepm, int weightopt, char model[],\
       for(i=1;i<=n;i++) weight[i]=1.0;                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     }                    int popforecast, int estepm ,\
     /*-calculation of age at interview from date of interview and age at death -*/                    double jprev1, double mprev1,double anprev1, \
     agev=matrix(1,maxwav,1,imx);                    double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
     for (i=1; i<=imx; i++) {  
       for(m=2; (m<= maxwav); m++) {     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
          anint[m][i]=9999;  </ul>");
          s[m][i]=-1;     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 ",
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;             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"));
     for (i=1; i<=imx; i++)  {     fprintf(fichtm,"\
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
       for(m=1; (m<= maxwav); m++){             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
         if(s[m][i] >0){     fprintf(fichtm,"\
           if (s[m][i] >= nlstate+1) {   - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
             if(agedc[i]>0)     <a href=\"%s\">%s</a> <br>\n</li>",
               if(moisdc[i]!=99 && andc[i]!=9999)             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
                 agev[m][i]=agedc[i];  
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/  
            else {  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
               if (andc[i]!=9999){  
               printf("Warning negative age at death: %d line:%d\n",num[i],i);   m=cptcoveff;
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
               agev[m][i]=-1;  
               }   jj1=0;
             }   for(k1=1; k1<=m;k1++){
           }     for(i1=1; i1<=ncodemax[k1];i1++){
           else if(s[m][i] !=9){ /* Should no more exist */       jj1++;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);       if (cptcovn > 0) {
             if(mint[m][i]==99 || anint[m][i]==9999)         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
               agev[m][i]=1;         for (cpt=1; cpt<=cptcoveff;cpt++) 
             else if(agev[m][i] <agemin){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
               agemin=agev[m][i];         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/       }
             }       /* Pij */
             else if(agev[m][i] >agemax){       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
               agemax=agev[m][i];  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/       /* Quasi-incidences */
             }       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
             /*agev[m][i]=anint[m][i]-annais[i];*/   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
             /*   agev[m][i] = age[i]+2*m;*/  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
           }         /* Period (stable) prevalence in each health state */
           else { /* =9 */         for(cpt=1; cpt<nlstate;cpt++){
             agev[m][i]=1;           fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
             s[m][i]=-1;  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
           }         }
         }       for(cpt=1; cpt<=nlstate;cpt++) {
         else /*= 0 Unknown */          fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
           agev[m][i]=1;  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
       }       }
         } /* end i1 */
     }   }/* End k1 */
     for (i=1; i<=imx; i++)  {   fprintf(fichtm,"</ul>");
       for(m=1; (m<= maxwav); m++){  
         if (s[m][i] > (nlstate+ndeath)) {  
           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(fichtm,"\
           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);    \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
           goto end;   - 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,"\
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
     free_vector(severity,1,maxwav);   fprintf(fichtm,"\
     free_imatrix(outcome,1,maxwav+1,1,n);   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
     free_vector(moisnais,1,n);           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
     free_vector(annais,1,n);   fprintf(fichtm,"\
     /* free_matrix(mint,1,maxwav,1,n);   - 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): \
        free_matrix(anint,1,maxwav,1,n);*/     <a href=\"%s\">%s</a> <br>\n</li>",
     free_vector(moisdc,1,n);             estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
     free_vector(andc,1,n);   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>",
     wav=ivector(1,imx);             estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
     dh=imatrix(1,lastpass-firstpass+1,1,imx);   fprintf(fichtm,"\
     mw=imatrix(1,lastpass-firstpass+1,1,imx);   - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij 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"));
     /* Concatenates waves */   fprintf(fichtm,"\
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);   - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
       Tcode=ivector(1,100);   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
       ncodemax[1]=1;  
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  /*  if(popforecast==1) fprintf(fichtm,"\n */
        /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
    codtab=imatrix(1,100,1,10);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
    h=0;  /*      <br>",fileres,fileres,fileres,fileres); */
    m=pow(2,cptcoveff);  /*  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); */
    for(k=1;k<=cptcoveff; k++){   fflush(fichtm);
      for(i=1; i <=(m/pow(2,k));i++){   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
        for(j=1; j <= ncodemax[k]; j++){  
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){   m=cptcoveff;
            h++;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;  
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/   jj1=0;
          }   for(k1=1; k1<=m;k1++){
        }     for(i1=1; i1<=ncodemax[k1];i1++){
      }       jj1++;
    }       if (cptcovn > 0) {
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       codtab[1][2]=1;codtab[2][2]=2; */         for (cpt=1; cpt<=cptcoveff;cpt++) 
    /* for(i=1; i <=m ;i++){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
       for(k=1; k <=cptcovn; k++){         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);       }
       }       for(cpt=1; cpt<=nlstate;cpt++) {
       printf("\n");         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
       }  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
       scanf("%d",i);*/  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
           }
    /* Calculates basic frequencies. Computes observed prevalence at single age       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
        and prints on file fileres'p'. */  health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
         } /* end i1 */
       }/* End k1 */
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   fprintf(fichtm,"</ul>");
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   fflush(fichtm);
     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 */  /******************* Gnuplot file **************/
        void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
     /* 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] */    char dirfileres[132],optfileres[132];
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
     if(mle==1){  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  /*     printf("Problem with file %s",optionfilegnuplot); */
     }  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
      /*   } */
     /*--------- 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);    /*#ifdef windows */
      fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
    jk=1;    m=pow(2,cptcoveff);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    strcpy(dirfileres,optionfilefiname);
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    strcpy(optfileres,"vpl");
    for(i=1,jk=1; i <=nlstate; i++){   /* 1eme*/
      for(k=1; k <=(nlstate+ndeath); k++){    for (cpt=1; cpt<= nlstate ; cpt ++) {
        if (k != i)     for (k1=1; k1<= m ; k1 ++) {
          {       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
            printf("%d%d ",i,k);       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
            fprintf(ficlog,"%d%d ",i,k);       fprintf(ficgp,"set xlabel \"Age\" \n\
            fprintf(ficres,"%1d%1d ",i,k);  set ylabel \"Probability\" \n\
            for(j=1; j <=ncovmodel; j++){  set ter png small\n\
              printf("%f ",p[jk]);  set size 0.65,0.65\n\
              fprintf(ficlog,"%f ",p[jk]);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
              fprintf(ficres,"%f ",p[jk]);  
              jk++;       for (i=1; i<= nlstate ; i ++) {
            }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
            printf("\n");         else fprintf(ficgp," \%%*lf (\%%*lf)");
            fprintf(ficlog,"\n");       }
            fprintf(ficres,"\n");       fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 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)");
    if(mle==1){       } 
      /* Computing hessian and covariance matrix */       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
      ftolhess=ftol; /* Usually correct */       for (i=1; i<= nlstate ; i ++) {
      hesscov(matcov, p, npar, delti, ftolhess, func);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
    }         else fprintf(ficgp," \%%*lf (\%%*lf)");
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");       }  
    printf("# Scales (for hessian or gradient estimation)\n");       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");     }
    for(i=1,jk=1; i <=nlstate; i++){    }
      for(j=1; j <=nlstate+ndeath; j++){    /*2 eme*/
        if (j!=i) {    
          fprintf(ficres,"%1d%1d",i,j);    for (k1=1; k1<= m ; k1 ++) { 
          printf("%1d%1d",i,j);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
          fprintf(ficlog,"%1d%1d",i,j);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
          for(k=1; k<=ncovmodel;k++){      
            printf(" %.5e",delti[jk]);      for (i=1; i<= nlstate+1 ; i ++) {
            fprintf(ficlog," %.5e",delti[jk]);        k=2*i;
            fprintf(ficres," %.5e",delti[jk]);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
            jk++;        for (j=1; j<= nlstate+1 ; j ++) {
          }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
          printf("\n");          else fprintf(ficgp," \%%*lf (\%%*lf)");
          fprintf(ficlog,"\n");        }   
          fprintf(ficres,"\n");        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)");
    k=1;          else fprintf(ficgp," \%%*lf (\%%*lf)");
    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)        fprintf(ficgp,"\" t\"\" w l 0,");
      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(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
    fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");        for (j=1; j<= nlstate+1 ; j ++) {
    for(i=1;i<=npar;i++){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
      /*  if (k>nlstate) k=1;          else fprintf(ficgp," \%%*lf (\%%*lf)");
          i1=(i-1)/(ncovmodel*nlstate)+1;        }   
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
          printf("%s%d%d",alph[k],i1,tab[i]);*/        else fprintf(ficgp,"\" t\"\" w l 0,");
      fprintf(ficres,"%3d",i);      }
      if(mle==1)    }
        printf("%3d",i);    
      fprintf(ficlog,"%3d",i);    /*3eme*/
      for(j=1; j<=i;j++){    
        fprintf(ficres," %.5e",matcov[i][j]);    for (k1=1; k1<= m ; k1 ++) { 
        if(mle==1)      for (cpt=1; cpt<= nlstate ; cpt ++) {
          printf(" %.5e",matcov[i][j]);        /*       k=2+nlstate*(2*cpt-2); */
        fprintf(ficlog," %.5e",matcov[i][j]);        k=2+(nlstate+1)*(cpt-1);
      }        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
      fprintf(ficres,"\n");        fprintf(ficgp,"set ter png small\n\
      if(mle==1)  set size 0.65,0.65\n\
        printf("\n");  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
      fprintf(ficlog,"\n");        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
      k++;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
    }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
              fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
    while((c=getc(ficpar))=='#' && c!= EOF){          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
      ungetc(c,ficpar);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
      fgets(line, MAXLINE, ficpar);          
      puts(line);        */
      fputs(line,ficparo);        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);
    ungetc(c,ficpar);          /*      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);*/
    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;        fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
    if (fage <= 2) {      }
      bage = ageminpar;    }
      fage = agemaxpar;    
    }    /* CV preval stable (period) */
        for (k1=1; k1<= m ; k1 ++) { 
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      for (cpt=1; cpt<=nlstate ; cpt ++) {
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);        k=3;
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
            fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
    while((c=getc(ficpar))=='#' && c!= EOF){  set ter png small\nset size 0.65,0.65\n\
      ungetc(c,ficpar);  unset log y\n\
      fgets(line, MAXLINE, ficpar);  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
      puts(line);        
      fputs(line,ficparo);        for (i=1; i< nlstate ; i ++)
    }          fprintf(ficgp,"+$%d",k+i+1);
    ungetc(c,ficpar);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
          
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        l=3+(nlstate+ndeath)*cpt;
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        for (i=1; i< nlstate ; i ++) {
              l=3+(nlstate+ndeath)*cpt;
    while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficgp,"+$%d",l+i+1);
      ungetc(c,ficpar);        }
      fgets(line, MAXLINE, ficpar);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
      puts(line);      } 
      fputs(line,ficparo);    }  
    }    
    ungetc(c,ficpar);    /* proba elementaires */
      for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        if (k != i) {
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
   fscanf(ficpar,"pop_based=%d\n",&popbased);            jk++; 
   fprintf(ficparo,"pop_based=%d\n",popbased);              fprintf(ficgp,"\n");
   fprintf(ficres,"pop_based=%d\n",popbased);            }
          }
   while((c=getc(ficpar))=='#' && c!= EOF){      }
     ungetc(c,ficpar);     }
     fgets(line, MAXLINE, ficpar);  
     puts(line);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
     fputs(line,ficparo);       for(jk=1; jk <=m; jk++) {
   }         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
   ungetc(c,ficpar);         if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);         else
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);           fprintf(ficgp,"\nset title \"Probability\"\n");
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
 while((c=getc(ficpar))=='#' && c!= EOF){           k3=i;
     ungetc(c,ficpar);           for(k=1; k<=(nlstate+ndeath); k++) {
     fgets(line, MAXLINE, ficpar);             if (k != k2){
     puts(line);               if(ng==2)
     fputs(line,ficparo);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   }               else
   ungetc(c,ficpar);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);               for(j=3; j <=ncovmodel; j++) {
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                 }
                  else
 /*------------ gnuplot -------------*/                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   strcpy(optionfilegnuplot,optionfilefiname);               }
   strcat(optionfilegnuplot,".gp");               fprintf(ficgp,")/(1");
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {               
     printf("Problem with file %s",optionfilegnuplot);               for(k1=1; k1 <=nlstate; k1++){   
   }                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
   fclose(ficgp);                 ij=1;
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);                 for(j=3; j <=ncovmodel; j++){
 /*--------- index.htm --------*/                   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]]]);
   strcpy(optionfilehtm,optionfile);                     ij++;
   strcat(optionfilehtm,".htm");                   }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {                   else
     printf("Problem with %s \n",optionfilehtm), exit(0);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   }                 }
                  fprintf(ficgp,")");
   fprintf(fichtm,"<body> <font size=\"2\">%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               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
 \n               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
 Total number of observations=%d <br>\n               i=i+ncovmodel;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n             }
 <hr  size=\"2\" color=\"#EC5E5E\">           } /* end k */
  <ul><li><h4>Parameter files</h4>\n         } /* end k2 */
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n       } /* end jk */
  - Log file of the run: <a href=\"%s\">%s</a><br>\n     } /* end ng */
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);     fflush(ficgp); 
   fclose(fichtm);  }  /* end gnuplot */
   
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);  
    /*************** Moving average **************/
 /*------------ free_vector  -------------*/  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
  chdir(path);  
      int i, cpt, cptcod;
  free_ivector(wav,1,imx);    int modcovmax =1;
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    int mobilavrange, mob;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      double age;
  free_ivector(num,1,n);  
  free_vector(agedc,1,n);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
  /*free_matrix(covar,1,NCOVMAX,1,n);*/                             a covariate has 2 modalities */
  fclose(ficparo);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
  fclose(ficres);  
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
   /*--------------- Prevalence limit --------------*/      else mobilavrange=mobilav;
        for (age=bage; age<=fage; age++)
   strcpy(filerespl,"pl");        for (i=1; i<=nlstate;i++)
   strcat(filerespl,fileres);          for (cptcod=1;cptcod<=modcovmax;cptcod++)
   if((ficrespl=fopen(filerespl,"w"))==NULL) {            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;      /* We keep the original values on the extreme ages bage, fage and for 
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;         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. 
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      */ 
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);      for (mob=3;mob <=mobilavrange;mob=mob+2){
   fprintf(ficrespl,"#Prevalence limit\n");        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
   fprintf(ficrespl,"#Age ");          for (i=1; i<=nlstate;i++){
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
   fprintf(ficrespl,"\n");              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                  for (cpt=1;cpt<=(mob-1)/2;cpt++){
   prlim=matrix(1,nlstate,1,nlstate);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                }
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            }
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          }
   k=0;        }/* end age */
   agebase=ageminpar;      }/* end mob */
   agelim=agemaxpar;    }else return -1;
   ftolpl=1.e-10;    return 0;
   i1=cptcoveff;  }/* End movingaverage */
   if (cptcovn < 1){i1=1;}  
   
   for(cptcov=1;cptcov<=i1;cptcov++){  /************** Forecasting ******************/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  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){
         k=k+1;    /* proj1, year, month, day of starting projection 
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/       agemin, agemax range of age
         fprintf(ficrespl,"\n#******");       dateprev1 dateprev2 range of dates during which prevalence is computed
         printf("\n#******");       anproj2 year of en of projection (same day and month as proj1).
         fprintf(ficlog,"\n#******");    */
         for(j=1;j<=cptcoveff;j++) {    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int *popage;
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double agec; /* generic age */
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
         }    double *popeffectif,*popcount;
         fprintf(ficrespl,"******\n");    double ***p3mat;
         printf("******\n");    double ***mobaverage;
         fprintf(ficlog,"******\n");    char fileresf[FILENAMELENGTH];
          
         for (age=agebase; age<=agelim; age++){    agelim=AGESUP;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
           fprintf(ficrespl,"%.0f",age );   
           for(i=1; i<=nlstate;i++)    strcpy(fileresf,"f"); 
           fprintf(ficrespl," %.5f", prlim[i][i]);    strcat(fileresf,fileres);
           fprintf(ficrespl,"\n");    if((ficresf=fopen(fileresf,"w"))==NULL) {
         }      printf("Problem with forecast resultfile: %s\n", fileresf);
       }      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }    }
   fclose(ficrespl);    printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   /*------------- h Pij x at various ages ------------*/  
      if (cptcoveff==0) ncodemax[cptcoveff]=1;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    if (mobilav!=0) {
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   printf("Computing pij: result on file '%s' \n", filerespij);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);      }
      }
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   /*if (stepm<=24) stepsize=2;*/    stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
   agelim=AGESUP;    if(estepm < stepm){
   hstepm=stepsize*YEARM; /* Every year of age */      printf ("Problem %d lower than %d\n",estepm, stepm);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    }
     else  hstepm=estepm;   
   /* hstepm=1;   aff par mois*/  
     hstepm=hstepm/stepm; 
   k=0;    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
   for(cptcov=1;cptcov<=i1;cptcov++){                                 fractional in yp1 */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    anprojmean=yp;
       k=k+1;    yp2=modf((yp1*12),&yp);
         fprintf(ficrespij,"\n#****** ");    mprojmean=yp;
         for(j=1;j<=cptcoveff;j++)    yp1=modf((yp2*30.5),&yp);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    jprojmean=yp;
         fprintf(ficrespij,"******\n");    if(jprojmean==0) jprojmean=1;
            if(mprojmean==0) jprojmean=1;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    i1=cptcoveff;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    if (cptcovn < 1){i1=1;}
     
           /*      nhstepm=nhstepm*YEARM; aff par mois*/    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficresf,"#****** Routine prevforecast **\n");
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    /*            if (h==(int)(YEARM*yearp)){ */
           fprintf(ficrespij,"# Age");    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
           for(i=1; i<=nlstate;i++)      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
             for(j=1; j<=nlstate+ndeath;j++)        k=k+1;
               fprintf(ficrespij," %1d-%1d",i,j);        fprintf(ficresf,"\n#******");
           fprintf(ficrespij,"\n");        for(j=1;j<=cptcoveff;j++) {
            for (h=0; h<=nhstepm; h++){          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(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        }
             for(i=1; i<=nlstate;i++)        fprintf(ficresf,"******\n");
               for(j=1; j<=nlstate+ndeath;j++)        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);        for(j=1; j<=nlstate+ndeath;j++){ 
             fprintf(ficrespij,"\n");          for(i=1; i<=nlstate;i++)              
              }            fprintf(ficresf," p%d%d",i,j);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficresf," p.%d",j);
           fprintf(ficrespij,"\n");        }
         }        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
     }          fprintf(ficresf,"\n");
   }          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);          for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
   fclose(ficrespij);            nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
   /*---------- Forecasting ------------------*/            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
   if((stepm == 1) && (strcmp(model,".")==0)){          
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);            for (h=0; h<=nhstepm; h++){
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);              if (h*hstepm/YEARM*stepm ==yearp) {
   }                fprintf(ficresf,"\n");
   else{                for(j=1;j<=cptcoveff;j++) 
     erreur=108;                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
     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(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
     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);              } 
   }              for(j=1; j<=nlstate+ndeath;j++) {
                  ppij=0.;
                 for(i=1; i<=nlstate;i++) {
   /*---------- Health expectancies and variances ------------*/                  if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
   strcpy(filerest,"t");                  else {
   strcat(filerest,fileres);                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
   if((ficrest=fopen(filerest,"w"))==NULL) {                  }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                  if (h*hstepm/YEARM*stepm== yearp) {
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
   }                  }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                } /* end i */
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);                if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
   strcpy(filerese,"e");              }/* end j */
   strcat(filerese,fileres);            } /* end h */
   if((ficreseij=fopen(filerese,"w"))==NULL) {            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          } /* end agec */
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        } /* end yearp */
   }      } /* end cptcod */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    } /* end  cptcov */
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);         
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcpy(fileresv,"v");  
   strcat(fileresv,fileres);    fclose(ficresf);
   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);  /************** Forecasting *****not tested NB*************/
   }  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){
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   calagedate=-1;    int *popage;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
   k=0;    double ***p3mat,***tabpop,***tabpopprev;
   for(cptcov=1;cptcov<=i1;cptcov++){    double ***mobaverage;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    char filerespop[FILENAMELENGTH];
       k=k+1;  
       fprintf(ficrest,"\n#****** ");    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(j=1;j<=cptcoveff;j++)    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    agelim=AGESUP;
       fprintf(ficrest,"******\n");    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
       fprintf(ficreseij,"\n#****** ");    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       for(j=1;j<=cptcoveff;j++)    
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
       fprintf(ficreseij,"******\n");    strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
       fprintf(ficresvij,"\n#****** ");    if((ficrespop=fopen(filerespop,"w"))==NULL) {
       for(j=1;j<=cptcoveff;j++)      printf("Problem with forecast resultfile: %s\n", filerespop);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficresvij,"******\n");    }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
       oldm=oldms;savm=savms;  
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      if (cptcoveff==0) ncodemax[cptcoveff]=1;
    
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    if (mobilav!=0) {
       oldm=oldms;savm=savms;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
       if(popbased==1){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
        }      }
     }
    
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    stepsize=(int) (stepm+YEARM-1)/YEARM;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    if (stepm<=12) stepsize=1;
       fprintf(ficrest,"\n");    
     agelim=AGESUP;
       epj=vector(1,nlstate+1);    
       for(age=bage; age <=fage ;age++){    hstepm=1;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    hstepm=hstepm/stepm; 
         if (popbased==1) {    
           for(i=1; i<=nlstate;i++)    if (popforecast==1) {
             prlim[i][i]=probs[(int)age][i][k];      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);
         fprintf(ficrest," %4.0f",age);      } 
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      popage=ivector(0,AGESUP);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      popeffectif=vector(0,AGESUP);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];      popcount=vector(0,AGESUP);
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/      
           }      i=1;   
           epj[nlstate+1] +=epj[j];      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
         }     
       imx=i;
         for(i=1, vepp=0.;i <=nlstate;i++)      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[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(cptcov=1,k=0;cptcov<=i2;cptcov++){
         for(j=1;j <=nlstate;j++){     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));        k=k+1;
         }        fprintf(ficrespop,"\n#******");
         fprintf(ficrest,"\n");        for(j=1;j<=cptcoveff;j++) {
       }          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
     }        }
   }        fprintf(ficrespop,"******\n");
 free_matrix(mint,1,maxwav,1,n);        fprintf(ficrespop,"# Age");
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
     free_vector(weight,1,n);        if (popforecast==1)  fprintf(ficrespop," [Population]");
   fclose(ficreseij);        
   fclose(ficresvij);        for (cpt=0; cpt<=0;cpt++) { 
   fclose(ficrest);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   fclose(ficpar);          
   free_vector(epj,1,nlstate+1);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
              nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   /*------- Variance limit prevalence------*/              nhstepm = nhstepm/hstepm; 
             
   strcpy(fileresvpl,"vpl");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   strcat(fileresvpl,fileres);            oldm=oldms;savm=savms;
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);          
     exit(0);            for (h=0; h<=nhstepm; h++){
   }              if (h==(int) (calagedatem+YEARM*cpt)) {
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
   k=0;              for(j=1; j<=nlstate+ndeath;j++) {
   for(cptcov=1;cptcov<=i1;cptcov++){                kk1=0.;kk2=0;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                for(i=1; i<=nlstate;i++) {              
       k=k+1;                  if (mobilav==1) 
       fprintf(ficresvpl,"\n#****** ");                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
       for(j=1;j<=cptcoveff;j++)                  else {
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
       fprintf(ficresvpl,"******\n");                  }
                      }
       varpl=matrix(1,nlstate,(int) bage, (int) fage);                if (h==(int)(calagedatem+12*cpt)){
       oldm=oldms;savm=savms;                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                    /*fprintf(ficrespop," %.3f", kk1);
     }                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
  }                }
               }
   fclose(ficresvpl);              for(i=1; i<=nlstate;i++){
                 kk1=0.;
   /*---------- End : free ----------------*/                  for(j=1; j<=nlstate;j++){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                    }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);              }
    
                if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);            }
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);          }
          }
   free_matrix(matcov,1,npar,1,npar);   
   free_vector(delti,1,npar);    /******/
   free_matrix(agev,1,maxwav,1,imx);  
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   fprintf(fichtm,"\n</body>");          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   fclose(fichtm);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   fclose(ficgp);            nhstepm = nhstepm/hstepm; 
              
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if(erreur >0){            oldm=oldms;savm=savms;
     printf("End of Imach with error or warning %d\n",erreur);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);            for (h=0; h<=nhstepm; h++){
   }else{              if (h==(int) (calagedatem+YEARM*cpt)) {
    printf("End of Imach\n");                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
    fprintf(ficlog,"End of Imach\n");              } 
   }              for(j=1; j<=nlstate+ndeath;j++) {
   printf("See log file on %s\n",filelog);                kk1=0.;kk2=0;
   fclose(ficlog);                for(i=1; i<=nlstate;i++) {              
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                  }
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
   /*printf("Total time was %d uSec.\n", total_usecs);*/              }
   /*------ End -----------*/            }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
  end:        }
 #ifdef windows     } 
   /* chdir(pathcd);*/    }
 #endif   
  /*system("wgnuplot graph.plt");*/    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  /*system("../gp37mgw/wgnuplot graph.plt");*/  
  /*system("cd ../gp37mgw");*/    if (popforecast==1) {
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      free_ivector(popage,0,AGESUP);
  strcpy(plotcmd,GNUPLOTPROGRAM);      free_vector(popeffectif,0,AGESUP);
  strcat(plotcmd," ");      free_vector(popcount,0,AGESUP);
  strcat(plotcmd,optionfilegnuplot);    }
  system(plotcmd);    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 #ifdef windows    fclose(ficrespop);
   while (z[0] != 'q') {  } /* End of popforecast */
     /* chdir(path); */  
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");  int fileappend(FILE *fichier, char *optionfich)
     scanf("%s",z);  {
     if (z[0] == 'c') system("./imach");    if((fichier=fopen(optionfich,"a"))==NULL) {
     else if (z[0] == 'e') system(optionfilehtm);      printf("Problem with file: %s\n", optionfich);
     else if (z[0] == 'g') system(plotcmd);      fprintf(ficlog,"Problem with file: %s\n", optionfich);
     else if (z[0] == 'q') exit(0);      return (0);
   }    }
 #endif    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], cc[32];
     int i,j, k, l, 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;
   }
   
   /******************* 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 m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     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\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);
   
   } 
   
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*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, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     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 kk1, kk2;
     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];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char  *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_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.tv_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';
      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("Problem creating directory or it already exists %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);
   
     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.tv_sec-start_time.tv_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\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     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++;
       puts(line);
       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++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     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);
       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 guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         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",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);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         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);
   
       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++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       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 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     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);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     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;
       }
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         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 '%d' at line number %d %s 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);
           exit(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.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           exit(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 %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         exit(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.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         exit(1);
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       lval=strtol(strb,&endptr,10); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight.  Exiting.\n",lval, i,line,linei);
         exit(1);
       }
       weight[i]=(double)(lval); 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self).  Exiting.\n",lval,linei, i,line,j);
           exit(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 */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        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]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         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 */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*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);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     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++;
           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\n",(int)moisdc[i],(int)andc[i],num[i],i);
           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\n",(int)moisdc[i],(int)andc[i],num[i],i);
           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;
                 }
               }
           }
           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(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     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);     
           goto end;
         }
       }
     }
   
     /*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); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     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 */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],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);*/
       
     /*------------ 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");
     }
     /*  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,"<body>\n<title>IMaCh Cov %s</title>\n <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",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <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",\
             fileres,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);
       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]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       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);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       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);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
     
       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("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",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);
         puts(line);
         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);
         puts(line);
         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);
         puts(line);
         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);
         puts(line);
         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) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       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); */
         /*      } */
       }
     
   
       /*---------- 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(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);
   
       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);
   
       /* 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);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           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(ficreseij,"\n#****** ");
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][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(ficreseij,"******\n");
           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;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
           cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
           }
   
           pstamp(ficrest);
           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# 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 (popbased==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,1,15,1,2);
       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(ficreseij);
       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++){
           k=k+1;
           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 */
     free_matrix(prlim,1,nlstate,1,nlstate);
       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,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
       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);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     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(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  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>",strstart, strtend);
     fclose(fichtm);
     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");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error 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("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       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.1.52  
changed lines
  Added in v.1.121


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