Diff for /imach/src/imach.c between versions 1.50 and 1.101

version 1.50, 2002/06/26 23:25:02 version 1.101, 2004/09/15 10:38:38
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.101  2004/09/15 10:38:38  brouard
      Fix on curr_time
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.100  2004/07/12 18:29:06  brouard
   first survey ("cross") where individuals from different ages are    Add version for Mac OS X. Just define UNIX in Makefile
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.99  2004/06/05 08:57:40  brouard
   second wave of interviews ("longitudinal") which measure each change    *** empty log message ***
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.98  2004/05/16 15:05:56  brouard
   model. More health states you consider, more time is necessary to reach the    New version 0.97 . First attempt to estimate force of mortality
   Maximum Likelihood of the parameters involved in the model.  The    directly from the data i.e. without the need of knowing the health
   simplest model is the multinomial logistic model where pij is the    state at each age, but using a Gompertz model: log u =a + b*age .
   probability to be observed in state j at the second wave    This is the basic analysis of mortality and should be done before any
   conditional to be observed in state i at the first wave. Therefore    other analysis, in order to test if the mortality estimated from the
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    cross-longitudinal survey is different from the mortality estimated
   'age' is age and 'sex' is a covariate. If you want to have a more    from other sources like vital statistic data.
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    The same imach parameter file can be used but the option for mle should be -3.
   you to do it.  More covariates you add, slower the  
   convergence.    Agnès, who wrote this part of the code, tried to keep most of the
     former routines in order to include the new code within the former code.
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    The output is very simple: only an estimate of the intercept and of
   identical for each individual. Also, if a individual missed an    the slope with 95% confident intervals.
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Current limitations:
     A) Even if you enter covariates, i.e. with the
   hPijx is the probability to be observed in state i at age x+h    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   conditional to the observed state i at age x. The delay 'h' can be    B) There is no computation of Life Expectancy nor Life Table.
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    Revision 1.97  2004/02/20 13:25:42  lievre
   semester or year) is model as a multinomial logistic.  The hPx    Version 0.96d. Population forecasting command line is (temporarily)
   matrix is simply the matrix product of nh*stepm elementary matrices    suppressed.
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Revision 1.96  2003/07/15 15:38:55  brouard
     * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   Also this programme outputs the covariance matrix of the parameters but also    rewritten within the same printf. Workaround: many printfs.
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.95  2003/07/08 07:54:34  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    * imach.c (Repository):
            Institut national d'études démographiques, Paris.    (Repository): Using imachwizard code to output a more meaningful covariance
   This software have been partly granted by Euro-REVES, a concerted action    matrix (cov(a12,c31) instead of numbers.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.94  2003/06/27 13:00:02  brouard
   software can be distributed freely for non commercial use. Latest version    Just cleaning
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.93  2003/06/25 16:33:55  brouard
      (Module): On windows (cygwin) function asctime_r doesn't
 #include <math.h>    exist so I changed back to asctime which exists.
 #include <stdio.h>    (Module): Version 0.96b
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 #define MAXLINE 256    exist so I changed back to asctime which exists.
 #define GNUPLOTPROGRAM "gnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.91  2003/06/25 15:30:29  brouard
 #define FILENAMELENGTH 80    * imach.c (Repository): Duplicated warning errors corrected.
 /*#define DEBUG*/    (Repository): Elapsed time after each iteration is now output. It
 #define windows    helps to forecast when convergence will be reached. Elapsed time
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    is stamped in powell.  We created a new html file for the graphs
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    concerning matrix of covariance. It has extension -cov.htm.
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.90  2003/06/24 12:34:15  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 #define NINTERVMAX 8    of the covariance matrix to be input.
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.89  2003/06/24 12:30:52  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    (Module): Some bugs corrected for windows. Also, when
 #define MAXN 20000    mle=-1 a template is output in file "or"mypar.txt with the design
 #define YEARM 12. /* Number of months per year */    of the covariance matrix to be input.
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.88  2003/06/23 17:54:56  brouard
 #ifdef windows    * 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.
 #define DIRSEPARATOR '\\'  
 #define ODIRSEPARATOR '/'    Revision 1.87  2003/06/18 12:26:01  brouard
 #else    Version 0.96
 #define DIRSEPARATOR '/'  
 #define ODIRSEPARATOR '\\'    Revision 1.86  2003/06/17 20:04:08  brouard
 #endif    (Module): Change position of html and gnuplot routines and added
     routine fileappend.
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";  
 int erreur; /* Error number */    Revision 1.85  2003/06/17 13:12:43  brouard
 int nvar;    * imach.c (Repository): Check when date of death was earlier that
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    current date of interview. It may happen when the death was just
 int npar=NPARMAX;    prior to the death. In this case, dh was negative and likelihood
 int nlstate=2; /* Number of live states */    was wrong (infinity). We still send an "Error" but patch by
 int ndeath=1; /* Number of dead states */    assuming that the date of death was just one stepm after the
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    interview.
 int popbased=0;    (Repository): Because some people have very long ID (first column)
     we changed int to long in num[] and we added a new lvector for
 int *wav; /* Number of waves for this individuual 0 is possible */    memory allocation. But we also truncated to 8 characters (left
 int maxwav; /* Maxim number of waves */    truncation)
 int jmin, jmax; /* min, max spacing between 2 waves */    (Repository): No more line truncation errors.
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.84  2003/06/13 21:44:43  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    * imach.c (Repository): Replace "freqsummary" at a correct
 double jmean; /* Mean space between 2 waves */    place. It differs from routine "prevalence" which may be called
 double **oldm, **newm, **savm; /* Working pointers to matrices */    many times. Probs is memory consuming and must be used with
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    parcimony.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 FILE *ficlog;  
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    Revision 1.83  2003/06/10 13:39:11  lievre
 FILE *ficresprobmorprev;    *** empty log message ***
 FILE *fichtm; /* Html File */  
 FILE *ficreseij;    Revision 1.82  2003/06/05 15:57:20  brouard
 char filerese[FILENAMELENGTH];    Add log in  imach.c and  fullversion number is now printed.
 FILE  *ficresvij;  
 char fileresv[FILENAMELENGTH];  */
 FILE  *ficresvpl;  /*
 char fileresvpl[FILENAMELENGTH];     Interpolated Markov Chain
 char title[MAXLINE];  
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    Short summary of the programme:
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    
     This program computes Healthy Life Expectancies from
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 char filelog[FILENAMELENGTH]; /* Log file */    first survey ("cross") where individuals from different ages are
 char filerest[FILENAMELENGTH];    interviewed on their health status or degree of disability (in the
 char fileregp[FILENAMELENGTH];    case of a health survey which is our main interest) -2- at least a
 char popfile[FILENAMELENGTH];    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    computed from the time spent in each health state according to a
     model. More health states you consider, more time is necessary to reach the
 #define NR_END 1    Maximum Likelihood of the parameters involved in the model.  The
 #define FREE_ARG char*    simplest model is the multinomial logistic model where pij is the
 #define FTOL 1.0e-10    probability to be observed in state j at the second wave
     conditional to be observed in state i at the first wave. Therefore
 #define NRANSI    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #define ITMAX 200    'age' is age and 'sex' is a covariate. If you want to have a more
     complex model than "constant and age", you should modify the program
 #define TOL 2.0e-4    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
 #define CGOLD 0.3819660    convergence.
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    The advantage of this computer programme, compared to a simple
     multinomial logistic model, is clear when the delay between waves is not
 #define GOLD 1.618034    identical for each individual. Also, if a individual missed an
 #define GLIMIT 100.0    intermediate interview, the information is lost, but taken into
 #define TINY 1.0e-20    account using an interpolation or extrapolation.  
   
 static double maxarg1,maxarg2;    hPijx is the probability to be observed in state i at age x+h
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    conditional to the observed state i at age x. The delay 'h' can be
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    split into an exact number (nh*stepm) of unobserved intermediate
      states. This elementary transition (by month, quarter,
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    semester or year) is modelled as a multinomial logistic.  The hPx
 #define rint(a) floor(a+0.5)    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
 static double sqrarg;    hPijx.
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the stable prevalence. 
 int imx;    
 int stepm;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 /* Stepm, step in month: minimum step interpolation*/             Institut national d'études démographiques, Paris.
     This software have been partly granted by Euro-REVES, a concerted action
 int estepm;    from the European Union.
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 int m,nb;    can be accessed at http://euroreves.ined.fr/imach .
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 double **pmmij, ***probs, ***mobaverage;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 double dateintmean=0;    
     **********************************************************************/
 double *weight;  /*
 int **s; /* Status */    main
 double *agedc, **covar, idx;    read parameterfile
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    read datafile
     concatwav
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    freqsummary
 double ftolhess; /* Tolerance for computing hessian */    if (mle >= 1)
       mlikeli
 /**************** split *************************/    print results files
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    if mle==1 
 {       computes hessian
    char *s;                             /* pointer */    read end of parameter file: agemin, agemax, bage, fage, estepm
    int  l1, l2;                         /* length counters */        begin-prev-date,...
     open gnuplot file
    l1 = strlen( path );                 /* length of path */    open html file
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    stable prevalence
    s= strrchr( path, DIRSEPARATOR );            /* find last / */     for age prevalim()
    if ( s == NULL ) {                   /* no directory, so use current */    h Pij x
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)    variance of p varprob
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/    forecasting if prevfcast==1 prevforecast call prevalence()
 #if     defined(__bsd__)                /* get current working directory */    health expectancies
       extern char       *getwd( );    Variance-covariance of DFLE
     prevalence()
       if ( getwd( dirc ) == NULL ) {     movingaverage()
 #else    varevsij() 
       extern char       *getcwd( );    if popbased==1 varevsij(,popbased)
     total life expectancies
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Variance of stable prevalence
 #endif   end
          return( GLOCK_ERROR_GETCWD );  */
       }  
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */   
       l2 = strlen( s );                 /* length of filename */  #include <math.h>
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #include <stdio.h>
       strcpy( name, s );                /* save file name */  #include <stdlib.h>
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #include <unistd.h>
       dirc[l1-l2] = 0;                  /* add zero */  
    }  /* #include <sys/time.h> */
    l1 = strlen( dirc );                 /* length of directory */  #include <time.h>
 #ifdef windows  #include "timeval.h"
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else  /* #include <libintl.h> */
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  /* #define _(String) gettext (String) */
 #endif  
    s = strrchr( name, '.' );            /* find last / */  #define MAXLINE 256
    s++;  #define GNUPLOTPROGRAM "gnuplot"
    strcpy(ext,s);                       /* save extension */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
    l1= strlen( name);  #define FILENAMELENGTH 132
    l2= strlen( s)+1;  /*#define DEBUG*/
    strncpy( finame, name, l1-l2);  /*#define windows*/
    finame[l1-l2]= 0;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
    return( 0 );                         /* we're done */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 }  
   #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 /******************************************/  
   #define NINTERVMAX 8
 void replace(char *s, char*t)  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 {  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   int i;  #define NCOVMAX 8 /* Maximum number of covariates */
   int lg=20;  #define MAXN 20000
   i=0;  #define YEARM 12. /* Number of months per year */
   lg=strlen(t);  #define AGESUP 130
   for(i=0; i<= lg; i++) {  #define AGEBASE 40
     (s[i] = t[i]);  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
     if (t[i]== '\\') s[i]='/';  #ifdef UNIX
   }  #define DIRSEPARATOR '/'
 }  #define ODIRSEPARATOR '\\'
   #else
 int nbocc(char *s, char occ)  #define DIRSEPARATOR '\\'
 {  #define ODIRSEPARATOR '/'
   int i,j=0;  #endif
   int lg=20;  
   i=0;  /* $Id$ */
   lg=strlen(s);  /* $State$ */
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;  char version[]="Imach version 0.97b, May 2004, INED-EUROREVES ";
   }  char fullversion[]="$Revision$ $Date$"; 
   return j;  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 }  int nvar;
   int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 void cutv(char *u,char *v, char*t, char occ)  int npar=NPARMAX;
 {  int nlstate=2; /* Number of live states */
   /* cuts string t into u and v where u is ended by char occ excluding it  int ndeath=1; /* Number of dead states */
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
      gives u="abcedf" and v="ghi2j" */  int popbased=0;
   int i,lg,j,p=0;  
   i=0;  int *wav; /* Number of waves for this individuual 0 is possible */
   for(j=0; j<=strlen(t)-1; j++) {  int maxwav; /* Maxim number of waves */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  int jmin, jmax; /* min, max spacing between 2 waves */
   }  int gipmx, gsw; /* Global variables on the number of contributions 
                      to the likelihood and the sum of weights (done by funcone)*/
   lg=strlen(t);  int mle, weightopt;
   for(j=0; j<p; j++) {  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
     (u[j] = t[j]);  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
      u[p]='\0';             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
    for(j=0; j<= lg; j++) {  double **oldm, **newm, **savm; /* Working pointers to matrices */
     if (j>=(p+1))(v[j-p-1] = t[j]);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   }  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 }  FILE *ficlog, *ficrespow;
   int globpr; /* Global variable for printing or not */
 /********************** nrerror ********************/  double fretone; /* Only one call to likelihood */
   long ipmx; /* Number of contributions */
 void nrerror(char error_text[])  double sw; /* Sum of weights */
 {  char filerespow[FILENAMELENGTH];
   fprintf(stderr,"ERREUR ...\n");  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   fprintf(stderr,"%s\n",error_text);  FILE *ficresilk;
   exit(1);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 }  FILE *ficresprobmorprev;
 /*********************** vector *******************/  FILE *fichtm, *fichtmcov; /* Html File */
 double *vector(int nl, int nh)  FILE *ficreseij;
 {  char filerese[FILENAMELENGTH];
   double *v;  FILE  *ficresvij;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  char fileresv[FILENAMELENGTH];
   if (!v) nrerror("allocation failure in vector");  FILE  *ficresvpl;
   return v-nl+NR_END;  char fileresvpl[FILENAMELENGTH];
 }  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 /************************ free vector ******************/  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 void free_vector(double*v, int nl, int nh)  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 {  char command[FILENAMELENGTH];
   free((FREE_ARG)(v+nl-NR_END));  int  outcmd=0;
 }  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  char filelog[FILENAMELENGTH]; /* Log file */
 {  char filerest[FILENAMELENGTH];
   int *v;  char fileregp[FILENAMELENGTH];
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  char popfile[FILENAMELENGTH];
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 }  
   struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 /******************free ivector **************************/  struct timezone tzp;
 void free_ivector(int *v, long nl, long nh)  extern int gettimeofday();
 {  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   free((FREE_ARG)(v+nl-NR_END));  long time_value;
 }  extern long time();
   char strcurr[80], strfor[80];
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #define NR_END 1
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  #define FREE_ARG char*
 {  #define FTOL 1.0e-10
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;  #define NRANSI 
    #define ITMAX 200 
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #define TOL 2.0e-4 
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  #define CGOLD 0.3819660 
   m -= nrl;  #define ZEPS 1.0e-10 
    #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
    
   /* allocate rows and set pointers to them */  #define GOLD 1.618034 
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #define GLIMIT 100.0 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define TINY 1.0e-20 
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  static double maxarg1,maxarg2;
    #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
      
   /* return pointer to array of pointers to rows */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   return m;  #define rint(a) floor(a+0.5)
 }  
   static double sqrarg;
 /****************** free_imatrix *************************/  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 void free_imatrix(m,nrl,nrh,ncl,nch)  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       int **m;  int agegomp= AGEGOMP;
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */  int imx; 
 {  int stepm=1;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  /* Stepm, step in month: minimum step interpolation*/
   free((FREE_ARG) (m+nrl-NR_END));  
 }  int estepm;
   /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  int m,nb;
 {  long *num;
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   double **m;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  double *ageexmed,*agecens;
   if (!m) nrerror("allocation failure 1 in matrix()");  double dateintmean=0;
   m += NR_END;  
   m -= nrl;  double *weight;
   int **s; /* Status */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  double *agedc, **covar, idx;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   double ftolhess; /* Tolerance for computing hessian */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;  /**************** split *************************/
 }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
 /*************************free matrix ************************/    /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)       the name of the file (name), its extension only (ext) and its first part of the name (finame)
 {    */ 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    char  *ss;                            /* pointer */
   free((FREE_ARG)(m+nrl-NR_END));    int   l1, l2;                         /* length counters */
 }  
     l1 = strlen(path );                   /* length of path */
 /******************* ma3x *******************************/    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 {    if ( ss == NULL ) {                   /* no directory, so use current */
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   double ***m;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       /* get current working directory */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));      /*    extern  char* getcwd ( char *buf , int len);*/
   if (!m) nrerror("allocation failure 1 in matrix()");      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   m += NR_END;        return( GLOCK_ERROR_GETCWD );
   m -= nrl;      }
       strcpy( name, path );               /* we've got it */
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    } else {                              /* strip direcotry from path */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      ss++;                               /* after this, the filename */
   m[nrl] += NR_END;      l2 = strlen( ss );                  /* length of filename */
   m[nrl] -= ncl;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, ss );         /* save file name */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    }
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    l1 = strlen( dirc );                  /* length of directory */
   m[nrl][ncl] += NR_END;    /*#ifdef windows
   m[nrl][ncl] -= nll;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   for (j=ncl+1; j<=nch; j++)  #else
     m[nrl][j]=m[nrl][j-1]+nlay;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
    #endif
   for (i=nrl+1; i<=nrh; i++) {    */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    ss = strrchr( name, '.' );            /* find last / */
     for (j=ncl+1; j<=nch; j++)    if (ss >0){
       m[i][j]=m[i][j-1]+nlay;      ss++;
   }      strcpy(ext,ss);                     /* save extension */
   return m;      l1= strlen( name);
 }      l2= strlen(ss)+1;
       strncpy( finame, name, l1-l2);
 /*************************free ma3x ************************/      finame[l1-l2]= 0;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    }
 {    return( 0 );                          /* we're done */
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  }
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  
 }  /******************************************/
   
 /***************** f1dim *************************/  void replace_back_to_slash(char *s, char*t)
 extern int ncom;  {
 extern double *pcom,*xicom;    int i;
 extern double (*nrfunc)(double []);    int lg=0;
      i=0;
 double f1dim(double x)    lg=strlen(t);
 {    for(i=0; i<= lg; i++) {
   int j;      (s[i] = t[i]);
   double f;      if (t[i]== '\\') s[i]='/';
   double *xt;    }
    }
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  int nbocc(char *s, char occ)
   f=(*nrfunc)(xt);  {
   free_vector(xt,1,ncom);    int i,j=0;
   return f;    int lg=20;
 }    i=0;
     lg=strlen(s);
 /*****************brent *************************/    for(i=0; i<= lg; i++) {
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    if  (s[i] == occ ) j++;
 {    }
   int iter;    return j;
   double a,b,d,etemp;  }
   double fu,fv,fw,fx;  
   double ftemp;  void cutv(char *u,char *v, char*t, char occ)
   double p,q,r,tol1,tol2,u,v,w,x,xm;  {
   double e=0.0;    /* cuts string t into u and v where u is ended by char occ excluding it
         and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   a=(ax < cx ? ax : cx);       gives u="abcedf" and v="ghi2j" */
   b=(ax > cx ? ax : cx);    int i,lg,j,p=0;
   x=w=v=bx;    i=0;
   fw=fv=fx=(*f)(x);    for(j=0; j<=strlen(t)-1; j++) {
   for (iter=1;iter<=ITMAX;iter++) {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     xm=0.5*(a+b);    }
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    lg=strlen(t);
     printf(".");fflush(stdout);    for(j=0; j<p; j++) {
     fprintf(ficlog,".");fflush(ficlog);      (u[j] = t[j]);
 #ifdef DEBUG    }
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);       u[p]='\0';
     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(j=0; j<= lg; j++) {
 #endif      if (j>=(p+1))(v[j-p-1] = t[j]);
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    }
       *xmin=x;  }
       return fx;  
     }  /********************** nrerror ********************/
     ftemp=fu;  
     if (fabs(e) > tol1) {  void nrerror(char error_text[])
       r=(x-w)*(fx-fv);  {
       q=(x-v)*(fx-fw);    fprintf(stderr,"ERREUR ...\n");
       p=(x-v)*q-(x-w)*r;    fprintf(stderr,"%s\n",error_text);
       q=2.0*(q-r);    exit(EXIT_FAILURE);
       if (q > 0.0) p = -p;  }
       q=fabs(q);  /*********************** vector *******************/
       etemp=e;  double *vector(int nl, int nh)
       e=d;  {
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    double *v;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       else {    if (!v) nrerror("allocation failure in vector");
         d=p/q;    return v-nl+NR_END;
         u=x+d;  }
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  /************************ free vector ******************/
       }  void free_vector(double*v, int nl, int nh)
     } else {  {
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    free((FREE_ARG)(v+nl-NR_END));
     }  }
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);  /************************ivector *******************************/
     if (fu <= fx) {  int *ivector(long nl,long nh)
       if (u >= x) a=x; else b=x;  {
       SHFT(v,w,x,u)    int *v;
         SHFT(fv,fw,fx,fu)    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
         } else {    if (!v) nrerror("allocation failure in ivector");
           if (u < x) a=u; else b=u;    return v-nl+NR_END;
           if (fu <= fw || w == x) {  }
             v=w;  
             w=u;  /******************free ivector **************************/
             fv=fw;  void free_ivector(int *v, long nl, long nh)
             fw=fu;  {
           } else if (fu <= fv || v == x || v == w) {    free((FREE_ARG)(v+nl-NR_END));
             v=u;  }
             fv=fu;  
           }  /************************lvector *******************************/
         }  long *lvector(long nl,long nh)
   }  {
   nrerror("Too many iterations in brent");    long *v;
   *xmin=x;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   return fx;    if (!v) nrerror("allocation failure in ivector");
 }    return v-nl+NR_END;
   }
 /****************** mnbrak ***********************/  
   /******************free lvector **************************/
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  void free_lvector(long *v, long nl, long nh)
             double (*func)(double))  {
 {    free((FREE_ARG)(v+nl-NR_END));
   double ulim,u,r,q, dum;  }
   double fu;  
    /******************* imatrix *******************************/
   *fa=(*func)(*ax);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   *fb=(*func)(*bx);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   if (*fb > *fa) {  { 
     SHFT(dum,*ax,*bx,dum)    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       SHFT(dum,*fb,*fa,dum)    int **m; 
       }    
   *cx=(*bx)+GOLD*(*bx-*ax);    /* allocate pointers to rows */ 
   *fc=(*func)(*cx);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   while (*fb > *fc) {    if (!m) nrerror("allocation failure 1 in matrix()"); 
     r=(*bx-*ax)*(*fb-*fc);    m += NR_END; 
     q=(*bx-*cx)*(*fb-*fa);    m -= nrl; 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    
     ulim=(*bx)+GLIMIT*(*cx-*bx);    /* allocate rows and set pointers to them */ 
     if ((*bx-u)*(u-*cx) > 0.0) {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       fu=(*func)(u);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     } else if ((*cx-u)*(u-ulim) > 0.0) {    m[nrl] += NR_END; 
       fu=(*func)(u);    m[nrl] -= ncl; 
       if (fu < *fc) {    
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
           SHFT(*fb,*fc,fu,(*func)(u))    
           }    /* return pointer to array of pointers to rows */ 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    return m; 
       u=ulim;  } 
       fu=(*func)(u);  
     } else {  /****************** free_imatrix *************************/
       u=(*cx)+GOLD*(*cx-*bx);  void free_imatrix(m,nrl,nrh,ncl,nch)
       fu=(*func)(u);        int **m;
     }        long nch,ncl,nrh,nrl; 
     SHFT(*ax,*bx,*cx,u)       /* free an int matrix allocated by imatrix() */ 
       SHFT(*fa,*fb,*fc,fu)  { 
       }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 }    free((FREE_ARG) (m+nrl-NR_END)); 
   } 
 /*************** linmin ************************/  
   /******************* matrix *******************************/
 int ncom;  double **matrix(long nrl, long nrh, long ncl, long nch)
 double *pcom,*xicom;  {
 double (*nrfunc)(double []);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
      double **m;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double brent(double ax, double bx, double cx,    if (!m) nrerror("allocation failure 1 in matrix()");
                double (*f)(double), double tol, double *xmin);    m += NR_END;
   double f1dim(double x);    m -= nrl;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  
               double *fc, double (*func)(double));    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   int j;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double xx,xmin,bx,ax;    m[nrl] += NR_END;
   double fx,fb,fa;    m[nrl] -= ncl;
    
   ncom=n;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   pcom=vector(1,n);    return m;
   xicom=vector(1,n);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   nrfunc=func;     */
   for (j=1;j<=n;j++) {  }
     pcom[j]=p[j];  
     xicom[j]=xi[j];  /*************************free matrix ************************/
   }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   ax=0.0;  {
   xx=1.0;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    free((FREE_ARG)(m+nrl-NR_END));
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  }
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  /******************* ma3x *******************************/
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 #endif  {
   for (j=1;j<=n;j++) {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     xi[j] *= xmin;    double ***m;
     p[j] += xi[j];  
   }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   free_vector(xicom,1,n);    if (!m) nrerror("allocation failure 1 in matrix()");
   free_vector(pcom,1,n);    m += NR_END;
 }    m -= nrl;
   
 /*************** powell ************************/    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
             double (*func)(double []))    m[nrl] += NR_END;
 {    m[nrl] -= ncl;
   void linmin(double p[], double xi[], int n, double *fret,  
               double (*func)(double []));    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   double fp,fptt;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   double *xits;    m[nrl][ncl] += NR_END;
   pt=vector(1,n);    m[nrl][ncl] -= nll;
   ptt=vector(1,n);    for (j=ncl+1; j<=nch; j++) 
   xit=vector(1,n);      m[nrl][j]=m[nrl][j-1]+nlay;
   xits=vector(1,n);    
   *fret=(*func)(p);    for (i=nrl+1; i<=nrh; i++) {
   for (j=1;j<=n;j++) pt[j]=p[j];      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   for (*iter=1;;++(*iter)) {      for (j=ncl+1; j<=nch; j++) 
     fp=(*fret);        m[i][j]=m[i][j-1]+nlay;
     ibig=0;    }
     del=0.0;    return m; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     for (i=1;i<=n;i++)    */
       printf(" %d %.12f",i, p[i]);  }
     fprintf(ficlog," %d %.12f",i, p[i]);  
     printf("\n");  /*************************free ma3x ************************/
     fprintf(ficlog,"\n");  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     for (i=1;i<=n;i++) {  {
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       fptt=(*fret);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 #ifdef DEBUG    free((FREE_ARG)(m+nrl-NR_END));
       printf("fret=%lf \n",*fret);  }
       fprintf(ficlog,"fret=%lf \n",*fret);  
 #endif  /*************** function subdirf ***********/
       printf("%d",i);fflush(stdout);  char *subdirf(char fileres[])
       fprintf(ficlog,"%d",i);fflush(ficlog);  {
       linmin(p,xit,n,fret,func);    /* Caution optionfilefiname is hidden */
       if (fabs(fptt-(*fret)) > del) {    strcpy(tmpout,optionfilefiname);
         del=fabs(fptt-(*fret));    strcat(tmpout,"/"); /* Add to the right */
         ibig=i;    strcat(tmpout,fileres);
       }    return tmpout;
 #ifdef DEBUG  }
       printf("%d %.12e",i,(*fret));  
       fprintf(ficlog,"%d %.12e",i,(*fret));  /*************** function subdirf2 ***********/
       for (j=1;j<=n;j++) {  char *subdirf2(char fileres[], char *preop)
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  {
         printf(" x(%d)=%.12e",j,xit[j]);    
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);    /* Caution optionfilefiname is hidden */
       }    strcpy(tmpout,optionfilefiname);
       for(j=1;j<=n;j++) {    strcat(tmpout,"/");
         printf(" p=%.12e",p[j]);    strcat(tmpout,preop);
         fprintf(ficlog," p=%.12e",p[j]);    strcat(tmpout,fileres);
       }    return tmpout;
       printf("\n");  }
       fprintf(ficlog,"\n");  
 #endif  /*************** function subdirf3 ***********/
     }  char *subdirf3(char fileres[], char *preop, char *preop2)
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  {
 #ifdef DEBUG    
       int k[2],l;    /* Caution optionfilefiname is hidden */
       k[0]=1;    strcpy(tmpout,optionfilefiname);
       k[1]=-1;    strcat(tmpout,"/");
       printf("Max: %.12e",(*func)(p));    strcat(tmpout,preop);
       fprintf(ficlog,"Max: %.12e",(*func)(p));    strcat(tmpout,preop2);
       for (j=1;j<=n;j++) {    strcat(tmpout,fileres);
         printf(" %.12e",p[j]);    return tmpout;
         fprintf(ficlog," %.12e",p[j]);  }
       }  
       printf("\n");  /***************** f1dim *************************/
       fprintf(ficlog,"\n");  extern int ncom; 
       for(l=0;l<=1;l++) {  extern double *pcom,*xicom;
         for (j=1;j<=n;j++) {  extern double (*nrfunc)(double []); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];   
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  double f1dim(double x) 
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  { 
         }    int j; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    double f;
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    double *xt; 
       }   
 #endif    xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
       free_vector(xit,1,n);    free_vector(xt,1,ncom); 
       free_vector(xits,1,n);    return f; 
       free_vector(ptt,1,n);  } 
       free_vector(pt,1,n);  
       return;  /*****************brent *************************/
     }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  { 
     for (j=1;j<=n;j++) {    int iter; 
       ptt[j]=2.0*p[j]-pt[j];    double a,b,d,etemp;
       xit[j]=p[j]-pt[j];    double fu,fv,fw,fx;
       pt[j]=p[j];    double ftemp;
     }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     fptt=(*func)(ptt);    double e=0.0; 
     if (fptt < fp) {   
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    a=(ax < cx ? ax : cx); 
       if (t < 0.0) {    b=(ax > cx ? ax : cx); 
         linmin(p,xit,n,fret,func);    x=w=v=bx; 
         for (j=1;j<=n;j++) {    fw=fv=fx=(*f)(x); 
           xi[j][ibig]=xi[j][n];    for (iter=1;iter<=ITMAX;iter++) { 
           xi[j][n]=xit[j];      xm=0.5*(a+b); 
         }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 #ifdef DEBUG      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      printf(".");fflush(stdout);
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      fprintf(ficlog,".");fflush(ficlog);
         for(j=1;j<=n;j++){  #ifdef DEBUG
           printf(" %.12e",xit[j]);      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," %.12e",xit[j]);      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)))) { */
         printf("\n");  #endif
         fprintf(ficlog,"\n");      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 #endif        *xmin=x; 
       }        return fx; 
     }      } 
   }      ftemp=fu;
 }      if (fabs(e) > tol1) { 
         r=(x-w)*(fx-fv); 
 /**** Prevalence limit ****************/        q=(x-v)*(fx-fw); 
         p=(x-v)*q-(x-w)*r; 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        q=2.0*(q-r); 
 {        if (q > 0.0) p = -p; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        q=fabs(q); 
      matrix by transitions matrix until convergence is reached */        etemp=e; 
         e=d; 
   int i, ii,j,k;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   double min, max, maxmin, maxmax,sumnew=0.;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double **matprod2();        else { 
   double **out, cov[NCOVMAX], **pmij();          d=p/q; 
   double **newm;          u=x+d; 
   double agefin, delaymax=50 ; /* Max number of years to converge */          if (u-a < tol2 || b-u < tol2) 
             d=SIGN(tol1,xm-x); 
   for (ii=1;ii<=nlstate+ndeath;ii++)        } 
     for (j=1;j<=nlstate+ndeath;j++){      } else { 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     }      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
    cov[1]=1.;      fu=(*f)(u); 
        if (fu <= fx) { 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        if (u >= x) a=x; else b=x; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        SHFT(v,w,x,u) 
     newm=savm;          SHFT(fv,fw,fx,fu) 
     /* Covariates have to be included here again */          } else { 
      cov[2]=agefin;            if (u < x) a=u; else b=u; 
              if (fu <= fw || w == x) { 
       for (k=1; k<=cptcovn;k++) {              v=w; 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];              w=u; 
         /*      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]]);*/              fv=fw; 
       }              fw=fu; 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];            } else if (fu <= fv || v == x || v == w) { 
       for (k=1; k<=cptcovprod;k++)              v=u; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];              fv=fu; 
             } 
       /*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]);*/    nrerror("Too many iterations in brent"); 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    *xmin=x; 
     return fx; 
     savm=oldm;  } 
     oldm=newm;  
     maxmax=0.;  /****************** mnbrak ***********************/
     for(j=1;j<=nlstate;j++){  
       min=1.;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       max=0.;              double (*func)(double)) 
       for(i=1; i<=nlstate; i++) {  { 
         sumnew=0;    double ulim,u,r,q, dum;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    double fu; 
         prlim[i][j]= newm[i][j]/(1-sumnew);   
         max=FMAX(max,prlim[i][j]);    *fa=(*func)(*ax); 
         min=FMIN(min,prlim[i][j]);    *fb=(*func)(*bx); 
       }    if (*fb > *fa) { 
       maxmin=max-min;      SHFT(dum,*ax,*bx,dum) 
       maxmax=FMAX(maxmax,maxmin);        SHFT(dum,*fb,*fa,dum) 
     }        } 
     if(maxmax < ftolpl){    *cx=(*bx)+GOLD*(*bx-*ax); 
       return prlim;    *fc=(*func)(*cx); 
     }    while (*fb > *fc) { 
   }      r=(*bx-*ax)*(*fb-*fc); 
 }      q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 /*************** transition probabilities ***************/        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      if ((*bx-u)*(u-*cx) > 0.0) { 
 {        fu=(*func)(u); 
   double s1, s2;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   /*double t34;*/        fu=(*func)(u); 
   int i,j,j1, nc, ii, jj;        if (fu < *fc) { 
           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     for(i=1; i<= nlstate; i++){            SHFT(*fb,*fc,fu,(*func)(u)) 
     for(j=1; j<i;j++){            } 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         /*s2 += param[i][j][nc]*cov[nc];*/        u=ulim; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        fu=(*func)(u); 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      } else { 
       }        u=(*cx)+GOLD*(*cx-*bx); 
       ps[i][j]=s2;        fu=(*func)(u); 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      } 
     }      SHFT(*ax,*bx,*cx,u) 
     for(j=i+1; j<=nlstate+ndeath;j++){        SHFT(*fa,*fb,*fc,fu) 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        } 
         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);*/  
       }  /*************** linmin ************************/
       ps[i][j]=s2;  
     }  int ncom; 
   }  double *pcom,*xicom;
     /*ps[3][2]=1;*/  double (*nrfunc)(double []); 
    
   for(i=1; i<= nlstate; i++){  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
      s1=0;  { 
     for(j=1; j<i; j++)    double brent(double ax, double bx, double cx, 
       s1+=exp(ps[i][j]);                 double (*f)(double), double tol, double *xmin); 
     for(j=i+1; j<=nlstate+ndeath; j++)    double f1dim(double x); 
       s1+=exp(ps[i][j]);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     ps[i][i]=1./(s1+1.);                double *fc, double (*func)(double)); 
     for(j=1; j<i; j++)    int j; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    double xx,xmin,bx,ax; 
     for(j=i+1; j<=nlstate+ndeath; j++)    double fx,fb,fa;
       ps[i][j]= exp(ps[i][j])*ps[i][i];   
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    ncom=n; 
   } /* end i */    pcom=vector(1,n); 
     xicom=vector(1,n); 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    nrfunc=func; 
     for(jj=1; jj<= nlstate+ndeath; jj++){    for (j=1;j<=n;j++) { 
       ps[ii][jj]=0;      pcom[j]=p[j]; 
       ps[ii][ii]=1;      xicom[j]=xi[j]; 
     }    } 
   }    ax=0.0; 
     xx=1.0; 
     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     for(jj=1; jj<= nlstate+ndeath; jj++){  #ifdef DEBUG
      printf("%lf ",ps[ii][jj]);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
    }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     printf("\n ");  #endif
     }    for (j=1;j<=n;j++) { 
     printf("\n ");printf("%lf ",cov[2]);*/      xi[j] *= xmin; 
 /*      p[j] += xi[j]; 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    } 
   goto end;*/    free_vector(xicom,1,n); 
     return ps;    free_vector(pcom,1,n); 
 }  } 
   
 /**************** Product of 2 matrices ******************/  char *asc_diff_time(long time_sec, char ascdiff[])
   {
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    long sec_left, days, hours, minutes;
 {    days = (time_sec) / (60*60*24);
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    sec_left = (time_sec) % (60*60*24);
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    hours = (sec_left) / (60*60) ;
   /* in, b, out are matrice of pointers which should have been initialized    sec_left = (sec_left) %(60*60);
      before: only the contents of out is modified. The function returns    minutes = (sec_left) /60;
      a pointer to pointers identical to out */    sec_left = (sec_left) % (60);
   long i, j, k;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   for(i=nrl; i<= nrh; i++)    return ascdiff;
     for(k=ncolol; k<=ncoloh; k++)  }
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];  /*************** powell ************************/
   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   return out;              double (*func)(double [])) 
 }  { 
     void linmin(double p[], double xi[], int n, double *fret, 
                 double (*func)(double [])); 
 /************* Higher Matrix Product ***************/    int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    double fp,fptt;
 {    double *xits;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    int niterf, itmp;
      duration (i.e. until  
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    pt=vector(1,n); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    ptt=vector(1,n); 
      (typically every 2 years instead of every month which is too big).    xit=vector(1,n); 
      Model is determined by parameters x and covariates have to be    xits=vector(1,n); 
      included manually here.    *fret=(*func)(p); 
     for (j=1;j<=n;j++) pt[j]=p[j]; 
      */    for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
   int i, j, d, h, k;      ibig=0; 
   double **out, cov[NCOVMAX];      del=0.0; 
   double **newm;      last_time=curr_time;
       (void) gettimeofday(&curr_time,&tzp);
   /* Hstepm could be zero and should return the unit matrix */      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);
   for (i=1;i<=nlstate+ndeath;i++)      /*    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);
     for (j=1;j<=nlstate+ndeath;j++){      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       oldm[i][j]=(i==j ? 1.0 : 0.0);      */
       po[i][j][0]=(i==j ? 1.0 : 0.0);     for (i=1;i<=n;i++) {
     }        printf(" %d %.12f",i, p[i]);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        fprintf(ficlog," %d %.12lf",i, p[i]);
   for(h=1; h <=nhstepm; h++){        fprintf(ficrespow," %.12lf", p[i]);
     for(d=1; d <=hstepm; d++){      }
       newm=savm;      printf("\n");
       /* Covariates have to be included here again */      fprintf(ficlog,"\n");
       cov[1]=1.;      fprintf(ficrespow,"\n");fflush(ficrespow);
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      if(*iter <=3){
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        tm = *localtime(&curr_time.tv_sec);
       for (k=1; k<=cptcovage;k++)        strcpy(strcurr,asctime(&tm));
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /*       asctime_r(&tm,strcurr); */
       for (k=1; k<=cptcovprod;k++)        forecast_time=curr_time; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        itmp = strlen(strcurr);
         if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           strcurr[itmp-1]='\0';
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        for(niterf=10;niterf<=30;niterf+=10){
                    pmij(pmmij,cov,ncovmodel,x,nlstate));          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
       savm=oldm;          tmf = *localtime(&forecast_time.tv_sec);
       oldm=newm;  /*      asctime_r(&tmf,strfor); */
     }          strcpy(strfor,asctime(&tmf));
     for(i=1; i<=nlstate+ndeath; i++)          itmp = strlen(strfor);
       for(j=1;j<=nlstate+ndeath;j++) {          if(strfor[itmp-1]=='\n')
         po[i][j][h]=newm[i][j];          strfor[itmp-1]='\0';
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);          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);
          */          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);
       }        }
   } /* end h */      }
   return po;      for (i=1;i<=n;i++) { 
 }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         fptt=(*fret); 
   #ifdef DEBUG
 /*************** log-likelihood *************/        printf("fret=%lf \n",*fret);
 double func( double *x)        fprintf(ficlog,"fret=%lf \n",*fret);
 {  #endif
   int i, ii, j, k, mi, d, kk;        printf("%d",i);fflush(stdout);
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        fprintf(ficlog,"%d",i);fflush(ficlog);
   double **out;        linmin(p,xit,n,fret,func); 
   double sw; /* Sum of weights */        if (fabs(fptt-(*fret)) > del) { 
   double lli; /* Individual log likelihood */          del=fabs(fptt-(*fret)); 
   long ipmx;          ibig=i; 
   /*extern weight */        } 
   /* We are differentiating ll according to initial status */  #ifdef DEBUG
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        printf("%d %.12e",i,(*fret));
   /*for(i=1;i<imx;i++)        fprintf(ficlog,"%d %.12e",i,(*fret));
     printf(" %d\n",s[4][i]);        for (j=1;j<=n;j++) {
   */          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   cov[1]=1.;          printf(" x(%d)=%.12e",j,xit[j]);
           fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   for(k=1; k<=nlstate; k++) ll[k]=0.;        }
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        for(j=1;j<=n;j++) {
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];          printf(" p=%.12e",p[j]);
     for(mi=1; mi<= wav[i]-1; mi++){          fprintf(ficlog," p=%.12e",p[j]);
       for (ii=1;ii<=nlstate+ndeath;ii++)        }
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        printf("\n");
       for(d=0; d<dh[mi][i]; d++){        fprintf(ficlog,"\n");
         newm=savm;  #endif
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      } 
         for (kk=1; kk<=cptcovage;kk++) {      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  #ifdef DEBUG
         }        int k[2],l;
                k[0]=1;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        k[1]=-1;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        printf("Max: %.12e",(*func)(p));
         savm=oldm;        fprintf(ficlog,"Max: %.12e",(*func)(p));
         oldm=newm;        for (j=1;j<=n;j++) {
                  printf(" %.12e",p[j]);
                  fprintf(ficlog," %.12e",p[j]);
       } /* end mult */        }
              printf("\n");
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        fprintf(ficlog,"\n");
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        for(l=0;l<=1;l++) {
       ipmx +=1;          for (j=1;j<=n;j++) {
       sw += weight[i];            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     } /* end of wave */            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   } /* end of individual */          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        }
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  #endif
   return -l;  
 }  
         free_vector(xit,1,n); 
         free_vector(xits,1,n); 
 /*********** Maximum Likelihood Estimation ***************/        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        return; 
 {      } 
   int i,j, iter;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   double **xi,*delti;      for (j=1;j<=n;j++) { 
   double fret;        ptt[j]=2.0*p[j]-pt[j]; 
   xi=matrix(1,npar,1,npar);        xit[j]=p[j]-pt[j]; 
   for (i=1;i<=npar;i++)        pt[j]=p[j]; 
     for (j=1;j<=npar;j++)      } 
       xi[i][j]=(i==j ? 1.0 : 0.0);      fptt=(*func)(ptt); 
   printf("Powell\n");  fprintf(ficlog,"Powell\n");      if (fptt < fp) { 
   powell(p,xi,npar,ftol,&iter,&fret,func);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         if (t < 0.0) { 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          linmin(p,xit,n,fret,func); 
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));          for (j=1;j<=n;j++) { 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));            xi[j][ibig]=xi[j][n]; 
             xi[j][n]=xit[j]; 
 }          }
   #ifdef DEBUG
 /**** Computes Hessian and covariance matrix ***/          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 {          for(j=1;j<=n;j++){
   double  **a,**y,*x,pd;            printf(" %.12e",xit[j]);
   double **hess;            fprintf(ficlog," %.12e",xit[j]);
   int i, j,jk;          }
   int *indx;          printf("\n");
           fprintf(ficlog,"\n");
   double hessii(double p[], double delta, int theta, double delti[]);  #endif
   double hessij(double p[], double delti[], int i, int j);        }
   void lubksb(double **a, int npar, int *indx, double b[]) ;      } 
   void ludcmp(double **a, int npar, int *indx, double *d) ;    } 
   } 
   hess=matrix(1,npar,1,npar);  
   /**** Prevalence limit (stable prevalence)  ****************/
   printf("\nCalculation of the hessian matrix. Wait...\n");  
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   for (i=1;i<=npar;i++){  {
     printf("%d",i);fflush(stdout);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     fprintf(ficlog,"%d",i);fflush(ficlog);       matrix by transitions matrix until convergence is reached */
     hess[i][i]=hessii(p,ftolhess,i,delti);  
     /*printf(" %f ",p[i]);*/    int i, ii,j,k;
     /*printf(" %lf ",hess[i][i]);*/    double min, max, maxmin, maxmax,sumnew=0.;
   }    double **matprod2();
      double **out, cov[NCOVMAX], **pmij();
   for (i=1;i<=npar;i++) {    double **newm;
     for (j=1;j<=npar;j++)  {    double agefin, delaymax=50 ; /* Max number of years to converge */
       if (j>i) {  
         printf(".%d%d",i,j);fflush(stdout);    for (ii=1;ii<=nlstate+ndeath;ii++)
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);      for (j=1;j<=nlstate+ndeath;j++){
         hess[i][j]=hessij(p,delti,i,j);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         hess[j][i]=hess[i][j];          }
         /*printf(" %lf ",hess[i][j]);*/  
       }     cov[1]=1.;
     }   
   }   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   printf("\n");    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   fprintf(ficlog,"\n");      newm=savm;
       /* Covariates have to be included here again */
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");       cov[2]=agefin;
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");    
          for (k=1; k<=cptcovn;k++) {
   a=matrix(1,npar,1,npar);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   y=matrix(1,npar,1,npar);          /*      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]]);*/
   x=vector(1,npar);        }
   indx=ivector(1,npar);        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   for (i=1;i<=npar;i++)        for (k=1; k<=cptcovprod;k++)
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   ludcmp(a,npar,indx,&pd);  
         /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   for (j=1;j<=npar;j++) {        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     for (i=1;i<=npar;i++) x[i]=0;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     x[j]=1;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){      savm=oldm;
       matcov[i][j]=x[i];      oldm=newm;
     }      maxmax=0.;
   }      for(j=1;j<=nlstate;j++){
         min=1.;
   printf("\n#Hessian matrix#\n");        max=0.;
   fprintf(ficlog,"\n#Hessian matrix#\n");        for(i=1; i<=nlstate; i++) {
   for (i=1;i<=npar;i++) {          sumnew=0;
     for (j=1;j<=npar;j++) {          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       printf("%.3e ",hess[i][j]);          prlim[i][j]= newm[i][j]/(1-sumnew);
       fprintf(ficlog,"%.3e ",hess[i][j]);          max=FMAX(max,prlim[i][j]);
     }          min=FMIN(min,prlim[i][j]);
     printf("\n");        }
     fprintf(ficlog,"\n");        maxmin=max-min;
   }        maxmax=FMAX(maxmax,maxmin);
       }
   /* Recompute Inverse */      if(maxmax < ftolpl){
   for (i=1;i<=npar;i++)        return prlim;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      }
   ludcmp(a,npar,indx,&pd);    }
   }
   /*  printf("\n#Hessian matrix recomputed#\n");  
   /*************** transition probabilities ***************/ 
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     x[j]=1;  {
     lubksb(a,npar,indx,x);    double s1, s2;
     for (i=1;i<=npar;i++){    /*double t34;*/
       y[i][j]=x[i];    int i,j,j1, nc, ii, jj;
       printf("%.3e ",y[i][j]);  
       fprintf(ficlog,"%.3e ",y[i][j]);      for(i=1; i<= nlstate; i++){
     }        for(j=1; j<i;j++){
     printf("\n");          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     fprintf(ficlog,"\n");            /*s2 += param[i][j][nc]*cov[nc];*/
   }            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   */  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
           }
   free_matrix(a,1,npar,1,npar);          ps[i][j]=s2;
   free_matrix(y,1,npar,1,npar);  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
   free_vector(x,1,npar);        }
   free_ivector(indx,1,npar);        for(j=i+1; j<=nlstate+ndeath;j++){
   free_matrix(hess,1,npar,1,npar);          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
             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); */
 }          }
           ps[i][j]=s2;
 /*************** hessian matrix ****************/        }
 double hessii( double x[], double delta, int theta, double delti[])      }
 {      /*ps[3][2]=1;*/
   int i;      
   int l=1, lmax=20;      for(i=1; i<= nlstate; i++){
   double k1,k2;        s1=0;
   double p2[NPARMAX+1];        for(j=1; j<i; j++)
   double res;          s1+=exp(ps[i][j]);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        for(j=i+1; j<=nlstate+ndeath; j++)
   double fx;          s1+=exp(ps[i][j]);
   int k=0,kmax=10;        ps[i][i]=1./(s1+1.);
   double l1;        for(j=1; j<i; j++)
           ps[i][j]= exp(ps[i][j])*ps[i][i];
   fx=func(x);        for(j=i+1; j<=nlstate+ndeath; j++)
   for (i=1;i<=npar;i++) p2[i]=x[i];          ps[i][j]= exp(ps[i][j])*ps[i][i];
   for(l=0 ; l <=lmax; l++){        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     l1=pow(10,l);      } /* end i */
     delts=delt;      
     for(k=1 ; k <kmax; k=k+1){      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       delt = delta*(l1*k);        for(jj=1; jj<= nlstate+ndeath; jj++){
       p2[theta]=x[theta] +delt;          ps[ii][jj]=0;
       k1=func(p2)-fx;          ps[ii][ii]=1;
       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 */  
        /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
 #ifdef DEBUG  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
       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);  /*         printf("ddd %lf ",ps[ii][jj]); */
       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  /*       printf("\n "); */
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  /*        } */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  /*        printf("\n ");printf("%lf ",cov[2]); */
         k=kmax;         /*
       }        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        goto end;*/
         k=kmax; l=lmax*10.;      return ps;
       }  }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  
         delts=delt;  /**************** Product of 2 matrices ******************/
       }  
     }  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   }  {
   delti[theta]=delts;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   return res;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
      /* in, b, out are matrice of pointers which should have been initialized 
 }       before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
 double hessij( double x[], double delti[], int thetai,int thetaj)    long i, j, k;
 {    for(i=nrl; i<= nrh; i++)
   int i;      for(k=ncolol; k<=ncoloh; k++)
   int l=1, l1, lmax=20;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   double k1,k2,k3,k4,res,fx;          out[i][k] +=in[i][j]*b[j][k];
   double p2[NPARMAX+1];  
   int k;    return out;
   }
   fx=func(x);  
   for (k=1; k<=2; k++) {  
     for (i=1;i<=npar;i++) p2[i]=x[i];  /************* Higher Matrix Product ***************/
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     k1=func(p2)-fx;  {
      /* Computes the transition matrix starting at age 'age' over 
     p2[thetai]=x[thetai]+delti[thetai]/k;       'nhstepm*hstepm*stepm' months (i.e. until
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     k2=func(p2)-fx;       nhstepm*hstepm matrices. 
         Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     p2[thetai]=x[thetai]-delti[thetai]/k;       (typically every 2 years instead of every month which is too big 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;       for the memory).
     k3=func(p2)-fx;       Model is determined by parameters x and covariates have to be 
         included manually here. 
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;       */
     k4=func(p2)-fx;  
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    int i, j, d, h, k;
 #ifdef DEBUG    double **out, cov[NCOVMAX];
     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);    double **newm;
     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  
 #endif    /* Hstepm could be zero and should return the unit matrix */
   }    for (i=1;i<=nlstate+ndeath;i++)
   return res;      for (j=1;j<=nlstate+ndeath;j++){
 }        oldm[i][j]=(i==j ? 1.0 : 0.0);
         po[i][j][0]=(i==j ? 1.0 : 0.0);
 /************** Inverse of matrix **************/      }
 void ludcmp(double **a, int n, int *indx, double *d)    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 {    for(h=1; h <=nhstepm; h++){
   int i,imax,j,k;      for(d=1; d <=hstepm; d++){
   double big,dum,sum,temp;        newm=savm;
   double *vv;        /* Covariates have to be included here again */
          cov[1]=1.;
   vv=vector(1,n);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   *d=1.0;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   for (i=1;i<=n;i++) {        for (k=1; k<=cptcovage;k++)
     big=0.0;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for (j=1;j<=n;j++)        for (k=1; k<=cptcovprod;k++)
       if ((temp=fabs(a[i][j])) > big) big=temp;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  
     vv[i]=1.0/big;  
   }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   for (j=1;j<=n;j++) {        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     for (i=1;i<j;i++) {        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       sum=a[i][j];                     pmij(pmmij,cov,ncovmodel,x,nlstate));
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        savm=oldm;
       a[i][j]=sum;        oldm=newm;
     }      }
     big=0.0;      for(i=1; i<=nlstate+ndeath; i++)
     for (i=j;i<=n;i++) {        for(j=1;j<=nlstate+ndeath;j++) {
       sum=a[i][j];          po[i][j][h]=newm[i][j];
       for (k=1;k<j;k++)          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
         sum -= a[i][k]*a[k][j];           */
       a[i][j]=sum;        }
       if ( (dum=vv[i]*fabs(sum)) >= big) {    } /* end h */
         big=dum;    return po;
         imax=i;  }
       }  
     }  
     if (j != imax) {  /*************** log-likelihood *************/
       for (k=1;k<=n;k++) {  double func( double *x)
         dum=a[imax][k];  {
         a[imax][k]=a[j][k];    int i, ii, j, k, mi, d, kk;
         a[j][k]=dum;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       }    double **out;
       *d = -(*d);    double sw; /* Sum of weights */
       vv[imax]=vv[j];    double lli; /* Individual log likelihood */
     }    int s1, s2;
     indx[j]=imax;    double bbh, survp;
     if (a[j][j] == 0.0) a[j][j]=TINY;    long ipmx;
     if (j != n) {    /*extern weight */
       dum=1.0/(a[j][j]);    /* We are differentiating ll according to initial status */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     }    /*for(i=1;i<imx;i++) 
   }      printf(" %d\n",s[4][i]);
   free_vector(vv,1,n);  /* Doesn't work */    */
 ;    cov[1]=1.;
 }  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
 void lubksb(double **a, int n, int *indx, double b[])  
 {    if(mle==1){
   int i,ii=0,ip,j;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double sum;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
   for (i=1;i<=n;i++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
     ip=indx[i];            for (j=1;j<=nlstate+ndeath;j++){
     sum=b[ip];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     b[ip]=b[i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (ii)            }
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          for(d=0; d<dh[mi][i]; d++){
     else if (sum) ii=i;            newm=savm;
     b[i]=sum;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   }            for (kk=1; kk<=cptcovage;kk++) {
   for (i=n;i>=1;i--) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     sum=b[i];            }
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     b[i]=sum/a[i][i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
 }            oldm=newm;
           } /* end mult */
 /************ Frequencies ********************/        
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 {  /* Some frequencies */          /* But now since version 0.9 we anticipate for bias at large stepm.
             * If stepm is larger than one month (smallest stepm) and if the exact delay 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   int first;           * the nearest (and in case of equal distance, to the lowest) interval but now
   double ***freq; /* Frequencies */           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   double *pp;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   double pos, k2, dateintsum=0,k2cpt=0;           * probability in order to take into account the bias as a fraction of the way
   FILE *ficresp;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   char fileresp[FILENAMELENGTH];           * -stepm/2 to stepm/2 .
             * For stepm=1 the results are the same as for previous versions of Imach.
   pp=vector(1,nlstate);           * For stepm > 1 the results are less biased than in previous versions. 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);           */
   strcpy(fileresp,"p");          s1=s[mw[mi][i]][i];
   strcat(fileresp,fileres);          s2=s[mw[mi+1][i]][i];
   if((ficresp=fopen(fileresp,"w"))==NULL) {          bbh=(double)bh[mi][i]/(double)stepm; 
     printf("Problem with prevalence resultfile: %s\n", fileresp);          /* bias bh is positive if real duration
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);           * is higher than the multiple of stepm and negative otherwise.
     exit(0);           */
   }          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          if( s2 > nlstate){ 
   j1=0;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
                 to the likelihood is the probability to die between last step unit time and current 
   j=cptcoveff;               step unit time, which is also equal to probability to die before dh 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}               minus probability to die before dh-stepm . 
                In version up to 0.92 likelihood was computed
   first=1;          as if date of death was unknown. Death was treated as any other
           health state: the date of the interview describes the actual state
   for(k1=1; k1<=j;k1++){          and not the date of a change in health state. The former idea was
     for(i1=1; i1<=ncodemax[k1];i1++){          to consider that at each interview the state was recorded
       j1++;          (healthy, disable or death) and IMaCh was corrected; but when we
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          introduced the exact date of death then we should have modified
         scanf("%d", i);*/          the contribution of an exact death to the likelihood. This new
       for (i=-1; i<=nlstate+ndeath; i++)            contribution is smaller and very dependent of the step unit
         for (jk=-1; jk<=nlstate+ndeath; jk++)            stepm. It is no more the probability to die between last interview
           for(m=agemin; m <= agemax+3; m++)          and month of death but the probability to survive from last
             freq[i][jk][m]=0;          interview up to one month before death multiplied by the
                probability to die within a month. Thanks to Chris
       dateintsum=0;          Jackson for correcting this bug.  Former versions increased
       k2cpt=0;          mortality artificially. The bad side is that we add another loop
       for (i=1; i<=imx; i++) {          which slows down the processing. The difference can be up to 10%
         bool=1;          lower mortality.
         if  (cptcovn>0) {            */
           for (z1=1; z1<=cptcoveff; z1++)            lli=log(out[s1][s2] - savm[s1][s2]);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          }else{
               bool=0;            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 */
         if (bool==1) {          } 
           for(m=firstpass; m<=lastpass; m++){          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
             k2=anint[m][i]+(mint[m][i]/12.);          /*if(lli ==000.0)*/
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          /*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); */
               if(agev[m][i]==0) agev[m][i]=agemax+1;          ipmx +=1;
               if(agev[m][i]==1) agev[m][i]=agemax+2;          sw += weight[i];
               if (m<lastpass) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        } /* end of wave */
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      } /* end of individual */
               }    }  else if(mle==2){
                    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                 dateintsum=dateintsum+k2;        for(mi=1; mi<= wav[i]-1; mi++){
                 k2cpt++;          for (ii=1;ii<=nlstate+ndeath;ii++)
               }            for (j=1;j<=nlstate+ndeath;j++){
             }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            }
       }          for(d=0; d<=dh[mi][i]; d++){
                    newm=savm;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
       if  (cptcovn>0) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         fprintf(ficresp, "\n#********** Variable ");            }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         fprintf(ficresp, "**********\n#");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
       for(i=1; i<=nlstate;i++)            oldm=newm;
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          } /* end mult */
       fprintf(ficresp, "\n");        
                s1=s[mw[mi][i]][i];
       for(i=(int)agemin; i <= (int)agemax+3; i++){          s2=s[mw[mi+1][i]][i];
         if(i==(int)agemax+3){          bbh=(double)bh[mi][i]/(double)stepm; 
           fprintf(ficlog,"Total");          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         }else{          ipmx +=1;
           if(first==1){          sw += weight[i];
             first=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             printf("See log file for details...\n");        } /* end of wave */
           }      } /* end of individual */
           fprintf(ficlog,"Age %d", i);    }  else if(mle==3){  /* exponential inter-extrapolation */
         }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for(jk=1; jk <=nlstate ; jk++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        for(mi=1; mi<= wav[i]-1; mi++){
             pp[jk] += freq[jk][m][i];          for (ii=1;ii<=nlstate+ndeath;ii++)
         }            for (j=1;j<=nlstate+ndeath;j++){
         for(jk=1; jk <=nlstate ; jk++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(m=-1, pos=0; m <=0 ; m++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             pos += freq[jk][m][i];            }
           if(pp[jk]>=1.e-10){          for(d=0; d<dh[mi][i]; d++){
             if(first==1){            newm=savm;
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             }            for (kk=1; kk<=cptcovage;kk++) {
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           }else{            }
             if(first==1)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            savm=oldm;
           }            oldm=newm;
         }          } /* end mult */
         
         for(jk=1; jk <=nlstate ; jk++){          s1=s[mw[mi][i]][i];
           for(m=0, 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]>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;
         for(jk=1,pos=0; jk <=nlstate ; jk++)          sw += weight[i];
           pos += pp[jk];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for(jk=1; jk <=nlstate ; jk++){        } /* end of wave */
           if(pos>=1.e-5){      } /* end of individual */
             if(first==1)    }else if (mle==4){  /* ml=4 no inter-extrapolation */
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           }else{        for(mi=1; mi<= wav[i]-1; mi++){
             if(first==1)          for (ii=1;ii<=nlstate+ndeath;ii++)
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            for (j=1;j<=nlstate+ndeath;j++){
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           }              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++){
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            newm=savm;
               probs[i][jk][j1]= pp[jk]/pos;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
               /*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 (kk=1; kk<=cptcovage;kk++) {
             }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             else            }
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          
           }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                    savm=oldm;
         for(jk=-1; jk <=nlstate+ndeath; jk++)            oldm=newm;
           for(m=-1; m <=nlstate+ndeath; m++)          } /* end mult */
             if(freq[jk][m][i] !=0 ) {        
             if(first==1)          s1=s[mw[mi][i]][i];
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          s2=s[mw[mi+1][i]][i];
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);          if( s2 > nlstate){ 
             }            lli=log(out[s1][s2] - savm[s1][s2]);
         if(i <= (int) agemax)          }else{
           fprintf(ficresp,"\n");            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         if(first==1)          }
           printf("Others in log...\n");          ipmx +=1;
         fprintf(ficlog,"\n");          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   }        } /* end of wave */
   dateintmean=dateintsum/k2cpt;      } /* end of individual */
      }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   fclose(ficresp);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   free_vector(pp,1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
   /* End of Freq */            for (j=1;j<=nlstate+ndeath;j++){
 }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
 /************ Prevalence ********************/            }
 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(d=0; d<dh[mi][i]; d++){
 {  /* Some frequencies */            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;            for (kk=1; kk<=cptcovage;kk++) {
   double ***freq; /* Frequencies */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double *pp;            }
   double pos, k2;          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   pp=vector(1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            savm=oldm;
              oldm=newm;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          } /* end mult */
   j1=0;        
            s1=s[mw[mi][i]][i];
   j=cptcoveff;          s2=s[mw[mi+1][i]][i];
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
            ipmx +=1;
   for(k1=1; k1<=j;k1++){          sw += weight[i];
     for(i1=1; i1<=ncodemax[k1];i1++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       j1++;          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
              } /* end of wave */
       for (i=-1; i<=nlstate+ndeath; i++)        } /* end of individual */
         for (jk=-1; jk<=nlstate+ndeath; jk++)      } /* End of if */
           for(m=agemin; m <= agemax+3; m++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
             freq[i][jk][m]=0;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
          l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       for (i=1; i<=imx; i++) {    return -l;
         bool=1;  }
         if  (cptcovn>0) {  
           for (z1=1; z1<=cptcoveff; z1++)  /*************** log-likelihood *************/
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  double funcone( double *x)
               bool=0;  {
         }    /* Same as likeli but slower because of a lot of printf and if */
         if (bool==1) {    int i, ii, j, k, mi, d, kk;
           for(m=firstpass; m<=lastpass; m++){    double l, ll[NLSTATEMAX], cov[NCOVMAX];
             k2=anint[m][i]+(mint[m][i]/12.);    double **out;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    double lli; /* Individual log likelihood */
               if(agev[m][i]==0) agev[m][i]=agemax+1;    double llt;
               if(agev[m][i]==1) agev[m][i]=agemax+2;    int s1, s2;
               if (m<lastpass) {    double bbh, survp;
                 if (calagedate>0)    /*extern weight */
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    /* We are differentiating ll according to initial status */
                 else    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    /*for(i=1;i<imx;i++) 
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];      printf(" %d\n",s[4][i]);
               }    */
             }    cov[1]=1.;
           }  
         }    for(k=1; k<=nlstate; k++) ll[k]=0.;
       }  
       for(i=(int)agemin; i <= (int)agemax+3; i++){    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for(jk=1; jk <=nlstate ; jk++){      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      for(mi=1; mi<= wav[i]-1; mi++){
             pp[jk] += freq[jk][m][i];        for (ii=1;ii<=nlstate+ndeath;ii++)
         }          for (j=1;j<=nlstate+ndeath;j++){
         for(jk=1; jk <=nlstate ; jk++){            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(m=-1, pos=0; m <=0 ; m++)            savm[ii][j]=(ii==j ? 1.0 : 0.0);
             pos += freq[jk][m][i];          }
         }        for(d=0; d<dh[mi][i]; d++){
                  newm=savm;
         for(jk=1; jk <=nlstate ; jk++){          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          for (kk=1; kk<=cptcovage;kk++) {
             pp[jk] += freq[jk][m][i];            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }          }
                  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                  savm=oldm;
         for(jk=1; jk <=nlstate ; jk++){              oldm=newm;
           if( i <= (int) agemax){        } /* end mult */
             if(pos>=1.e-5){        
               probs[i][jk][j1]= pp[jk]/pos;        s1=s[mw[mi][i]][i];
             }        s2=s[mw[mi+1][i]][i];
           }        bbh=(double)bh[mi][i]/(double)stepm; 
         }/* end jk */        /* bias is positive if real duration
       }/* end i */         * is higher than the multiple of stepm and negative otherwise.
     } /* end i1 */         */
   } /* end k1 */        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
          } else if (mle==1){
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   free_vector(pp,1,nlstate);        } else if(mle==2){
            lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
 }  /* End of Freq */        } else if(mle==3){  /* exponential inter-extrapolation */
           lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
 /************* Waves Concatenation ***************/        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           lli=log(out[s1][s2]); /* Original formula */
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
 {          lli=log(out[s1][s2]); /* Original formula */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        } /* End of if */
      Death is a valid wave (if date is known).        ipmx +=1;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        sw += weight[i];
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      and mw[mi+1][i]. dh depends on stepm.  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
      */        if(globpr){
           fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
   int i, mi, m;   %10.6f %10.6f %10.6f ", \
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
      double sum=0., jmean=0.;*/                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   int first;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   int j, k=0,jk, ju, jl;            llt +=ll[k]*gipmx/gsw;
   double sum=0.;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   first=0;          }
   jmin=1e+5;          fprintf(ficresilk," %10.6f\n", -llt);
   jmax=-1;        }
   jmean=0.;      } /* end of wave */
   for(i=1; i<=imx; i++){    } /* end of individual */
     mi=0;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     m=firstpass;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     while(s[m][i] <= nlstate){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       if(s[m][i]>=1)    if(globpr==0){ /* First time we count the contributions and weights */
         mw[++mi][i]=m;      gipmx=ipmx;
       if(m >=lastpass)      gsw=sw;
         break;    }
       else    return -l;
         m++;  }
     }/* end while */  
     if (s[m][i] > nlstate){  
       mi++;     /* Death is another wave */  /*************** function likelione ***********/
       /* if(mi==0)  never been interviewed correctly before death */  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
          /* Only death is a correct wave */  {
       mw[mi][i]=m;    /* This routine should help understanding what is done with 
     }       the selection of individuals/waves and
        to check the exact contribution to the likelihood.
     wav[i]=mi;       Plotting could be done.
     if(mi==0){     */
       if(first==0){    int k;
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);  
         first=1;    if(*globpri !=0){ /* Just counts and sums, no printings */
       }      strcpy(fileresilk,"ilk"); 
       if(first==1){      strcat(fileresilk,fileres);
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       }        printf("Problem with resultfile: %s\n", fileresilk);
     } /* end mi==0 */        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   }      }
       fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
   for(i=1; i<=imx; i++){      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     for(mi=1; mi<wav[i];mi++){      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       if (stepm <=0)      for(k=1; k<=nlstate; k++) 
         dh[mi][i]=1;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       else{      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
         if (s[mw[mi+1][i]][i] > nlstate) {    }
           if (agedc[i] < 2*AGESUP) {  
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    *fretone=(*funcone)(p);
           if(j==0) j=1;  /* Survives at least one month after exam */    if(*globpri !=0){
           k=k+1;      fclose(ficresilk);
           if (j >= jmax) jmax=j;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
           if (j <= jmin) jmin=j;      fflush(fichtm); 
           sum=sum+j;    } 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    return;
           }  }
         }  
         else{  
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  /*********** Maximum Likelihood Estimation ***************/
           k=k+1;  
           if (j >= jmax) jmax=j;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
           else if (j <= jmin)jmin=j;  {
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    int i,j, iter;
           sum=sum+j;    double **xi;
         }    double fret;
         jk= j/stepm;    double fretone; /* Only one call to likelihood */
         jl= j -jk*stepm;    /*  char filerespow[FILENAMELENGTH];*/
         ju= j -(jk+1)*stepm;    xi=matrix(1,npar,1,npar);
         if(jl <= -ju)    for (i=1;i<=npar;i++)
           dh[mi][i]=jk;      for (j=1;j<=npar;j++)
         else        xi[i][j]=(i==j ? 1.0 : 0.0);
           dh[mi][i]=jk+1;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
         if(dh[mi][i]==0)    strcpy(filerespow,"pow"); 
           dh[mi][i]=1; /* At least one step */    strcat(filerespow,fileres);
       }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     }      printf("Problem with resultfile: %s\n", filerespow);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   jmean=sum/k;    }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    for (i=1;i<=nlstate;i++)
  }      for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
 /*********** Tricode ****************************/    fprintf(ficrespow,"\n");
 void tricode(int *Tvar, int **nbcode, int imx)  
 {    powell(p,xi,npar,ftol,&iter,&fret,func);
   int Ndum[20],ij=1, k, j, i;  
   int cptcode=0;    fclose(ficrespow);
   cptcoveff=0;    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));
   for (k=0; k<19; k++) Ndum[k]=0;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   for (k=1; k<=7; k++) ncodemax[k]=0;  
   }
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  
     for (i=1; i<=imx; i++) {  /**** Computes Hessian and covariance matrix ***/
       ij=(int)(covar[Tvar[j]][i]);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       Ndum[ij]++;  {
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    double  **a,**y,*x,pd;
       if (ij > cptcode) cptcode=ij;    double **hess;
     }    int i, j,jk;
     int *indx;
     for (i=0; i<=cptcode; i++) {  
       if(Ndum[i]!=0) ncodemax[j]++;    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);
     ij=1;    void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
     double gompertz(double p[]);
     for (i=1; i<=ncodemax[j]; i++) {    hess=matrix(1,npar,1,npar);
       for (k=0; k<=19; k++) {  
         if (Ndum[k] != 0) {    printf("\nCalculation of the hessian matrix. Wait...\n");
           nbcode[Tvar[j]][ij]=k;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
              for (i=1;i<=npar;i++){
           ij++;      printf("%d",i);fflush(stdout);
         }      fprintf(ficlog,"%d",i);fflush(ficlog);
         if (ij > ncodemax[j]) break;     
       }         hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     }      
   }        /*  printf(" %f ",p[i]);
           printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
  for (k=0; k<19; k++) Ndum[k]=0;    }
     
  for (i=1; i<=ncovmodel-2; i++) {    for (i=1;i<=npar;i++) {
    ij=Tvar[i];      for (j=1;j<=npar;j++)  {
    Ndum[ij]++;        if (j>i) { 
  }          printf(".%d%d",i,j);fflush(stdout);
           fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
  ij=1;          hess[i][j]=hessij(p,delti,i,j,func,npar);
  for (i=1; i<=10; i++) {          
    if((Ndum[i]!=0) && (i<=ncovcol)){          hess[j][i]=hess[i][j];    
      Tvaraff[ij]=i;          /*printf(" %lf ",hess[i][j]);*/
      ij++;        }
    }      }
  }    }
      printf("\n");
  cptcoveff=ij-1;    fprintf(ficlog,"\n");
 }  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
 /*********** Health Expectancies ****************/    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     
 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 )    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
 {    x=vector(1,npar);
   /* Health expectancies */    indx=ivector(1,npar);
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;    for (i=1;i<=npar;i++)
   double age, agelim, hf;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   double ***p3mat,***varhe;    ludcmp(a,npar,indx,&pd);
   double **dnewm,**doldm;  
   double *xp;    for (j=1;j<=npar;j++) {
   double **gp, **gm;      for (i=1;i<=npar;i++) x[i]=0;
   double ***gradg, ***trgradg;      x[j]=1;
   int theta;      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);        matcov[i][j]=x[i];
   xp=vector(1,npar);      }
   dnewm=matrix(1,nlstate*2,1,npar);    }
   doldm=matrix(1,nlstate*2,1,nlstate*2);  
      printf("\n#Hessian matrix#\n");
   fprintf(ficreseij,"# Health expectancies\n");    fprintf(ficlog,"\n#Hessian matrix#\n");
   fprintf(ficreseij,"# Age");    for (i=1;i<=npar;i++) { 
   for(i=1; i<=nlstate;i++)      for (j=1;j<=npar;j++) { 
     for(j=1; j<=nlstate;j++)        printf("%.3e ",hess[i][j]);
       fprintf(ficreseij," %1d-%1d (SE)",i,j);        fprintf(ficlog,"%.3e ",hess[i][j]);
   fprintf(ficreseij,"\n");      }
       printf("\n");
   if(estepm < stepm){      fprintf(ficlog,"\n");
     printf ("Problem %d lower than %d\n",estepm, stepm);    }
   }  
   else  hstepm=estepm;      /* Recompute Inverse */
   /* We compute the life expectancy from trapezoids spaced every estepm months    for (i=1;i<=npar;i++)
    * This is mainly to measure the difference between two models: for example      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
    * if stepm=24 months pijx are given only every 2 years and by summing them    ludcmp(a,npar,indx,&pd);
    * we are calculating an estimate of the Life Expectancy assuming a linear  
    * progression inbetween and thus overestimating or underestimating according    /*  printf("\n#Hessian matrix recomputed#\n");
    * to the curvature of the survival function. If, for the same date, we  
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    for (j=1;j<=npar;j++) {
    * to compare the new estimate of Life expectancy with the same linear      for (i=1;i<=npar;i++) x[i]=0;
    * hypothesis. A more precise result, taking into account a more precise      x[j]=1;
    * curvature will be obtained if estepm is as small as stepm. */      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
   /* For example we decided to compute the life expectancy with the smallest unit */        y[i][j]=x[i];
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        printf("%.3e ",y[i][j]);
      nhstepm is the number of hstepm from age to agelim        fprintf(ficlog,"%.3e ",y[i][j]);
      nstepm is the number of stepm from age to agelin.      }
      Look at hpijx to understand the reason of that which relies in memory size      printf("\n");
      and note for a fixed period like estepm months */      fprintf(ficlog,"\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  
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    free_matrix(a,1,npar,1,npar);
      results. So we changed our mind and took the option of the best precision.    free_matrix(y,1,npar,1,npar);
   */    free_vector(x,1,npar);
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
   agelim=AGESUP;  
   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 */  /*************** hessian matrix ****************/
     /* if (stepm >= YEARM) hstepm=1;*/  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int i;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    int l=1, lmax=20;
     gp=matrix(0,nhstepm,1,nlstate*2);    double k1,k2;
     gm=matrix(0,nhstepm,1,nlstate*2);    double p2[NPARMAX+1];
     double res;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    double fx;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      int k=0,kmax=10;
      double l1;
   
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
     /* Computing Variances of health expectancies */    for(l=0 ; l <=lmax; l++){
       l1=pow(10,l);
      for(theta=1; theta <=npar; theta++){      delts=delt;
       for(i=1; i<=npar; i++){      for(k=1 ; k <kmax; k=k+1){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        delt = delta*(l1*k);
       }        p2[theta]=x[theta] +delt;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          k1=func(p2)-fx;
          p2[theta]=x[theta]-delt;
       cptj=0;        k2=func(p2)-fx;
       for(j=1; j<= nlstate; j++){        /*res= (k1-2.0*fx+k2)/delt/delt; */
         for(i=1; i<=nlstate; i++){        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
           cptj=cptj+1;        
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){  #ifdef DEBUG
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
           }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         }  #endif
       }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
              if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
                k=kmax;
       for(i=1; i<=npar; i++)        }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            k=kmax; l=lmax*10.;
              }
       cptj=0;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       for(j=1; j<= nlstate; j++){          delts=delt;
         for(i=1;i<=nlstate;i++){        }
           cptj=cptj+1;      }
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    }
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    delti[theta]=delts;
           }    return res; 
         }    
       }  }
       for(j=1; j<= nlstate*2; j++)  
         for(h=0; h<=nhstepm-1; h++){  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  {
         }    int i;
      }    int l=1, l1, lmax=20;
        double k1,k2,k3,k4,res,fx;
 /* End theta */    double p2[NPARMAX+1];
     int k;
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);  
     fx=func(x);
      for(h=0; h<=nhstepm-1; h++)    for (k=1; k<=2; k++) {
       for(j=1; j<=nlstate*2;j++)      for (i=1;i<=npar;i++) p2[i]=x[i];
         for(theta=1; theta <=npar; theta++)      p2[thetai]=x[thetai]+delti[thetai]/k;
           trgradg[h][j][theta]=gradg[h][theta][j];      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
            k1=func(p2)-fx;
     
      for(i=1;i<=nlstate*2;i++)      p2[thetai]=x[thetai]+delti[thetai]/k;
       for(j=1;j<=nlstate*2;j++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         varhe[i][j][(int)age] =0.;      k2=func(p2)-fx;
     
      printf("%d|",(int)age);fflush(stdout);      p2[thetai]=x[thetai]-delti[thetai]/k;
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
      for(h=0;h<=nhstepm-1;h++){      k3=func(p2)-fx;
       for(k=0;k<=nhstepm-1;k++){    
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);      p2[thetai]=x[thetai]-delti[thetai]/k;
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         for(i=1;i<=nlstate*2;i++)      k4=func(p2)-fx;
           for(j=1;j<=nlstate*2;j++)      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;  #ifdef DEBUG
       }      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     }      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);
     /* Computing expectancies */  #endif
     for(i=1; i<=nlstate;i++)    }
       for(j=1; j<=nlstate;j++)    return res;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){  }
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;  
            /************** Inverse of matrix **************/
 /* 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]);*/  void ludcmp(double **a, int n, int *indx, double *d) 
   { 
         }    int i,imax,j,k; 
     double big,dum,sum,temp; 
     fprintf(ficreseij,"%3.0f",age );    double *vv; 
     cptj=0;   
     for(i=1; i<=nlstate;i++)    vv=vector(1,n); 
       for(j=1; j<=nlstate;j++){    *d=1.0; 
         cptj++;    for (i=1;i<=n;i++) { 
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      big=0.0; 
       }      for (j=1;j<=n;j++) 
     fprintf(ficreseij,"\n");        if ((temp=fabs(a[i][j])) > big) big=temp; 
          if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     free_matrix(gm,0,nhstepm,1,nlstate*2);      vv[i]=1.0/big; 
     free_matrix(gp,0,nhstepm,1,nlstate*2);    } 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    for (j=1;j<=n;j++) { 
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);      for (i=1;i<j;i++) { 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        sum=a[i][j]; 
   }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   printf("\n");        a[i][j]=sum; 
   fprintf(ficlog,"\n");      } 
       big=0.0; 
   free_vector(xp,1,npar);      for (i=j;i<=n;i++) { 
   free_matrix(dnewm,1,nlstate*2,1,npar);        sum=a[i][j]; 
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);        for (k=1;k<j;k++) 
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);          sum -= a[i][k]*a[k][j]; 
 }        a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
 /************ Variance ******************/          big=dum; 
 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)          imax=i; 
 {        } 
   /* Variance of health expectancies */      } 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      if (j != imax) { 
   /* double **newm;*/        for (k=1;k<=n;k++) { 
   double **dnewm,**doldm;          dum=a[imax][k]; 
   double **dnewmp,**doldmp;          a[imax][k]=a[j][k]; 
   int i, j, nhstepm, hstepm, h, nstepm ;          a[j][k]=dum; 
   int k, cptcode;        } 
   double *xp;        *d = -(*d); 
   double **gp, **gm;  /* for var eij */        vv[imax]=vv[j]; 
   double ***gradg, ***trgradg; /*for var eij */      } 
   double **gradgp, **trgradgp; /* for var p point j */      indx[j]=imax; 
   double *gpp, *gmp; /* for var p point j */      if (a[j][j] == 0.0) a[j][j]=TINY; 
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */      if (j != n) { 
   double ***p3mat;        dum=1.0/(a[j][j]); 
   double age,agelim, hf;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   int theta;      } 
   char digit[4];    } 
   char digitp[16];    free_vector(vv,1,n);  /* Doesn't work */
   ;
   char fileresprobmorprev[FILENAMELENGTH];  } 
   
   if(popbased==1)  void lubksb(double **a, int n, int *indx, double b[]) 
     strcpy(digitp,"-populbased-");  { 
   else    int i,ii=0,ip,j; 
     strcpy(digitp,"-stablbased-");    double sum; 
    
   strcpy(fileresprobmorprev,"prmorprev");    for (i=1;i<=n;i++) { 
   sprintf(digit,"%-d",ij);      ip=indx[i]; 
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/      sum=b[ip]; 
   strcat(fileresprobmorprev,digit); /* Tvar to be done */      b[ip]=b[i]; 
   strcat(fileresprobmorprev,digitp); /* Popbased or not */      if (ii) 
   strcat(fileresprobmorprev,fileres);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {      else if (sum) ii=i; 
     printf("Problem with resultfile: %s\n", fileresprobmorprev);      b[i]=sum; 
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);    } 
   }    for (i=n;i>=1;i--) { 
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);      sum=b[i]; 
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");      b[i]=sum/a[i][i]; 
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);    } 
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){  } 
     fprintf(ficresprobmorprev," p.%-d SE",j);  
     for(i=1; i<=nlstate;i++)  /************ Frequencies ********************/
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);  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)
   }    {  /* Some frequencies */
   fprintf(ficresprobmorprev,"\n");    
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    int first;
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);    double ***freq; /* Frequencies */
     exit(0);    double *pp, **prop;
   }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   else{    FILE *ficresp;
     fprintf(ficgp,"\n# Routine varevsij");    char fileresp[FILENAMELENGTH];
   }    
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {    pp=vector(1,nlstate);
     printf("Problem with html file: %s\n", optionfilehtm);    prop=matrix(1,nlstate,iagemin,iagemax+3);
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);    strcpy(fileresp,"p");
     exit(0);    strcat(fileresp,fileres);
   }    if((ficresp=fopen(fileresp,"w"))==NULL) {
   else{      printf("Problem with prevalence resultfile: %s\n", fileresp);
     fprintf(fichtm,"\n<li><h4> Computing step probabilities of dying and weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   }      exit(0);
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    }
     freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
   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");    j1=0;
   fprintf(ficresvij,"# Age");    
   for(i=1; i<=nlstate;i++)    j=cptcoveff;
     for(j=1; j<=nlstate;j++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  
   fprintf(ficresvij,"\n");    first=1;
   
   xp=vector(1,npar);    for(k1=1; k1<=j;k1++){
   dnewm=matrix(1,nlstate,1,npar);      for(i1=1; i1<=ncodemax[k1];i1++){
   doldm=matrix(1,nlstate,1,nlstate);        j1++;
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);          scanf("%d", i);*/
         for (i=-1; i<=nlstate+ndeath; i++)  
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   gpp=vector(nlstate+1,nlstate+ndeath);            for(m=iagemin; m <= iagemax+3; m++)
   gmp=vector(nlstate+1,nlstate+ndeath);              freq[i][jk][m]=0;
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/  
        for (i=1; i<=nlstate; i++)  
   if(estepm < stepm){        for(m=iagemin; m <= iagemax+3; m++)
     printf ("Problem %d lower than %d\n",estepm, stepm);          prop[i][m]=0;
   }        
   else  hstepm=estepm;          dateintsum=0;
   /* For example we decided to compute the life expectancy with the smallest unit */        k2cpt=0;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        for (i=1; i<=imx; i++) {
      nhstepm is the number of hstepm from age to agelim          bool=1;
      nstepm is the number of stepm from age to agelin.          if  (cptcovn>0) {
      Look at hpijx to understand the reason of that which relies in memory size            for (z1=1; z1<=cptcoveff; z1++) 
      and note for a fixed period like k years */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the                bool=0;
      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          if (bool==1){
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            for(m=firstpass; m<=lastpass; m++){
      results. So we changed our mind and took the option of the best precision.              k2=anint[m][i]+(mint[m][i]/12.);
   */              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   agelim = AGESUP;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                if (m<lastpass) {
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);                }
     gp=matrix(0,nhstepm,1,nlstate);                
     gm=matrix(0,nhstepm,1,nlstate);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
                   k2cpt++;
     for(theta=1; theta <=npar; theta++){                }
       for(i=1; i<=npar; i++){ /* Computes gradient */                /*}*/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            }
       }          }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);         
         /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)        if  (cptcovn>0) {
           prlim[i][i]=probs[(int)age][i][ij];          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#");
       for(j=1; j<= nlstate; j++){        }
         for(h=0; h<=nhstepm; h++){        for(i=1; i<=nlstate;i++) 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        fprintf(ficresp, "\n");
         }        
       }        for(i=iagemin; i <= iagemax+3; i++){
       /* This for computing forces of mortality (h=1)as a weighted average */          if(i==iagemax+3){
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){            fprintf(ficlog,"Total");
         for(i=1; i<= nlstate; i++)          }else{
           gpp[j] += prlim[i][i]*p3mat[i][j][1];            if(first==1){
       }                  first=0;
       /* end force of mortality */              printf("See log file for details...\n");
             }
       for(i=1; i<=npar; i++) /* Computes gradient */            fprintf(ficlog,"Age %d", i);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            for(jk=1; jk <=nlstate ; jk++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                pp[jk] += freq[jk][m][i]; 
       if (popbased==1) {          }
         for(i=1; i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){
           prlim[i][i]=probs[(int)age][i][ij];            for(m=-1, pos=0; m <=0 ; m++)
       }              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
       for(j=1; j<= nlstate; j++){              if(first==1){
         for(h=0; h<=nhstepm; h++){              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)              }
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         }            }else{
       }              if(first==1)
       /* This for computing force of mortality (h=1)as a weighted average */                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         for(i=1; i<= nlstate; i++)            }
           gmp[j] += prlim[i][i]*p3mat[i][j][1];          }
       }      
       /* end force of mortality */          for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       for(j=1; j<= nlstate; j++) /* vareij */              pp[jk] += freq[jk][m][i];
         for(h=0; h<=nhstepm; h++){          }       
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         }            pos += pp[jk];
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */            posprop += prop[jk][i];
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];          }
       }          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
     } /* End theta */              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
     for(h=0; h<=nhstepm; h++) /* veij */              if(first==1)
       for(j=1; j<=nlstate;j++)                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         for(theta=1; theta <=npar; theta++)              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           trgradg[h][j][theta]=gradg[h][theta][j];            }
             if( i <= iagemax){
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */              if(pos>=1.e-5){
       for(theta=1; theta <=npar; theta++)                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
         trgradgp[j][theta]=gradgp[theta][j];                /*probs[i][jk][j1]= pp[jk]/pos;*/
                 /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */              }
     for(i=1;i<=nlstate;i++)              else
       for(j=1;j<=nlstate;j++)                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
         vareij[i][j][(int)age] =0.;            }
           }
     for(h=0;h<=nhstepm;h++){          
       for(k=0;k<=nhstepm;k++){          for(jk=-1; jk <=nlstate+ndeath; jk++)
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);            for(m=-1; m <=nlstate+ndeath; m++)
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);              if(freq[jk][m][i] !=0 ) {
         for(i=1;i<=nlstate;i++)              if(first==1)
           for(j=1;j<=nlstate;j++)                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       }              }
     }          if(i <= iagemax)
             fprintf(ficresp,"\n");
     /* pptj */          if(first==1)
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);            printf("Others in log...\n");
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);          fprintf(ficlog,"\n");
     for(j=nlstate+1;j<=nlstate+ndeath;j++)        }
       for(i=nlstate+1;i<=nlstate+ndeath;i++)      }
         varppt[j][i]=doldmp[j][i];    }
     /* end ppptj */    dateintmean=dateintsum/k2cpt; 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);     
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);    fclose(ficresp);
      free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     if (popbased==1) {    free_vector(pp,1,nlstate);
       for(i=1; i<=nlstate;i++)    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
         prlim[i][i]=probs[(int)age][i][ij];    /* End of Freq */
     }  }
      
     /* This for computing force of mortality (h=1)as a weighted average */  /************ Prevalence ********************/
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){  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)
       for(i=1; i<= nlstate; i++)  {  
         gmp[j] += prlim[i][i]*p3mat[i][j][1];    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     }           in each health status at the date of interview (if between dateprev1 and dateprev2).
     /* end force of mortality */       We still use firstpass and lastpass as another selection.
     */
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);   
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));    double ***freq; /* Frequencies */
       for(i=1; i<=nlstate;i++){    double *pp, **prop;
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);    double pos,posprop; 
       }    double  y2; /* in fractional years */
     }    int iagemin, iagemax;
     fprintf(ficresprobmorprev,"\n");  
     iagemin= (int) agemin;
     fprintf(ficresvij,"%.0f ",age );    iagemax= (int) agemax;
     for(i=1; i<=nlstate;i++)    /*pp=vector(1,nlstate);*/
       for(j=1; j<=nlstate;j++){    prop=matrix(1,nlstate,iagemin,iagemax+3); 
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       }    j1=0;
     fprintf(ficresvij,"\n");    
     free_matrix(gp,0,nhstepm,1,nlstate);    j=cptcoveff;
     free_matrix(gm,0,nhstepm,1,nlstate);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    for(k1=1; k1<=j;k1++){
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(i1=1; i1<=ncodemax[k1];i1++){
   } /* End age */        j1++;
   free_vector(gpp,nlstate+1,nlstate+ndeath);        
   free_vector(gmp,nlstate+1,nlstate+ndeath);        for (i=1; i<=nlstate; i++)  
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);          for(m=iagemin; m <= iagemax+3; m++)
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/            prop[i][m]=0.0;
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");       
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */        for (i=1; i<=imx; i++) { /* Each individual */
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");          bool=1;
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);          if  (cptcovn>0) {
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);            for (z1=1; z1<=cptcoveff; z1++) 
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);                bool=0;
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);          } 
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   free_vector(xp,1,npar);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   free_matrix(doldm,1,nlstate,1,nlstate);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   free_matrix(dnewm,1,nlstate,1,npar);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);                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); 
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   fclose(ficresprobmorprev);                  /*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]]);*/
   fclose(ficgp);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   fclose(fichtm);                  prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
 }              }
             } /* end selection of waves */
 /************ 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=iagemin; i <= iagemax+3; i++){  
   /* Variance of prevalence limit */          
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   double **newm;            posprop += prop[jk][i]; 
   double **dnewm,**doldm;          } 
   int i, j, nhstepm, hstepm;  
   int k, cptcode;          for(jk=1; jk <=nlstate ; jk++){     
   double *xp;            if( i <=  iagemax){ 
   double *gp, *gm;              if(posprop>=1.e-5){ 
   double **gradg, **trgradg;                probs[i][jk][j1]= prop[jk][i]/posprop;
   double age,agelim;              } 
   int theta;            } 
              }/* end jk */ 
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");        }/* end i */ 
   fprintf(ficresvpl,"# Age");      } /* end i1 */
   for(i=1; i<=nlstate;i++)    } /* end k1 */
       fprintf(ficresvpl," %1d-%1d",i,i);    
   fprintf(ficresvpl,"\n");    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     /*free_vector(pp,1,nlstate);*/
   xp=vector(1,npar);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   dnewm=matrix(1,nlstate,1,npar);  }  /* End of prevalence */
   doldm=matrix(1,nlstate,1,nlstate);  
    /************* Waves Concatenation ***************/
   hstepm=1*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
   agelim = AGESUP;  {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       Death is a valid wave (if date is known).
     if (stepm >= YEARM) hstepm=1;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     gradg=matrix(1,npar,1,nlstate);       and mw[mi+1][i]. dh depends on stepm.
     gp=vector(1,nlstate);       */
     gm=vector(1,nlstate);  
     int i, mi, m;
     for(theta=1; theta <=npar; theta++){    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       for(i=1; i<=npar; i++){ /* Computes gradient */       double sum=0., jmean=0.;*/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    int first;
       }    int j, k=0,jk, ju, jl;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double sum=0.;
       for(i=1;i<=nlstate;i++)    first=0;
         gp[i] = prlim[i][i];    jmin=1e+5;
        jmax=-1;
       for(i=1; i<=npar; i++) /* Computes gradient */    jmean=0.;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    for(i=1; i<=imx; i++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      mi=0;
       for(i=1;i<=nlstate;i++)      m=firstpass;
         gm[i] = prlim[i][i];      while(s[m][i] <= nlstate){
         if(s[m][i]>=1)
       for(i=1;i<=nlstate;i++)          mw[++mi][i]=m;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        if(m >=lastpass)
     } /* End theta */          break;
         else
     trgradg =matrix(1,nlstate,1,npar);          m++;
       }/* end while */
     for(j=1; j<=nlstate;j++)      if (s[m][i] > nlstate){
       for(theta=1; theta <=npar; theta++)        mi++;     /* Death is another wave */
         trgradg[j][theta]=gradg[theta][j];        /* if(mi==0)  never been interviewed correctly before death */
            /* Only death is a correct wave */
     for(i=1;i<=nlstate;i++)        mw[mi][i]=m;
       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);      wav[i]=mi;
     for(i=1;i<=nlstate;i++)      if(mi==0){
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        nbwarn++;
         if(first==0){
     fprintf(ficresvpl,"%.0f ",age );          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     for(i=1; i<=nlstate;i++)          first=1;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        }
     fprintf(ficresvpl,"\n");        if(first==1){
     free_vector(gp,1,nlstate);          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
     free_vector(gm,1,nlstate);        }
     free_matrix(gradg,1,npar,1,nlstate);      } /* end mi==0 */
     free_matrix(trgradg,1,nlstate,1,npar);    } /* End individuals */
   } /* End age */  
     for(i=1; i<=imx; i++){
   free_vector(xp,1,npar);      for(mi=1; mi<wav[i];mi++){
   free_matrix(doldm,1,nlstate,1,npar);        if (stepm <=0)
   free_matrix(dnewm,1,nlstate,1,nlstate);          dh[mi][i]=1;
         else{
 }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             if (agedc[i] < 2*AGESUP) {
 /************ Variance of one-step probabilities  ******************/              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)              if(j==0) j=1;  /* Survives at least one month after exam */
 {              else if(j<0){
   int i, j=0,  i1, k1, l1, t, tj;                nberr++;
   int k2, l2, j1,  z1;                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]);
   int k=0,l, cptcode;                j=1; /* Temporary Dangerous patch */
   int first=1, first1;                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.\n  You MUST fix the contradiction between dates.\n",stepm);
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;                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]);
   double **dnewm,**doldm;                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.\n  You MUST fix the contradiction between dates.\n",stepm);
   double *xp;              }
   double *gp, *gm;              k=k+1;
   double **gradg, **trgradg;              if (j >= jmax) jmax=j;
   double **mu;              if (j <= jmin) jmin=j;
   double age,agelim, cov[NCOVMAX];              sum=sum+j;
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   int theta;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   char fileresprob[FILENAMELENGTH];            }
   char fileresprobcov[FILENAMELENGTH];          }
   char fileresprobcor[FILENAMELENGTH];          else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   double ***varpij;            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             k=k+1;
   strcpy(fileresprob,"prob");            if (j >= jmax) jmax=j;
   strcat(fileresprob,fileres);            else if (j <= jmin)jmin=j;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     printf("Problem with resultfile: %s\n", fileresprob);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);            if(j<0){
   }              nberr++;
   strcpy(fileresprobcov,"probcov");              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]);
   strcat(fileresprobcov,fileres);              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]);
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {            }
     printf("Problem with resultfile: %s\n", fileresprobcov);            sum=sum+j;
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);          }
   }          jk= j/stepm;
   strcpy(fileresprobcor,"probcor");          jl= j -jk*stepm;
   strcat(fileresprobcor,fileres);          ju= j -(jk+1)*stepm;
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     printf("Problem with resultfile: %s\n", fileresprobcor);            if(jl==0){
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);              dh[mi][i]=jk;
   }              bh[mi][i]=0;
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);            }else{ /* We want a negative bias in order to only have interpolation ie
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);                    * at the price of an extra matrix product in likelihood */
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);              dh[mi][i]=jk+1;
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);              bh[mi][i]=ju;
   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);          }else{
              if(jl <= -ju){
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");              dh[mi][i]=jk;
   fprintf(ficresprob,"# Age");              bh[mi][i]=jl;       /* bias is positive if real duration
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");                                   * is higher than the multiple of stepm and negative otherwise.
   fprintf(ficresprobcov,"# Age");                                   */
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");            }
   fprintf(ficresprobcov,"# Age");            else{
               dh[mi][i]=jk+1;
               bh[mi][i]=ju;
   for(i=1; i<=nlstate;i++)            }
     for(j=1; j<=(nlstate+ndeath);j++){            if(dh[mi][i]==0){
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);              dh[mi][i]=1; /* At least one step */
       fprintf(ficresprobcov," p%1d-%1d ",i,j);              bh[mi][i]=ju; /* At least one step */
       fprintf(ficresprobcor," p%1d-%1d ",i,j);              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
     }              }
   fprintf(ficresprob,"\n");          } /* end if mle */
   fprintf(ficresprobcov,"\n");        }
   fprintf(ficresprobcor,"\n");      } /* end wave */
   xp=vector(1,npar);    }
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    jmean=sum/k;
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);   }
   first=1;  
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {  /*********** Tricode ****************************/
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);  void tricode(int *Tvar, int **nbcode, int imx)
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);  {
     exit(0);    
   }    int Ndum[20],ij=1, k, j, i, maxncov=19;
   else{    int cptcode=0;
     fprintf(ficgp,"\n# Routine varprob");    cptcoveff=0; 
   }   
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {    for (k=0; k<maxncov; k++) Ndum[k]=0;
     printf("Problem with html file: %s\n", optionfilehtm);    for (k=1; k<=7; k++) ncodemax[k]=0;
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);  
     exit(0);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   else{                                 modality*/ 
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     fprintf(fichtm,"\n");        Ndum[ij]++; /*store the modality */
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     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");                                         Tvar[j]. If V=sex and male is 0 and 
     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");                                         female is 1, then  cptcode=1.*/
       }
   }  
       for (i=0; i<=cptcode; i++) {
          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 */
   cov[1]=1;      }
   tj=cptcoveff;  
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}      ij=1; 
   j1=0;      for (i=1; i<=ncodemax[j]; i++) {
   for(t=1; t<=tj;t++){        for (k=0; k<= maxncov; k++) {
     for(i1=1; i1<=ncodemax[t];i1++){          if (Ndum[k] != 0) {
       j1++;            nbcode[Tvar[j]][ij]=k; 
                  /* 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; */
       if  (cptcovn>0) {            
         fprintf(ficresprob, "\n#********** Variable ");            ij++;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          }
         fprintf(ficresprob, "**********\n#");          if (ij > ncodemax[j]) break; 
         fprintf(ficresprobcov, "\n#********** Variable ");        }  
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      } 
         fprintf(ficresprobcov, "**********\n#");    }  
          
         fprintf(ficgp, "\n#********** Variable ");   for (k=0; k< maxncov; k++) Ndum[k]=0;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficgp, "**********\n#");   for (i=1; i<=ncovmodel-2; i++) { 
             /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
             ij=Tvar[i];
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");     Ndum[ij]++;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);   }
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");  
           ij=1;
         fprintf(ficresprobcor, "\n#********** Variable ");       for (i=1; i<= maxncov; i++) {
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);     if((Ndum[i]!=0) && (i<=ncovcol)){
         fprintf(ficgp, "**********\n#");           Tvaraff[ij]=i; /*For printing */
       }       ij++;
           }
       for (age=bage; age<=fage; age ++){   }
         cov[2]=age;   
         for (k=1; k<=cptcovn;k++) {   cptcoveff=ij-1; /*Number of simple covariates*/
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];  }
         }  
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /*********** Health Expectancies ****************/
         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]]];  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 )
          
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));  {
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    /* Health expectancies */
         gp=vector(1,(nlstate)*(nlstate+ndeath));    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
         gm=vector(1,(nlstate)*(nlstate+ndeath));    double age, agelim, hf;
        double ***p3mat,***varhe;
         for(theta=1; theta <=npar; theta++){    double **dnewm,**doldm;
           for(i=1; i<=npar; i++)    double *xp;
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    double **gp, **gm;
              double ***gradg, ***trgradg;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    int theta;
            
           k=0;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
           for(i=1; i<= (nlstate); i++){    xp=vector(1,npar);
             for(j=1; j<=(nlstate+ndeath);j++){    dnewm=matrix(1,nlstate*nlstate,1,npar);
               k=k+1;    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
               gp[k]=pmmij[i][j];    
             }    fprintf(ficreseij,"# Health expectancies\n");
           }    fprintf(ficreseij,"# Age");
              for(i=1; i<=nlstate;i++)
           for(i=1; i<=npar; i++)      for(j=1; j<=nlstate;j++)
             xp[i] = x[i] - (i==theta ?delti[theta]:0);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
        fprintf(ficreseij,"\n");
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  
           k=0;    if(estepm < stepm){
           for(i=1; i<=(nlstate); i++){      printf ("Problem %d lower than %d\n",estepm, stepm);
             for(j=1; j<=(nlstate+ndeath);j++){    }
               k=k+1;    else  hstepm=estepm;   
               gm[k]=pmmij[i][j];    /* 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 
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)     * progression in between and thus overestimating or underestimating according
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];       * to the curvature of the survival function. If, for the same date, we 
         }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)     * hypothesis. A more precise result, taking into account a more precise
           for(theta=1; theta <=npar; theta++)     * curvature will be obtained if estepm is as small as stepm. */
             trgradg[j][theta]=gradg[theta][j];  
            /* For example we decided to compute the life expectancy with the smallest unit */
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);       nhstepm is the number of hstepm from age to agelim 
               nstepm is the number of stepm from age to agelin. 
         pmij(pmmij,cov,ncovmodel,x,nlstate);       Look at hpijx to understand the reason of that which relies in memory size
               and note for a fixed period like estepm months */
         k=0;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         for(i=1; i<=(nlstate); i++){       survival function given by stepm (the optimization length). Unfortunately it
           for(j=1; j<=(nlstate+ndeath);j++){       means that if the survival funtion is printed only each two years of age and if
             k=k+1;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
             mu[k][(int) age]=pmmij[i][j];       results. So we changed our mind and took the option of the best precision.
           }    */
         }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)  
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)    agelim=AGESUP;
             varpij[i][j][(int)age] = doldm[i][j];    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       /* nhstepm age range expressed in number of stepm */
         /*printf("\n%d ",(int)age);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      /* if (stepm >= YEARM) hstepm=1;*/
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
      }*/      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
         fprintf(ficresprob,"\n%d ",(int)age);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
         fprintf(ficresprobcov,"\n%d ",(int)age);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
         fprintf(ficresprobcor,"\n%d ",(int)age);  
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){   
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);  
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         }  
         i=0;      /* Computing  Variances of health expectancies */
         for (k=1; k<=(nlstate);k++){  
           for (l=1; l<=(nlstate+ndeath);l++){       for(theta=1; theta <=npar; theta++){
             i=i++;        for(i=1; i<=npar; i++){ 
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);        }
             for (j=1; j<=i;j++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);    
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));        cptj=0;
             }        for(j=1; j<= nlstate; j++){
           }          for(i=1; i<=nlstate; i++){
         }/* end of loop for state */            cptj=cptj+1;
       } /* end of loop for age */            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
               gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       /* Confidence intervalle of pij  */            }
       /*          }
       fprintf(ficgp,"\nset noparametric;unset label");        }
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");       
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");       
       fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);        for(i=1; i<=npar; i++) 
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);        
       */        cptj=0;
         for(j=1; j<= nlstate; j++){
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/          for(i=1;i<=nlstate;i++){
       first1=1;            cptj=cptj+1;
       for (k1=1; k1<=(nlstate);k1++){            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
         for (l1=1; l1<=(nlstate+ndeath);l1++){  
           if(l1==k1) continue;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           i=(k1-1)*(nlstate+ndeath)+l1;            }
           for (k2=1; k2<=(nlstate);k2++){          }
             for (l2=1; l2<=(nlstate+ndeath);l2++){        }
               if(l2==k2) continue;        for(j=1; j<= nlstate*nlstate; j++)
               j=(k2-1)*(nlstate+ndeath)+l2;          for(h=0; h<=nhstepm-1; h++){
               if(j<=i) continue;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
               for (age=bage; age<=fage; age ++){          }
                 if ((int)age %5==0){       } 
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;     
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;  /* End theta */
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;  
                   mu1=mu[i][(int) age]/stepm*YEARM ;       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
                   mu2=mu[j][(int) age]/stepm*YEARM;  
                   /* Computing eigen value of matrix of covariance */       for(h=0; h<=nhstepm-1; h++)
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));        for(j=1; j<=nlstate*nlstate;j++)
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));          for(theta=1; theta <=npar; theta++)
                   if(first1==1){            trgradg[h][j][theta]=gradg[h][theta][j];
                     first1=0;       
                     printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\nOthers in log...\n",v1,v2,cv12,lc1,lc2);  
                   }       for(i=1;i<=nlstate*nlstate;i++)
                   fprintf(ficlog,"Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);        for(j=1;j<=nlstate*nlstate;j++)
                   /* Eigen vectors */          varhe[i][j][(int)age] =0.;
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));  
                   v21=sqrt(1.-v11*v11);       printf("%d|",(int)age);fflush(stdout);
                   v12=-v21;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                   v22=v11;       for(h=0;h<=nhstepm-1;h++){
                   /*printf(fignu*/        for(k=0;k<=nhstepm-1;k++){
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
                   if(first==1){          for(i=1;i<=nlstate*nlstate;i++)
                     first=0;            for(j=1;j<=nlstate*nlstate;j++)
                     fprintf(ficgp,"\nset parametric;set nolabel");              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);        }
                     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>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);      /* Computing expectancies */
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);      for(i=1; i<=nlstate;i++)
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);        for(j=1; j<=nlstate;j++)
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
                     /*              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)) t \"%d\"",\            
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \  /* 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]);*/
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);  
                     */          }
                     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",\  
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \      fprintf(ficreseij,"%3.0f",age );
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));      cptj=0;
                   }else{      for(i=1; i<=nlstate;i++)
                     first=0;        for(j=1; j<=nlstate;j++){
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);          cptj++;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
                     /*        }
                     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)) t \"%d\"",\      fprintf(ficreseij,"\n");
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \     
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
                     */      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
                     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",\      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   }/* if first */    }
                 } /* age mod 5 */    printf("\n");
               } /* end loop age */    fprintf(ficlog,"\n");
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);  
               first=1;    free_vector(xp,1,npar);
             } /*l12 */    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
           } /* k12 */    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
         } /*l1 */    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
       }/* k1 */  }
     } /* loop covariates */  
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);  /************ Variance ******************/
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  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)
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  {
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);    /* Variance of health expectancies */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    /* double **newm;*/
   }    double **dnewm,**doldm;
   free_vector(xp,1,npar);    double **dnewmp,**doldmp;
   fclose(ficresprob);    int i, j, nhstepm, hstepm, h, nstepm ;
   fclose(ficresprobcov);    int k, cptcode;
   fclose(ficresprobcor);    double *xp;
   fclose(ficgp);    double **gp, **gm;  /* for var eij */
   fclose(fichtm);    double ***gradg, ***trgradg; /*for var eij */
 }    double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
 /******************* Printing html file ***********/    double ***p3mat;
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    double age,agelim, hf;
                   int lastpass, int stepm, int weightopt, char model[],\    double ***mobaverage;
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\    int theta;
                   int popforecast, int estepm ,\    char digit[4];
                   double jprev1, double mprev1,double anprev1, \    char digitp[25];
                   double jprev2, double mprev2,double anprev2){  
   int jj1, k1, i1, cpt;    char fileresprobmorprev[FILENAMELENGTH];
   /*char optionfilehtm[FILENAMELENGTH];*/  
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {    if(popbased==1){
     printf("Problem with %s \n",optionfilehtm), exit(0);      if(mobilav!=0)
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);        strcpy(digitp,"-populbased-mobilav-");
   }      else strcpy(digitp,"-populbased-nomobil-");
     }
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n    else 
  - 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      strcpy(digitp,"-stablbased-");
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n  
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n    if (mobilav!=0) {
  - Life expectancies by age and initial health status (estepm=%2d months):      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    <a href=\"e%s\">e%s</a> <br>\n</li>", \      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");      }
     }
  m=cptcoveff;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
  jj1=0;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
  for(k1=1; k1<=m;k1++){    strcat(fileresprobmorprev,digit); /* Tvar to be done */
    for(i1=1; i1<=ncodemax[k1];i1++){    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
      jj1++;    strcat(fileresprobmorprev,fileres);
      if (cptcovn > 0) {    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      printf("Problem with resultfile: %s\n", fileresprobmorprev);
        for (cpt=1; cpt<=cptcoveff;cpt++)      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    }
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    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);
      /* Pij */    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(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(ficresprobmorprev,"# Age cov=%-d",ij);
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        for(j=nlstate+1; j<=(nlstate+ndeath);j++){
      /* Quasi-incidences */      fprintf(ficresprobmorprev," p.%-d SE",j);
      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);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
        /* Stable prevalence in each health state */    }  
        for(cpt=1; cpt<nlstate;cpt++){    fprintf(ficresprobmorprev,"\n");
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    fprintf(ficgp,"\n# Routine varevsij");
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    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);
      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>    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
      }    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(fichtm,"\n<br>- Total life expectancy by age and    fprintf(ficresvij,"# Age");
 health expectancies in states (1) and (2): e%s%d.png<br>    for(i=1; i<=nlstate;i++)
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      for(j=1; j<=nlstate;j++)
    } /* end i1 */        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
  }/* End k1 */    fprintf(ficresvij,"\n");
  fprintf(fichtm,"</ul>");  
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n    doldm=matrix(1,nlstate,1,nlstate);
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n  
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    gpp=vector(nlstate+1,nlstate+ndeath);
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n    gmp=vector(nlstate+1,nlstate+ndeath);
  - 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);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
  if(popforecast==1) fprintf(fichtm,"\n    if(estepm < stepm){
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n      printf ("Problem %d lower than %d\n",estepm, stepm);
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    }
         <br>",fileres,fileres,fileres,fileres);    else  hstepm=estepm;   
  else    /* For example we decided to compute the life expectancy with the smallest unit */
    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);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
  m=cptcoveff;       Look at hpijx to understand the reason of that which relies in memory size
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}       and note for a fixed period like k years */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
  jj1=0;       survival function given by stepm (the optimization length). Unfortunately it
  for(k1=1; k1<=m;k1++){       means that if the survival funtion is printed every two years of age and if
    for(i1=1; i1<=ncodemax[k1];i1++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
      jj1++;       results. So we changed our mind and took the option of the best precision.
      if (cptcovn > 0) {    */
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
        for (cpt=1; cpt<=cptcoveff;cpt++)    agelim = AGESUP;
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
      }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
      for(cpt=1; cpt<=nlstate;cpt++) {      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
 interval) in state (%d): v%s%d%d.png <br>      gp=matrix(0,nhstepm,1,nlstate);
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        gm=matrix(0,nhstepm,1,nlstate);
      }  
    } /* end i1 */  
  }/* End k1 */      for(theta=1; theta <=npar; theta++){
  fprintf(fichtm,"</ul>");        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
 fclose(fichtm);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 }        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 /******************* Gnuplot file **************/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  
         if (popbased==1) {
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          if(mobilav ==0){
   int ng;            for(i=1; i<=nlstate;i++)
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {              prlim[i][i]=probs[(int)age][i][ij];
     printf("Problem with file %s",optionfilegnuplot);          }else{ /* mobilav */ 
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);            for(i=1; i<=nlstate;i++)
   }              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
 #ifdef windows        }
     fprintf(ficgp,"cd \"%s\" \n",pathc);    
 #endif        for(j=1; j<= nlstate; j++){
 m=pow(2,cptcoveff);          for(h=0; h<=nhstepm; h++){
              for(i=1, gp[h][j]=0.;i<=nlstate;i++)
  /* 1eme*/              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   for (cpt=1; cpt<= nlstate ; cpt ++) {          }
    for (k1=1; k1<= m ; k1 ++) {        }
         /* This for computing probability of death (h=1 means
 #ifdef windows           computed over hstepm matrices product = hstepm*stepm months) 
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);           as a weighted average of prlim.
      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);        */
 #endif        for(j=nlstate+1;j<=nlstate+ndeath;j++){
 #ifdef unix          for(i=1,gpp[j]=0.; i<= nlstate; i++)
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);        }    
 #endif        /* end probability of death */
   
 for (i=1; i<= nlstate ; i ++) {        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   else fprintf(ficgp," \%%*lf (\%%*lf)");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);   
     for (i=1; i<= nlstate ; i ++) {        if (popbased==1) {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          if(mobilav ==0){
   else fprintf(ficgp," \%%*lf (\%%*lf)");            for(i=1; i<=nlstate;i++)
 }              prlim[i][i]=probs[(int)age][i][ij];
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          }else{ /* mobilav */ 
      for (i=1; i<= nlstate ; i ++) {            for(i=1; i<=nlstate;i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              prlim[i][i]=mobaverage[(int)age][i][ij];
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }          }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  
 #ifdef unix        for(j=1; j<= nlstate; j++){
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");          for(h=0; h<=nhstepm; h++){
 #endif            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
    }              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   }          }
   /*2 eme*/        }
         /* This for computing probability of death (h=1 means
   for (k1=1; k1<= m ; k1 ++) {           computed over hstepm matrices product = hstepm*stepm months) 
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);           as a weighted average of prlim.
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);        */
            for(j=nlstate+1;j<=nlstate+ndeath;j++){
     for (i=1; i<= nlstate+1 ; i ++) {          for(i=1,gmp[j]=0.; i<= nlstate; i++)
       k=2*i;           gmp[j] += prlim[i][i]*p3mat[i][j][1];
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        }    
       for (j=1; j<= nlstate+1 ; j ++) {        /* end probability of death */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=1; j<= nlstate; j++) /* vareij */
 }            for(h=0; h<=nhstepm; h++){
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          }
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }    
       fprintf(ficgp,"\" t\"\" w l 0,");      } /* End theta */
      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 ++) {      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(h=0; h<=nhstepm; h++) /* veij */
 }          for(j=1; j<=nlstate;j++)
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          for(theta=1; theta <=npar; theta++)
       else fprintf(ficgp,"\" t\"\" w l 0,");            trgradg[h][j][theta]=gradg[h][theta][j];
     }  
   }      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
          for(theta=1; theta <=npar; theta++)
   /*3eme*/          trgradgp[j][theta]=gradgp[theta][j];
     
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<= nlstate ; cpt ++) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       k=2+nlstate*(2*cpt-2);      for(i=1;i<=nlstate;i++)
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        for(j=1;j<=nlstate;j++)
       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);          vareij[i][j][(int)age] =0.;
       /*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) ");      for(h=0;h<=nhstepm;h++){
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        for(k=0;k<=nhstepm;k++){
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
 */              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       for (i=1; i< nlstate ; i ++) {        }
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);      }
     
       }      /* pptj */
     }      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   }      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
        for(j=nlstate+1;j<=nlstate+ndeath;j++)
   /* CV preval stat */        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     for (k1=1; k1<= m ; k1 ++) {          varppt[j][i]=doldmp[j][i];
     for (cpt=1; cpt<nlstate ; cpt ++) {      /* end ppptj */
       k=3;      /*  x centered again */
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       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);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       for (i=1; i< nlstate ; i ++)      if (popbased==1) {
         fprintf(ficgp,"+$%d",k+i+1);        if(mobilav ==0){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          for(i=1; i<=nlstate;i++)
                  prlim[i][i]=probs[(int)age][i][ij];
       l=3+(nlstate+ndeath)*cpt;        }else{ /* mobilav */ 
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          for(i=1; i<=nlstate;i++)
       for (i=1; i< nlstate ; i ++) {            prlim[i][i]=mobaverage[(int)age][i][ij];
         l=3+(nlstate+ndeath)*cpt;        }
         fprintf(ficgp,"+$%d",l+i+1);      }
       }               
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        /* This for computing probability of death (h=1 means
     }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   }           as a weighted average of prlim.
        */
   /* proba elementaires */      for(j=nlstate+1;j<=nlstate+ndeath;j++){
    for(i=1,jk=1; i <=nlstate; i++){        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     for(k=1; k <=(nlstate+ndeath); k++){          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       if (k != i) {      }    
         for(j=1; j <=ncovmodel; j++){      /* end probability of death */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  
           jk++;      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
           fprintf(ficgp,"\n");      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         }        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
       }        for(i=1; i<=nlstate;i++){
     }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
    }        }
       } 
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/      fprintf(ficresprobmorprev,"\n");
      for(jk=1; jk <=m; jk++) {  
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);      fprintf(ficresvij,"%.0f ",age );
        if (ng==2)      for(i=1; i<=nlstate;i++)
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");        for(j=1; j<=nlstate;j++){
        else          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
          fprintf(ficgp,"\nset title \"Probability\"\n");        }
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);      fprintf(ficresvij,"\n");
        i=1;      free_matrix(gp,0,nhstepm,1,nlstate);
        for(k2=1; k2<=nlstate; k2++) {      free_matrix(gm,0,nhstepm,1,nlstate);
          k3=i;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
          for(k=1; k<=(nlstate+ndeath); k++) {      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
            if (k != k2){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              if(ng==2)    } /* End age */
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);    free_vector(gpp,nlstate+1,nlstate+ndeath);
              else    free_vector(gmp,nlstate+1,nlstate+ndeath);
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
              ij=1;    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
              for(j=3; j <=ncovmodel; j++) {    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
                  ij++;  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
                }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
                else  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
              }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
              fprintf(ficgp,")/(1");    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));
              for(k1=1; k1 <=nlstate; k1++){      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(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    /*  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);
                ij=1;  */
                for(j=3; j <=ncovmodel; j++){  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
                    ij++;    free_vector(xp,1,npar);
                  }    free_matrix(doldm,1,nlstate,1,nlstate);
                  else    free_matrix(dnewm,1,nlstate,1,npar);
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                }    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
                fprintf(ficgp,")");    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
              }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);    fclose(ficresprobmorprev);
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    fflush(ficgp);
              i=i+ncovmodel;    fflush(fichtm); 
            }  }  /* end varevsij */
          } /* end k */  
        } /* end k2 */  /************ Variance of prevlim ******************/
      } /* end jk */  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)
    } /* end ng */  {
    fclose(ficgp);    /* Variance of prevalence limit */
 }  /* end gnuplot */    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     double **dnewm,**doldm;
 /*************** Moving average **************/    int i, j, nhstepm, hstepm;
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    int k, cptcode;
     double *xp;
   int i, cpt, cptcod;    double *gp, *gm;
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    double **gradg, **trgradg;
       for (i=1; i<=nlstate;i++)    double age,agelim;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    int theta;
           mobaverage[(int)agedeb][i][cptcod]=0.;     
        fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    fprintf(ficresvpl,"# Age");
       for (i=1; i<=nlstate;i++){    for(i=1; i<=nlstate;i++)
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        fprintf(ficresvpl," %1d-%1d",i,i);
           for (cpt=0;cpt<=4;cpt++){    fprintf(ficresvpl,"\n");
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  
           }    xp=vector(1,npar);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    dnewm=matrix(1,nlstate,1,npar);
         }    doldm=matrix(1,nlstate,1,nlstate);
       }    
     }    hstepm=1*YEARM; /* Every year of age */
        hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
 }    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 /************** Forecasting ******************/      if (stepm >= YEARM) hstepm=1;
 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){      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
        gradg=matrix(1,npar,1,nlstate);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      gp=vector(1,nlstate);
   int *popage;      gm=vector(1,nlstate);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  
   double *popeffectif,*popcount;      for(theta=1; theta <=npar; theta++){
   double ***p3mat;        for(i=1; i<=npar; i++){ /* Computes gradient */
   char fileresf[FILENAMELENGTH];          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
  agelim=AGESUP;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;        for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      
          for(i=1; i<=npar; i++) /* Computes gradient */
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
   strcpy(fileresf,"f");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   strcat(fileresf,fileres);        for(i=1;i<=nlstate;i++)
   if((ficresf=fopen(fileresf,"w"))==NULL) {          gm[i] = prlim[i][i];
     printf("Problem with forecast resultfile: %s\n", fileresf);  
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);        for(i=1;i<=nlstate;i++)
   }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   printf("Computing forecasting: result on file '%s' \n", fileresf);      } /* End theta */
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);  
       trgradg =matrix(1,nlstate,1,npar);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
       for(j=1; j<=nlstate;j++)
   if (mobilav==1) {        for(theta=1; theta <=npar; theta++)
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          trgradg[j][theta]=gradg[theta][j];
     movingaverage(agedeb, fage, ageminpar, mobaverage);  
   }      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
   stepsize=(int) (stepm+YEARM-1)/YEARM;      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   if (stepm<=12) stepsize=1;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
        for(i=1;i<=nlstate;i++)
   agelim=AGESUP;        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
    
   hstepm=1;      fprintf(ficresvpl,"%.0f ",age );
   hstepm=hstepm/stepm;      for(i=1; i<=nlstate;i++)
   yp1=modf(dateintmean,&yp);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   anprojmean=yp;      fprintf(ficresvpl,"\n");
   yp2=modf((yp1*12),&yp);      free_vector(gp,1,nlstate);
   mprojmean=yp;      free_vector(gm,1,nlstate);
   yp1=modf((yp2*30.5),&yp);      free_matrix(gradg,1,npar,1,nlstate);
   jprojmean=yp;      free_matrix(trgradg,1,nlstate,1,npar);
   if(jprojmean==0) jprojmean=1;    } /* End age */
   if(mprojmean==0) jprojmean=1;  
      free_vector(xp,1,npar);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    free_matrix(doldm,1,nlstate,1,npar);
      free_matrix(dnewm,1,nlstate,1,nlstate);
   for(cptcov=1;cptcov<=i2;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  }
       k=k+1;  
       fprintf(ficresf,"\n#******");  /************ Variance of one-step probabilities  ******************/
       for(j=1;j<=cptcoveff;j++) {  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  {
       }    int i, j=0,  i1, k1, l1, t, tj;
       fprintf(ficresf,"******\n");    int k2, l2, j1,  z1;
       fprintf(ficresf,"# StartingAge FinalAge");    int k=0,l, cptcode;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    int first=1, first1;
          double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
          double **dnewm,**doldm;
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    double *xp;
         fprintf(ficresf,"\n");    double *gp, *gm;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      double **gradg, **trgradg;
     double **mu;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    double age,agelim, cov[NCOVMAX];
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
           nhstepm = nhstepm/hstepm;    int theta;
              char fileresprob[FILENAMELENGTH];
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    char fileresprobcov[FILENAMELENGTH];
           oldm=oldms;savm=savms;    char fileresprobcor[FILENAMELENGTH];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
            double ***varpij;
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {    strcpy(fileresprob,"prob"); 
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    strcat(fileresprob,fileres);
             }    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
             for(j=1; j<=nlstate+ndeath;j++) {      printf("Problem with resultfile: %s\n", fileresprob);
               kk1=0.;kk2=0;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
               for(i=1; i<=nlstate;i++) {                  }
                 if (mobilav==1)    strcpy(fileresprobcov,"probcov"); 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    strcat(fileresprobcov,fileres);
                 else {    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      printf("Problem with resultfile: %s\n", fileresprobcov);
                 }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
                    }
               }    strcpy(fileresprobcor,"probcor"); 
               if (h==(int)(calagedate+12*cpt)){    strcat(fileresprobcor,fileres);
                 fprintf(ficresf," %.3f", kk1);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
                              printf("Problem with resultfile: %s\n", fileresprobcor);
               }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
             }    }
           }    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
         }    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       }    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     }    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   }    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
            
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
   fclose(ficresf);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
 }    fprintf(ficresprobcov,"# Age");
 /************** Forecasting ******************/    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){    fprintf(ficresprobcov,"# Age");
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  
   int *popage;    for(i=1; i<=nlstate;i++)
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      for(j=1; j<=(nlstate+ndeath);j++){
   double *popeffectif,*popcount;        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   double ***p3mat,***tabpop,***tabpopprev;        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   char filerespop[FILENAMELENGTH];        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   /* fprintf(ficresprob,"\n");
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficresprobcov,"\n");
   agelim=AGESUP;    fprintf(ficresprobcor,"\n");
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;   */
     xp=vector(1,npar);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   strcpy(filerespop,"pop");    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   strcat(filerespop,fileres);    first=1;
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    fprintf(ficgp,"\n# Routine varprob");
     printf("Problem with forecast resultfile: %s\n", filerespop);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);    fprintf(fichtm,"\n");
   }  
   printf("Computing forecasting: result on file '%s' \n", filerespop);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    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.\
   if (mobilav==1) {   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    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. \
     movingaverage(agedeb, fage, ageminpar, mobaverage);  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   }  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
   stepsize=(int) (stepm+YEARM-1)/YEARM;   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
   if (stepm<=12) stepsize=1;   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
    To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   agelim=AGESUP;  
      cov[1]=1;
   hstepm=1;    tj=cptcoveff;
   hstepm=hstepm/stepm;    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
      j1=0;
   if (popforecast==1) {    for(t=1; t<=tj;t++){
     if((ficpop=fopen(popfile,"r"))==NULL) {      for(i1=1; i1<=ncodemax[t];i1++){ 
       printf("Problem with population file : %s\n",popfile);exit(0);        j1++;
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);        if  (cptcovn>0) {
     }          fprintf(ficresprob, "\n#********** Variable "); 
     popage=ivector(0,AGESUP);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     popeffectif=vector(0,AGESUP);          fprintf(ficresprob, "**********\n#\n");
     popcount=vector(0,AGESUP);          fprintf(ficresprobcov, "\n#********** Variable "); 
              for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     i=1;            fprintf(ficresprobcov, "**********\n#\n");
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;          
              fprintf(ficgp, "\n#********** Variable "); 
     imx=i;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          fprintf(ficgp, "**********\n#\n");
   }          
           
   for(cptcov=1;cptcov<=i2;cptcov++){          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       k=k+1;          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
       fprintf(ficrespop,"\n#******");          
       for(j=1;j<=cptcoveff;j++) {          fprintf(ficresprobcor, "\n#********** Variable ");    
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       }          fprintf(ficresprobcor, "**********\n#");    
       fprintf(ficrespop,"******\n");        }
       fprintf(ficrespop,"# Age");        
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);        for (age=bage; age<=fage; age ++){ 
       if (popforecast==1)  fprintf(ficrespop," [Population]");          cov[2]=age;
                for (k=1; k<=cptcovn;k++) {
       for (cpt=0; cpt<=0;cpt++) {            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            }
                  for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          for (k=1; k<=cptcovprod;k++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           nhstepm = nhstepm/hstepm;          
                    gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           oldm=oldms;savm=savms;          gp=vector(1,(nlstate)*(nlstate+ndeath));
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            gm=vector(1,(nlstate)*(nlstate+ndeath));
              
           for (h=0; h<=nhstepm; h++){          for(theta=1; theta <=npar; theta++){
             if (h==(int) (calagedate+YEARM*cpt)) {            for(i=1; i<=npar; i++)
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             }            
             for(j=1; j<=nlstate+ndeath;j++) {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
               kk1=0.;kk2=0;            
               for(i=1; i<=nlstate;i++) {                          k=0;
                 if (mobilav==1)            for(i=1; i<= (nlstate); i++){
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];              for(j=1; j<=(nlstate+ndeath);j++){
                 else {                k=k+1;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                gp[k]=pmmij[i][j];
                 }              }
               }            }
               if (h==(int)(calagedate+12*cpt)){            
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;            for(i=1; i<=npar; i++)
                   /*fprintf(ficrespop," %.3f", kk1);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      
               }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             }            k=0;
             for(i=1; i<=nlstate;i++){            for(i=1; i<=(nlstate); i++){
               kk1=0.;              for(j=1; j<=(nlstate+ndeath);j++){
                 for(j=1; j<=nlstate;j++){                k=k+1;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];                gm[k]=pmmij[i][j];
                 }              }
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];            }
             }       
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);          }
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
         }            for(theta=1; theta <=npar; theta++)
       }              trgradg[j][theta]=gradg[theta][j];
            
   /******/          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           nhstepm = nhstepm/hstepm;  
                    pmij(pmmij,cov,ncovmodel,x,nlstate);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          
           oldm=oldms;savm=savms;          k=0;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            for(i=1; i<=(nlstate); i++){
           for (h=0; h<=nhstepm; h++){            for(j=1; j<=(nlstate+ndeath);j++){
             if (h==(int) (calagedate+YEARM*cpt)) {              k=k+1;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);              mu[k][(int) age]=pmmij[i][j];
             }            }
             for(j=1; j<=nlstate+ndeath;j++) {          }
               kk1=0.;kk2=0;          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
               for(i=1; i<=nlstate;i++) {                          for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                  varpij[i][j][(int)age] = doldm[i][j];
               }  
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);          /*printf("\n%d ",(int)age);
             }            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
           }            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         }            }*/
       }  
    }          fprintf(ficresprob,"\n%d ",(int)age);
   }          fprintf(ficresprobcov,"\n%d ",(int)age);
            fprintf(ficresprobcor,"\n%d ",(int)age);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   if (popforecast==1) {            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     free_ivector(popage,0,AGESUP);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     free_vector(popeffectif,0,AGESUP);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     free_vector(popcount,0,AGESUP);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   }          }
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          i=0;
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for (k=1; k<=(nlstate);k++){
   fclose(ficrespop);            for (l=1; l<=(nlstate+ndeath);l++){ 
 }              i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
 /***********************************************/              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
 /**************** Main Program *****************/              for (j=1; j<=i;j++){
 /***********************************************/                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
 int main(int argc, char *argv[])              }
 {            }
           }/* end of loop for state */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        } /* end of loop for age */
   double agedeb, agefin,hf;  
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;        /* Confidence intervalle of pij  */
         /*
   double fret;          fprintf(ficgp,"\nset noparametric;unset label");
   double **xi,tmp,delta;          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   double dum; /* Dummy variable */          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);
   double ***p3mat;          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   int *indx;          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   char line[MAXLINE], linepar[MAXLINE];          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];        */
   int firstobs=1, lastobs=10;  
   int sdeb, sfin; /* Status at beginning and end */        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   int c,  h , cpt,l;        first1=1;
   int ju,jl, mi;        for (k2=1; k2<=(nlstate);k2++){
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            if(l2==k2) continue;
   int mobilav=0,popforecast=0;            j=(k2-1)*(nlstate+ndeath)+l2;
   int hstepm, nhstepm;            for (k1=1; k1<=(nlstate);k1++){
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
   double bage, fage, age, agelim, agebase;                i=(k1-1)*(nlstate+ndeath)+l1;
   double ftolpl=FTOL;                if(i<=j) continue;
   double **prlim;                for (age=bage; age<=fage; age ++){ 
   double *severity;                  if ((int)age %5==0){
   double ***param; /* Matrix of parameters */                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   double  *p;                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   double **matcov; /* Matrix of covariance */                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   double ***delti3; /* Scale */                    mu1=mu[i][(int) age]/stepm*YEARM ;
   double *delti; /* Scale */                    mu2=mu[j][(int) age]/stepm*YEARM;
   double ***eij, ***vareij;                    c12=cv12/sqrt(v1*v2);
   double **varpl; /* Variances of prevalence limits by age */                    /* Computing eigen value of matrix of covariance */
   double *epj, vepp;                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   double kk1, kk2;                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;                    /* Eigen vectors */
                      v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
   char *alph[]={"a","a","b","c","d","e"}, str[4];                    v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
   char z[1]="c", occ;                    tnalp=v21/v11;
 #include <sys/time.h>                    if(first1==1){
 #include <time.h>                      first1=0;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];                      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);
                      }
   /* long total_usecs;                    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);
   struct timeval start_time, end_time;                    /*printf(fignu*/
                      /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   getcwd(pathcd, size);                    if(first==1){
                       first=0;
   printf("\n%s",version);                      fprintf(ficgp,"\nset parametric;unset label");
   if(argc <=1){                      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);
     printf("\nEnter the parameter file name: ");                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     scanf("%s",pathtot);                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   }   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   else{  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
     strcpy(pathtot,argv[1]);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
   }                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   /*cygwin_split_path(pathtot,path,optionfile);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   /* cutv(path,optionfile,pathtot,'\\');*/                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);                      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",\
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   chdir(path);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   replace(pathc,path);                    }else{
                       first=0;
 /*-------- arguments in the command line --------*/                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   /* Log file */                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   strcat(filelog, optionfilefiname);                      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",\
   strcat(filelog,".log");    /* */                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   if((ficlog=fopen(filelog,"w"))==NULL)    {                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     printf("Problem with logfile %s\n",filelog);                    }/* if first */
     goto end;                  } /* age mod 5 */
   }                } /* end loop age */
   fprintf(ficlog,"Log filename:%s\n",filelog);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   fprintf(ficlog,"\n%s",version);                first=1;
   fprintf(ficlog,"\nEnter the parameter file name: ");              } /*l12 */
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);            } /* k12 */
   fflush(ficlog);          } /*l1 */
         }/* k1 */
   /* */      } /* loop covariates */
   strcpy(fileres,"r");    }
   strcat(fileres, optionfilefiname);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   strcat(fileres,".txt");    /* Other files have txt extension */    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
   /*---------arguments file --------*/    fclose(ficresprob);
     fclose(ficresprobcov);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    fclose(ficresprobcor);
     printf("Problem with optionfile %s\n",optionfile);    fflush(ficgp);
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);    fflush(fichtmcov);
     goto end;  }
   }  
   
   strcpy(filereso,"o");  /******************* Printing html file ***********/
   strcat(filereso,fileres);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   if((ficparo=fopen(filereso,"w"))==NULL) {                    int lastpass, int stepm, int weightopt, char model[],\
     printf("Problem with Output resultfile: %s\n", filereso);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);                    int popforecast, int estepm ,\
     goto end;                    double jprev1, double mprev1,double anprev1, \
   }                    double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
     ungetc(c,ficpar);   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
     fgets(line, MAXLINE, ficpar);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
     puts(line);     fprintf(fichtm,"\
     fputs(line,ficparo);   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
   }             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
   ungetc(c,ficpar);     fprintf(fichtm,"\
    - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
   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);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);     fprintf(fichtm,"\
   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);   - Life expectancies by age and initial health status (estepm=%2d months): \
 while((c=getc(ficpar))=='#' && c!= EOF){     <a href=\"%s\">%s</a> <br>\n</li>",
     ungetc(c,ficpar);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
     fgets(line, MAXLINE, ficpar);  
     puts(line);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     fputs(line,ficparo);  
   }   m=cptcoveff;
   ungetc(c,ficpar);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    
       jj1=0;
   covar=matrix(0,NCOVMAX,1,n);   for(k1=1; k1<=m;k1++){
   cptcovn=0;     for(i1=1; i1<=ncodemax[k1];i1++){
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;       jj1++;
        if (cptcovn > 0) {
   ncovmodel=2+cptcovn;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */         for (cpt=1; cpt<=cptcoveff;cpt++) 
             fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   /* Read guess parameters */         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   /* Reads comments: lines beginning with '#' */       }
   while((c=getc(ficpar))=='#' && c!= EOF){       /* Pij */
     ungetc(c,ficpar);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
     fgets(line, MAXLINE, ficpar);  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
     puts(line);       /* Quasi-incidences */
     fputs(line,ficparo);       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: %s%d2.png<br> \
   ungetc(c,ficpar);  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
           /* Stable prevalence in each health state */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);         for(cpt=1; cpt<nlstate;cpt++){
     for(i=1; i <=nlstate; i++)           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
     for(j=1; j <=nlstate+ndeath-1; j++){  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
       fscanf(ficpar,"%1d%1d",&i1,&j1);         }
       fprintf(ficparo,"%1d%1d",i1,j1);       for(cpt=1; cpt<=nlstate;cpt++) {
       if(mle==1)          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
         printf("%1d%1d",i,j);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
       fprintf(ficlog,"%1d%1d",i,j);       }
       for(k=1; k<=ncovmodel;k++){     } /* end i1 */
         fscanf(ficpar," %lf",&param[i][j][k]);   }/* End k1 */
         if(mle==1){   fprintf(fichtm,"</ul>");
           printf(" %lf",param[i][j][k]);  
           fprintf(ficlog," %lf",param[i][j][k]);  
         }   fprintf(fichtm,"\
         else  \n<br><li><h4> Result files (second order: variances)</h4>\n\
           fprintf(ficlog," %lf",param[i][j][k]);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
         fprintf(ficparo," %lf",param[i][j][k]);  
       }   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
       fscanf(ficpar,"\n");           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
       if(mle==1)   fprintf(fichtm,"\
         printf("\n");   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
       fprintf(ficlog,"\n");           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
       fprintf(ficparo,"\n");  
     }   fprintf(fichtm,"\
     - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
   p=param[1][1];   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
             estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
   /* Reads comments: lines beginning with '#' */   fprintf(fichtm,"\
   while((c=getc(ficpar))=='#' && c!= EOF){   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
     ungetc(c,ficpar);           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
     fgets(line, MAXLINE, ficpar);   fprintf(fichtm,"\
     puts(line);   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
     fputs(line,ficparo);           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   }  
   ungetc(c,ficpar);  /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  /*      <br>",fileres,fileres,fileres,fileres); */
   for(i=1; i <=nlstate; i++){  /*  else  */
     for(j=1; j <=nlstate+ndeath-1; j++){  /*    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); */
       fscanf(ficpar,"%1d%1d",&i1,&j1);   fflush(fichtm);
       printf("%1d%1d",i,j);   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
       fprintf(ficparo,"%1d%1d",i1,j1);  
       for(k=1; k<=ncovmodel;k++){   m=cptcoveff;
         fscanf(ficpar,"%le",&delti3[i][j][k]);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
         printf(" %le",delti3[i][j][k]);  
         fprintf(ficparo," %le",delti3[i][j][k]);   jj1=0;
       }   for(k1=1; k1<=m;k1++){
       fscanf(ficpar,"\n");     for(i1=1; i1<=ncodemax[k1];i1++){
       printf("\n");       jj1++;
       fprintf(ficparo,"\n");       if (cptcovn > 0) {
     }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   }         for (cpt=1; cpt<=cptcoveff;cpt++) 
   delti=delti3[1][1];           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   /* Reads comments: lines beginning with '#' */       }
   while((c=getc(ficpar))=='#' && c!= EOF){       for(cpt=1; cpt<=nlstate;cpt++) {
     ungetc(c,ficpar);         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
     fgets(line, MAXLINE, ficpar);  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
     puts(line);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
     fputs(line,ficparo);       }
   }       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   ungetc(c,ficpar);  health expectancies in states (1) and (2): %s%d.png<br>\
    <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
   matcov=matrix(1,npar,1,npar);     } /* end i1 */
   for(i=1; i <=npar; i++){   }/* End k1 */
     fscanf(ficpar,"%s",&str);   fprintf(fichtm,"</ul>");
     if(mle==1)   fflush(fichtm);
       printf("%s",str);  }
     fprintf(ficlog,"%s",str);  
     fprintf(ficparo,"%s",str);  /******************* Gnuplot file **************/
     for(j=1; j <=i; j++){  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
       fscanf(ficpar," %le",&matcov[i][j]);  
       if(mle==1){    char dirfileres[132],optfileres[132];
         printf(" %.5le",matcov[i][j]);    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
         fprintf(ficlog," %.5le",matcov[i][j]);    int ng;
       }  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
       else  /*     printf("Problem with file %s",optionfilegnuplot); */
         fprintf(ficlog," %.5le",matcov[i][j]);  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
       fprintf(ficparo," %.5le",matcov[i][j]);  /*   } */
     }  
     fscanf(ficpar,"\n");    /*#ifdef windows */
     if(mle==1)    fprintf(ficgp,"cd \"%s\" \n",pathc);
       printf("\n");      /*#endif */
     fprintf(ficlog,"\n");    m=pow(2,cptcoveff);
     fprintf(ficparo,"\n");  
   }    strcpy(dirfileres,optionfilefiname);
   for(i=1; i <=npar; i++)    strcpy(optfileres,"vpl");
     for(j=i+1;j<=npar;j++)   /* 1eme*/
       matcov[i][j]=matcov[j][i];    for (cpt=1; cpt<= nlstate ; cpt ++) {
         for (k1=1; k1<= m ; k1 ++) {
   if(mle==1)       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
     printf("\n");       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
   fprintf(ficlog,"\n");       fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
     /*-------- Rewriting paramater file ----------*/  set size 0.65,0.65\n\
      strcpy(rfileres,"r");    /* "Rparameterfile */  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/  
      strcat(rfileres,".");    /* */       for (i=1; i<= nlstate ; i ++) {
      strcat(rfileres,optionfilext);    /* Other files have txt extension */         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     if((ficres =fopen(rfileres,"w"))==NULL) {         else fprintf(ficgp," \%%*lf (\%%*lf)");
       printf("Problem writing new parameter file: %s\n", fileres);goto end;       }
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;       fprintf(ficgp,"\" t\"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 ++) {
     fprintf(ficres,"#%s\n",version);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
             else fprintf(ficgp," \%%*lf (\%%*lf)");
     /*-------- data file ----------*/       } 
     if((fic=fopen(datafile,"r"))==NULL)    {       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
       printf("Problem with datafile: %s\n", datafile);goto end;       for (i=1; i<= nlstate ; i ++) {
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     }         else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
     n= lastobs;       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
     severity = vector(1,maxwav);     }
     outcome=imatrix(1,maxwav+1,1,n);    }
     num=ivector(1,n);    /*2 eme*/
     moisnais=vector(1,n);    
     annais=vector(1,n);    for (k1=1; k1<= m ; k1 ++) { 
     moisdc=vector(1,n);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
     andc=vector(1,n);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
     agedc=vector(1,n);      
     cod=ivector(1,n);      for (i=1; i<= nlstate+1 ; i ++) {
     weight=vector(1,n);        k=2*i;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     mint=matrix(1,maxwav,1,n);        for (j=1; j<= nlstate+1 ; j ++) {
     anint=matrix(1,maxwav,1,n);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     s=imatrix(1,maxwav+1,1,n);          else fprintf(ficgp," \%%*lf (\%%*lf)");
     adl=imatrix(1,maxwav+1,1,n);            }   
     tab=ivector(1,NCOVMAX);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
     ncodemax=ivector(1,8);        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);
     i=1;        for (j=1; j<= nlstate+1 ; j ++) {
     while (fgets(line, MAXLINE, fic) != NULL)    {          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       if ((i >= firstobs) && (i <=lastobs)) {          else fprintf(ficgp," \%%*lf (\%%*lf)");
                }   
         for (j=maxwav;j>=1;j--){        fprintf(ficgp,"\" t\"\" w l 0,");
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
           strcpy(line,stra);        for (j=1; j<= nlstate+1 ; j ++) {
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }        }   
                if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        else fprintf(ficgp,"\" t\"\" w l 0,");
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      }
     }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    /*3eme*/
     
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    for (k1=1; k1<= m ; k1 ++) { 
         for (j=ncovcol;j>=1;j--){      for (cpt=1; cpt<= nlstate ; cpt ++) {
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        k=2+nlstate*(2*cpt-2);
         }        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         num[i]=atol(stra);        fprintf(ficgp,"set ter png small\n\
          set size 0.65,0.65\n\
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){  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);
           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,",\"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) ");
         i=i+1;          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       }          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     }          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     /* printf("ii=%d", ij);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
        scanf("%d",i);*/          
   imx=i-1; /* Number of individuals */        */
         for (i=1; i< nlstate ; i ++) {
   /* for (i=1; i<=imx; i++){          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);
     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;    /* CV preval stable (period) */
      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]));}*/    for (k1=1; k1<= m ; k1 ++) { 
        for (cpt=1; cpt<=nlstate ; cpt ++) {
          k=3;
   /* Calculation of the number of parameter from char model*/        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   Tprod=ivector(1,15);  set ter png small\nset size 0.65,0.65\n\
   Tvaraff=ivector(1,15);  unset log y\n\
   Tvard=imatrix(1,15,1,2);  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
   Tage=ivector(1,15);              
            for (i=1; i< nlstate ; i ++)
   if (strlen(model) >1){          fprintf(ficgp,"+$%d",k+i+1);
     j=0, j1=0, k1=1, k2=1;        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
     j=nbocc(model,'+');        
     j1=nbocc(model,'*');        l=3+(nlstate+ndeath)*cpt;
     cptcovn=j+1;        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
     cptcovprod=j1;        for (i=1; i< nlstate ; i ++) {
              l=3+(nlstate+ndeath)*cpt;
     strcpy(modelsav,model);          fprintf(ficgp,"+$%d",l+i+1);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        }
       printf("Error. Non available option model=%s ",model);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       fprintf(ficlog,"Error. Non available option model=%s ",model);      } 
       goto end;    }  
     }    
        /* proba elementaires */
     for(i=(j+1); i>=1;i--){    for(i=1,jk=1; i <=nlstate; i++){
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */      for(k=1; k <=(nlstate+ndeath); k++){
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */        if (k != i) {
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/          for(j=1; j <=ncovmodel; j++){
       /*scanf("%d",i);*/            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
       if (strchr(strb,'*')) {  /* Model includes a product */            jk++; 
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/            fprintf(ficgp,"\n");
         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;     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
             /*printf("stre=%s ", stre);*/       for(jk=1; jk <=m; jk++) {
         }         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
         else if (strcmp(strd,"age")==0) { /* or age*Vn */         if (ng==2)
           cptcovprod--;           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
           cutv(strb,stre,strc,'V');         else
           Tvar[i]=atoi(stre);           fprintf(ficgp,"\nset title \"Probability\"\n");
           cptcovage++;         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
           Tage[cptcovage]=i;         i=1;
         }         for(k2=1; k2<=nlstate; k2++) {
         else {  /* Age is not in the model */           k3=i;
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/           for(k=1; k<=(nlstate+ndeath); k++) {
           Tvar[i]=ncovcol+k1;             if (k != k2){
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */               if(ng==2)
           Tprod[k1]=i;                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
           Tvard[k1][1]=atoi(strc); /* m*/               else
           Tvard[k1][2]=atoi(stre); /* n */                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
           Tvar[cptcovn+k2]=Tvard[k1][1];               ij=1;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];               for(j=3; j <=ncovmodel; j++) {
           for (k=1; k<=lastobs;k++)                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
           k1++;                   ij++;
           k2=k2+2;                 }
         }                 else
       }                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       else { /* no more sum */               }
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/               fprintf(ficgp,")/(1");
        /*  scanf("%d",i);*/               
       cutv(strd,strc,strb,'V');               for(k1=1; k1 <=nlstate; k1++){   
       Tvar[i]=atoi(strc);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
       }                 ij=1;
       strcpy(modelsav,stra);                   for(j=3; j <=ncovmodel; j++){
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
         scanf("%d",i);*/                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     } /* end of loop + */                     ij++;
   } /* end model */                   }
                     else
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   printf("cptcovprod=%d ", cptcovprod);                 }
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);                 fprintf(ficgp,")");
   scanf("%d ",i);*/               }
     fclose(fic);               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     /*  if(mle==1){*/               i=i+ncovmodel;
     if (weightopt != 1) { /* Maximisation without weights*/             }
       for(i=1;i<=n;i++) weight[i]=1.0;           } /* end k */
     }         } /* end k2 */
     /*-calculation of age at interview from date of interview and age at death -*/       } /* end jk */
     agev=matrix(1,maxwav,1,imx);     } /* end ng */
      fflush(ficgp); 
     for (i=1; i<=imx; i++) {  }  /* end gnuplot */
       for(m=2; (m<= maxwav); m++) {  
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  
          anint[m][i]=9999;  /*************** Moving average **************/
          s[m][i]=-1;  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
        }  
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    int i, cpt, cptcod;
       }    int modcovmax =1;
     }    int mobilavrange, mob;
     double age;
     for (i=1; i<=imx; i++)  {  
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
       for(m=1; (m<= maxwav); m++){                             a covariate has 2 modalities */
         if(s[m][i] >0){    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
           if (s[m][i] >= nlstate+1) {  
             if(agedc[i]>0)    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
               if(moisdc[i]!=99 && andc[i]!=9999)      if(mobilav==1) mobilavrange=5; /* default */
                 agev[m][i]=agedc[i];      else mobilavrange=mobilav;
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/      for (age=bage; age<=fage; age++)
            else {        for (i=1; i<=nlstate;i++)
               if (andc[i]!=9999){          for (cptcod=1;cptcod<=modcovmax;cptcod++)
               printf("Warning negative age at death: %d line:%d\n",num[i],i);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);      /* We keep the original values on the extreme ages bage, fage and for 
               agev[m][i]=-1;         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
               }         we use a 5 terms etc. until the borders are no more concerned. 
             }      */ 
           }      for (mob=3;mob <=mobilavrange;mob=mob+2){
           else if(s[m][i] !=9){ /* Should no more exist */        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          for (i=1; i<=nlstate;i++){
             if(mint[m][i]==99 || anint[m][i]==9999)            for (cptcod=1;cptcod<=modcovmax;cptcod++){
               agev[m][i]=1;              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
             else if(agev[m][i] <agemin){                for (cpt=1;cpt<=(mob-1)/2;cpt++){
               agemin=agev[m][i];                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
             }                }
             else if(agev[m][i] >agemax){              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
               agemax=agev[m][i];            }
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/          }
             }        }/* end age */
             /*agev[m][i]=anint[m][i]-annais[i];*/      }/* end mob */
             /*   agev[m][i] = age[i]+2*m;*/    }else return -1;
           }    return 0;
           else { /* =9 */  }/* End movingaverage */
             agev[m][i]=1;  
             s[m][i]=-1;  
           }  /************** Forecasting ******************/
         }  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){
         else /*= 0 Unknown */    /* proj1, year, month, day of starting projection 
           agev[m][i]=1;       agemin, agemax range of age
       }       dateprev1 dateprev2 range of dates during which prevalence is computed
           anproj2 year of en of projection (same day and month as proj1).
     }    */
     for (i=1; i<=imx; i++)  {    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
       for(m=1; (m<= maxwav); m++){    int *popage;
         if (s[m][i] > (nlstate+ndeath)) {    double agec; /* generic age */
           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);      double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
           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);      double *popeffectif,*popcount;
           goto end;    double ***p3mat;
         }    double ***mobaverage;
       }    char fileresf[FILENAMELENGTH];
     }  
     agelim=AGESUP;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);   
     strcpy(fileresf,"f"); 
     free_vector(severity,1,maxwav);    strcat(fileresf,fileres);
     free_imatrix(outcome,1,maxwav+1,1,n);    if((ficresf=fopen(fileresf,"w"))==NULL) {
     free_vector(moisnais,1,n);      printf("Problem with forecast resultfile: %s\n", fileresf);
     free_vector(annais,1,n);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     /* free_matrix(mint,1,maxwav,1,n);    }
        free_matrix(anint,1,maxwav,1,n);*/    printf("Computing forecasting: result on file '%s' \n", fileresf);
     free_vector(moisdc,1,n);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
     free_vector(andc,1,n);  
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
      
     wav=ivector(1,imx);    if (mobilav!=0) {
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
            fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     /* Concatenates waves */        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      }
     }
   
       Tcode=ivector(1,100);    stepsize=(int) (stepm+YEARM-1)/YEARM;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    if (stepm<=12) stepsize=1;
       ncodemax[1]=1;    if(estepm < stepm){
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      printf ("Problem %d lower than %d\n",estepm, stepm);
          }
    codtab=imatrix(1,100,1,10);    else  hstepm=estepm;   
    h=0;  
    m=pow(2,cptcoveff);    hstepm=hstepm/stepm; 
      yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
    for(k=1;k<=cptcoveff; k++){                                 fractional in yp1 */
      for(i=1; i <=(m/pow(2,k));i++){    anprojmean=yp;
        for(j=1; j <= ncodemax[k]; j++){    yp2=modf((yp1*12),&yp);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    mprojmean=yp;
            h++;    yp1=modf((yp2*30.5),&yp);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    jprojmean=yp;
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/    if(jprojmean==0) jprojmean=1;
          }    if(mprojmean==0) jprojmean=1;
        }  
      }    i1=cptcoveff;
    }    if (cptcovn < 1){i1=1;}
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    
       codtab[1][2]=1;codtab[2][2]=2; */    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
    /* for(i=1; i <=m ;i++){    
       for(k=1; k <=cptcovn; k++){    fprintf(ficresf,"#****** Routine prevforecast **\n");
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);  
       }  /*            if (h==(int)(YEARM*yearp)){ */
       printf("\n");    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       }      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       scanf("%d",i);*/        k=k+1;
            fprintf(ficresf,"\n#******");
    /* Calculates basic frequencies. Computes observed prevalence at single age        for(j=1;j<=cptcoveff;j++) {
        and prints on file fileres'p'. */          fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
            fprintf(ficresf,"******\n");
            fprintf(ficresf,"# Covariate valuofcovar yearproj age");
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(j=1; j<=nlstate+ndeath;j++){ 
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(i=1; i<=nlstate;i++)              
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            fprintf(ficresf," p%d%d",i,j);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficresf," p.%d",j);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        }
              for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
     /* For Powell, parameters are in a vector p[] starting at p[1]          fprintf(ficresf,"\n");
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
     if(mle==1){            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);            nhstepm = nhstepm/hstepm; 
     }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                oldm=oldms;savm=savms;
     /*--------- results files --------------*/            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);          
              for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
    jk=1;                fprintf(ficresf,"\n");
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");                for(j=1;j<=cptcoveff;j++) 
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
    for(i=1,jk=1; i <=nlstate; i++){              } 
      for(k=1; k <=(nlstate+ndeath); k++){              for(j=1; j<=nlstate+ndeath;j++) {
        if (k != i)                ppij=0.;
          {                for(i=1; i<=nlstate;i++) {
            printf("%d%d ",i,k);                  if (mobilav==1) 
            fprintf(ficlog,"%d%d ",i,k);                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
            fprintf(ficres,"%1d%1d ",i,k);                  else {
            for(j=1; j <=ncovmodel; j++){                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
              printf("%f ",p[jk]);                  }
              fprintf(ficlog,"%f ",p[jk]);                  if (h*hstepm/YEARM*stepm== yearp) {
              fprintf(ficres,"%f ",p[jk]);                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
              jk++;                  }
            }                } /* end i */
            printf("\n");                if (h*hstepm/YEARM*stepm==yearp) {
            fprintf(ficlog,"\n");                  fprintf(ficresf," %.3f", ppij);
            fprintf(ficres,"\n");                }
          }              }/* end j */
      }            } /* end h */
    }            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    if(mle==1){          } /* end agec */
      /* Computing hessian and covariance matrix */        } /* end yearp */
      ftolhess=ftol; /* Usually correct */      } /* end cptcod */
      hesscov(matcov, p, npar, delti, ftolhess, func);    } /* end  cptcov */
    }         
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    printf("# Scales (for hessian or gradient estimation)\n");  
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");    fclose(ficresf);
    for(i=1,jk=1; i <=nlstate; i++){  }
      for(j=1; j <=nlstate+ndeath; j++){  
        if (j!=i) {  /************** Forecasting *****not tested NB*************/
          fprintf(ficres,"%1d%1d",i,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){
          printf("%1d%1d",i,j);    
          fprintf(ficlog,"%1d%1d",i,j);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
          for(k=1; k<=ncovmodel;k++){    int *popage;
            printf(" %.5e",delti[jk]);    double calagedatem, agelim, kk1, kk2;
            fprintf(ficlog," %.5e",delti[jk]);    double *popeffectif,*popcount;
            fprintf(ficres," %.5e",delti[jk]);    double ***p3mat,***tabpop,***tabpopprev;
            jk++;    double ***mobaverage;
          }    char filerespop[FILENAMELENGTH];
          printf("\n");  
          fprintf(ficlog,"\n");    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
          fprintf(ficres,"\n");    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        }    agelim=AGESUP;
      }    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
    }    
        prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    k=1;    
    fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    
    if(mle==1)    strcpy(filerespop,"pop"); 
      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");    strcat(filerespop,fileres);
    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");    if((ficrespop=fopen(filerespop,"w"))==NULL) {
    for(i=1;i<=npar;i++){      printf("Problem with forecast resultfile: %s\n", filerespop);
      /*  if (k>nlstate) k=1;      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
          i1=(i-1)/(ncovmodel*nlstate)+1;    }
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    printf("Computing forecasting: result on file '%s' \n", filerespop);
          printf("%s%d%d",alph[k],i1,tab[i]);*/    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
      fprintf(ficres,"%3d",i);  
      if(mle==1)    if (cptcoveff==0) ncodemax[cptcoveff]=1;
        printf("%3d",i);  
      fprintf(ficlog,"%3d",i);    if (mobilav!=0) {
      for(j=1; j<=i;j++){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        fprintf(ficres," %.5e",matcov[i][j]);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
        if(mle==1)        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
          printf(" %.5e",matcov[i][j]);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
        fprintf(ficlog," %.5e",matcov[i][j]);      }
      }    }
      fprintf(ficres,"\n");  
      if(mle==1)    stepsize=(int) (stepm+YEARM-1)/YEARM;
        printf("\n");    if (stepm<=12) stepsize=1;
      fprintf(ficlog,"\n");    
      k++;    agelim=AGESUP;
    }    
        hstepm=1;
    while((c=getc(ficpar))=='#' && c!= EOF){    hstepm=hstepm/stepm; 
      ungetc(c,ficpar);    
      fgets(line, MAXLINE, ficpar);    if (popforecast==1) {
      puts(line);      if((ficpop=fopen(popfile,"r"))==NULL) {
      fputs(line,ficparo);        printf("Problem with population file : %s\n",popfile);exit(0);
    }        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
    ungetc(c,ficpar);      } 
    estepm=0;      popage=ivector(0,AGESUP);
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);      popeffectif=vector(0,AGESUP);
    if (estepm==0 || estepm < stepm) estepm=stepm;      popcount=vector(0,AGESUP);
    if (fage <= 2) {      
      bage = ageminpar;      i=1;   
      fage = agemaxpar;      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
    }     
          imx=i;
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
    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);  
        for(cptcov=1,k=0;cptcov<=i2;cptcov++){
    while((c=getc(ficpar))=='#' && c!= EOF){     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
      ungetc(c,ficpar);        k=k+1;
      fgets(line, MAXLINE, ficpar);        fprintf(ficrespop,"\n#******");
      puts(line);        for(j=1;j<=cptcoveff;j++) {
      fputs(line,ficparo);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
    }        }
    ungetc(c,ficpar);        fprintf(ficrespop,"******\n");
          fprintf(ficrespop,"# Age");
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        if (popforecast==1)  fprintf(ficrespop," [Population]");
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        
            for (cpt=0; cpt<=0;cpt++) { 
    while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
      ungetc(c,ficpar);          
      fgets(line, MAXLINE, ficpar);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
      puts(line);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
      fputs(line,ficparo);            nhstepm = nhstepm/hstepm; 
    }            
    ungetc(c,ficpar);            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);  
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          
    dateprev2=anprev2+mprev2/12.+jprev2/365.;            for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
   fscanf(ficpar,"pop_based=%d\n",&popbased);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   fprintf(ficparo,"pop_based=%d\n",popbased);                } 
   fprintf(ficres,"pop_based=%d\n",popbased);                for(j=1; j<=nlstate+ndeath;j++) {
                  kk1=0.;kk2=0;
   while((c=getc(ficpar))=='#' && c!= EOF){                for(i=1; i<=nlstate;i++) {              
     ungetc(c,ficpar);                  if (mobilav==1) 
     fgets(line, MAXLINE, ficpar);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
     puts(line);                  else {
     fputs(line,ficparo);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
   }                  }
   ungetc(c,ficpar);                }
                 if (h==(int)(calagedatem+12*cpt)){
   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);                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
 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(ficrespop," %.3f", kk1);
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
 while((c=getc(ficpar))=='#' && c!= EOF){              for(i=1; i<=nlstate;i++){
     ungetc(c,ficpar);                kk1=0.;
     fgets(line, MAXLINE, ficpar);                  for(j=1; j<=nlstate;j++){
     puts(line);                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
     fputs(line,ficparo);                  }
   }                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
   ungetc(c,ficpar);              }
   
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;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);                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);            }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          }
         }
 /*------------ gnuplot -------------*/   
   strcpy(optionfilegnuplot,optionfilefiname);    /******/
   strcat(optionfilegnuplot,".gp");  
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
     printf("Problem with file %s",optionfilegnuplot);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   }          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   fclose(ficgp);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);            nhstepm = nhstepm/hstepm; 
 /*--------- index.htm --------*/            
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   strcpy(optionfilehtm,optionfile);            oldm=oldms;savm=savms;
   strcat(optionfilehtm,".htm");            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {            for (h=0; h<=nhstepm; h++){
     printf("Problem with %s \n",optionfilehtm), exit(0);              if (h==(int) (calagedatem+YEARM*cpt)) {
   }                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n              for(j=1; j<=nlstate+ndeath;j++) {
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n                kk1=0.;kk2=0;
 \n                for(i=1; i<=nlstate;i++) {              
 Total number of observations=%d <br>\n                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n                }
 <hr  size=\"2\" color=\"#EC5E5E\">                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
  <ul><li><h4>Parameter files</h4>\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            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  - 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);          }
   fclose(fichtm);        }
      } 
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);    }
     
 /*------------ free_vector  -------------*/    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  chdir(path);  
      if (popforecast==1) {
  free_ivector(wav,1,imx);      free_ivector(popage,0,AGESUP);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      free_vector(popeffectif,0,AGESUP);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        free_vector(popcount,0,AGESUP);
  free_ivector(num,1,n);    }
  free_vector(agedc,1,n);    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  fclose(ficparo);    fclose(ficrespop);
  fclose(ficres);  } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   /*--------------- Prevalence limit --------------*/  {
      if((fichier=fopen(optionfich,"a"))==NULL) {
   strcpy(filerespl,"pl");      printf("Problem with file: %s\n", optionfich);
   strcat(filerespl,fileres);      fprintf(ficlog,"Problem with file: %s\n", optionfich);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      return (0);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    }
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;    fflush(fichier);
   }    return (1);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  }
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);  
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");  /**************** function prwizard **********************/
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   fprintf(ficrespl,"\n");  {
    
   prlim=matrix(1,nlstate,1,nlstate);    /* Wizard to print covariance matrix template */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    char ca[32], cb[32], cc[32];
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int numlinepar;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
   k=0;    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   agebase=ageminpar;    fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   agelim=agemaxpar;    for(i=1; i <=nlstate; i++){
   ftolpl=1.e-10;      jj=0;
   i1=cptcoveff;      for(j=1; j <=nlstate+ndeath; j++){
   if (cptcovn < 1){i1=1;}        if(j==i) continue;
         jj++;
   for(cptcov=1;cptcov<=i1;cptcov++){        /*ca[0]= k+'a'-1;ca[1]='\0';*/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        printf("%1d%1d",i,j);
         k=k+1;        fprintf(ficparo,"%1d%1d",i,j);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        for(k=1; k<=ncovmodel;k++){
         fprintf(ficrespl,"\n#******");          /*        printf(" %lf",param[i][j][k]); */
         printf("\n#******");          /*        fprintf(ficparo," %lf",param[i][j][k]); */
         fprintf(ficlog,"\n#******");          printf(" 0.");
         for(j=1;j<=cptcoveff;j++) {          fprintf(ficparo," 0.");
           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]]);        printf("\n");
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficparo,"\n");
         }      }
         fprintf(ficrespl,"******\n");    }
         printf("******\n");    printf("# Scales (for hessian or gradient estimation)\n");
         fprintf(ficlog,"******\n");    fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
            npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
         for (age=agebase; age<=agelim; age++){    for(i=1; i <=nlstate; i++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      jj=0;
           fprintf(ficrespl,"%.0f",age );      for(j=1; j <=nlstate+ndeath; j++){
           for(i=1; i<=nlstate;i++)        if(j==i) continue;
           fprintf(ficrespl," %.5f", prlim[i][i]);        jj++;
           fprintf(ficrespl,"\n");        fprintf(ficparo,"%1d%1d",i,j);
         }        printf("%1d%1d",i,j);
       }        fflush(stdout);
     }        for(k=1; k<=ncovmodel;k++){
   fclose(ficrespl);          /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
   /*------------- h Pij x at various ages ------------*/          printf(" 0.");
            fprintf(ficparo," 0.");
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        numlinepar++;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        printf("\n");
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;        fprintf(ficparo,"\n");
   }      }
   printf("Computing pij: result on file '%s' \n", filerespij);    }
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);    printf("# Covariance matrix\n");
    /* # 121 Var(a12)\n\ */
   stepsize=(int) (stepm+YEARM-1)/YEARM;  /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /*if (stepm<=24) stepsize=2;*/  /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   agelim=AGESUP;  /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   hstepm=stepsize*YEARM; /* Every year of age */  /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  /* # 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" */
   /* hstepm=1;   aff par mois*/    fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
   k=0;    /* # 121 Var(a12)\n\ */
   for(cptcov=1;cptcov<=i1;cptcov++){    /* # 122 Cov(b12,a12) Var(b12)\n\ */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    /* #   ...\n\ */
       k=k+1;    /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
         fprintf(ficrespij,"\n#****** ");    
         for(j=1;j<=cptcoveff;j++)    for(itimes=1;itimes<=2;itimes++){
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      jj=0;
         fprintf(ficrespij,"******\n");      for(i=1; i <=nlstate; i++){
                for(j=1; j <=nlstate+ndeath; j++){
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          if(j==i) continue;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          for(k=1; k<=ncovmodel;k++){
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
           /*      nhstepm=nhstepm*YEARM; aff par mois*/            if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              fprintf(ficparo,"#%1d%1d%d",i,j,k);
           oldm=oldms;savm=savms;            }else{
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                printf("%1d%1d%d",i,j,k);
           fprintf(ficrespij,"# Age");              fprintf(ficparo,"%1d%1d%d",i,j,k);
           for(i=1; i<=nlstate;i++)              /*  printf(" %.5le",matcov[i][j]); */
             for(j=1; j<=nlstate+ndeath;j++)            }
               fprintf(ficrespij," %1d-%1d",i,j);            ll=0;
           fprintf(ficrespij,"\n");            for(li=1;li <=nlstate; li++){
            for (h=0; h<=nhstepm; h++){              for(lj=1;lj <=nlstate+ndeath; lj++){
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );                if(lj==li) continue;
             for(i=1; i<=nlstate;i++)                for(lk=1;lk<=ncovmodel;lk++){
               for(j=1; j<=nlstate+ndeath;j++)                  ll++;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);                  if(ll<=jj){
             fprintf(ficrespij,"\n");                    cb[0]= lk +'a'-1;cb[1]='\0';
              }                    if(ll<jj){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                      if(itimes==1){
           fprintf(ficrespij,"\n");                        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.");
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);                      }
                     }else{
   fclose(ficrespij);                      if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
   /*---------- Forecasting ------------------*/                      }else{
   if((stepm == 1) && (strcmp(model,".")==0)){                        printf(" 0.");
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);                        fprintf(ficparo," 0.");
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);                      }
   }                    }
   else{                  }
     erreur=108;                } /* end lk */
     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);              } /* end lj */
     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);            } /* end li */
   }            printf("\n");
              fprintf(ficparo,"\n");
             numlinepar++;
   /*---------- Health expectancies and variances ------------*/          } /* end k*/
         } /*end j */
   strcpy(filerest,"t");      } /* end i */
   strcat(filerest,fileres);    } /* end itimes */
   if((ficrest=fopen(filerest,"w"))==NULL) {  
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  } /* end of prwizard */
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;  /******************* Gompertz Likelihood ******************************/
   }  double gompertz(double x[])
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  { 
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);    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++) {
   strcpy(filerese,"e");      sump=sump+weight[i];
   strcat(filerese,fileres);      sump=sump+1;
   if((ficreseij=fopen(filerese,"w"))==NULL) {      num=num+1;
     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);    /* for (i=1; i<=imx; i++) 
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);       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]);*/
   
   strcpy(fileresv,"v");    for (i=0;i<=imx-1 ; i++)
   strcat(fileresv,fileres);      {
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        if (cens[i]==1 & wav[i]>1)
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);          A=-x[1]/(x[2])*
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);            (exp(x[2]/YEARM*(agecens[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)));
   }        
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        if (cens[i]==0 & wav[i]>1)
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          A=-x[1]/(x[2])*
   calagedate=-1;               (exp(x[2]/YEARM*(agedc[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)))
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            +log(x[1]/YEARM)+x[2]/YEARM*(agedc[i]*12-agegomp*12)+log(YEARM);      
         
   k=0;        if (wav[i]>1 & agecens[i]>15) {
   for(cptcov=1;cptcov<=i1;cptcov++){          L=L+A*weight[i];
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          /*      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]);*/
       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]]);   /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
       fprintf(ficrest,"******\n");   
     return -2*L*num/sump;
       fprintf(ficreseij,"\n#****** ");  }
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /******************* Printing html file ***********/
       fprintf(ficreseij,"******\n");  void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
       fprintf(ficresvij,"\n#****** ");                    int imx,  double p[],double **matcov){
       for(j=1;j<=cptcoveff;j++)    int i;
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficresvij,"******\n");    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);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    for (i=1;i<=2;i++) 
       oldm=oldms;savm=savms;      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]));
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
      fprintf(fichtm,"</ul>");
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    fflush(fichtm);
       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);  
       if(popbased==1){  /******************* Gnuplot file **************/
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);  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;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    int ng;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  
       fprintf(ficrest,"\n");  
     /*#ifdef windows */
       epj=vector(1,nlstate+1);    fprintf(ficgp,"cd \"%s\" \n",pathc);
       for(age=bage; age <=fage ;age++){      /*#endif */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
         if (popbased==1) {  
           for(i=1; i<=nlstate;i++)    strcpy(dirfileres,optionfilefiname);
             prlim[i][i]=probs[(int)age][i][k];    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(ficrest," %4.0f",age);    fprintf(ficgp, "set ter png small\n set log y\n"); 
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    fprintf(ficgp, "set size 0.65,0.65\n");
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
             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++)  /**************** Main Program *****************/
             vepp += vareij[i][j][(int)age];  /***********************************************/
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));  
         for(j=1;j <=nlstate;j++){  int main(int argc, char *argv[])
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));  {
         }    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
         fprintf(ficrest,"\n");    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
       }    int jj, ll, li, lj, lk, imk;
     }    int numlinepar=0; /* Current linenumber of parameter file */
   }    int itimes;
 free_matrix(mint,1,maxwav,1,n);    int NDIM=2;
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  
     free_vector(weight,1,n);    char ca[32], cb[32], cc[32];
   fclose(ficreseij);    /*  FILE *fichtm; *//* Html File */
   fclose(ficresvij);    /* FILE *ficgp;*/ /*Gnuplot File */
   fclose(ficrest);    double agedeb, agefin,hf;
   fclose(ficpar);    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   free_vector(epj,1,nlstate+1);  
      double fret;
   /*------- Variance limit prevalence------*/      double **xi,tmp,delta;
   
   strcpy(fileresvpl,"vpl");    double dum; /* Dummy variable */
   strcat(fileresvpl,fileres);    double ***p3mat;
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    double ***mobaverage;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    int *indx;
     exit(0);    char line[MAXLINE], linepar[MAXLINE];
   }    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    char pathr[MAXLINE], pathimach[MAXLINE]; 
     int firstobs=1, lastobs=10;
   k=0;    int sdeb, sfin; /* Status at beginning and end */
   for(cptcov=1;cptcov<=i1;cptcov++){    int c,  h , cpt,l;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int ju,jl, mi;
       k=k+1;    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
       fprintf(ficresvpl,"\n#****** ");    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
       for(j=1;j<=cptcoveff;j++)    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int mobilav=0,popforecast=0;
       fprintf(ficresvpl,"******\n");    int hstepm, nhstepm;
          double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
       oldm=oldms;savm=savms;  
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    double bage, fage, age, agelim, agebase;
     }    double ftolpl=FTOL;
  }    double **prlim;
     double *severity;
   fclose(ficresvpl);    double ***param; /* Matrix of parameters */
     double  *p;
   /*---------- End : free ----------------*/    double **matcov; /* Matrix of covariance */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    double ***delti3; /* Scale */
      double *delti; /* Scale */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    double ***eij, ***vareij;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    double **varpl; /* Variances of prevalence limits by age */
      double *epj, vepp;
      double kk1, kk2;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    double **ximort;
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    char *alph[]={"a","a","b","c","d","e"}, str[4];
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    int *dcwave;
    
   free_matrix(matcov,1,npar,1,npar);    char z[1]="c", occ;
   free_vector(delti,1,npar);  
   free_matrix(agev,1,maxwav,1,imx);    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    char strstart[80], *strt, strtend[80];
     char *stratrunc;
   fprintf(fichtm,"\n</body>");    int lstra;
   fclose(fichtm);  
   fclose(ficgp);    long total_usecs;
     
   /*   setlocale (LC_ALL, ""); */
   if(erreur >0){  /*   bindtextdomain (PACKAGE, LOCALEDIR); */
     printf("End of Imach with error or warning %d\n",erreur);  /*   textdomain (PACKAGE); */
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);  /*   setlocale (LC_CTYPE, ""); */
   }else{  /*   setlocale (LC_MESSAGES, ""); */
    printf("End of Imach\n");  
    fprintf(ficlog,"End of Imach\n");    /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
   }    (void) gettimeofday(&start_time,&tzp);
   printf("See log file on %s\n",filelog);    curr_time=start_time;
   fclose(ficlog);    tm = *localtime(&start_time.tv_sec);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    tmg = *gmtime(&start_time.tv_sec);
      strcpy(strstart,asctime(&tm));
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/  
   /*printf("Total time was %d uSec.\n", total_usecs);*/  /*  printf("Localtime (at start)=%s",strstart); */
   /*------ End -----------*/  /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
  end:  /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
 #ifdef windows  /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /* chdir(pathcd);*/  /*   tp.tv_sec = mktime(&tmg); */
 #endif  /*   strt=asctime(&tmg); */
  /*system("wgnuplot graph.plt");*/  /*   printf("Time(after) =%s",strstart);  */
  /*system("../gp37mgw/wgnuplot graph.plt");*/  /*  (void) time (&time_value);
  /*system("cd ../gp37mgw");*/  *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  *  tm = *localtime(&time_value);
  strcpy(plotcmd,GNUPLOTPROGRAM);  *  strstart=asctime(&tm);
  strcat(plotcmd," ");  *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
  strcat(plotcmd,optionfilegnuplot);  */
  system(plotcmd);  
     nberr=0; /* Number of errors and warnings */
 #ifdef windows    nbwarn=0;
   while (z[0] != 'q') {    getcwd(pathcd, size);
     /* chdir(path); */  
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    printf("\n%s\n%s",version,fullversion);
     scanf("%s",z);    if(argc <=1){
     if (z[0] == 'c') system("./imach");      printf("\nEnter the parameter file name: ");
     else if (z[0] == 'e') system(optionfilehtm);      scanf("%s",pathtot);
     else if (z[0] == 'g') system(plotcmd);    }
     else if (z[0] == 'q') exit(0);    else{
   }      strcpy(pathtot,argv[1]);
 #endif    }
 }    /*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],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     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 with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with 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;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); 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;
       }
     }
     /* 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 parameter 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);
     fclose(fic);*/
   
       /*  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){
           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\
    - 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,\
             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);
   
     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 (j=1; j<=lastpass; j++)
           if (s[j][i]>nlstate) {
             dcwave[i]=j;
             /*    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;
           
           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]=0.1; p[2]=0.1;
       /*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]));
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov);
     } /* 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,path); /* 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  (stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficrespl,"#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*/
   
       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);
   
       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 LEs with variances: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total LEs with variances: 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(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#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficreseij,"******\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, delti, matcov);  
    
           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);
           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);
           }
   
    
           fprintf(ficrest,"#Total LEs with variances: 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(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of stable prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of 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);
           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(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);
   
   
     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\nLocaltime 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 -----------*/
   
     chdir(path);
     strcpy(plotcmd,"\"");
     strcat(plotcmd,pathimach);
     strcat(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd,"\"");
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     if((outcmd=system(plotcmd)) != 0){
       printf(" 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.1.50  
changed lines
  Added in v.1.101


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