Diff for /imach/src/imach.c between versions 1.52 and 1.103

version 1.52, 2002/07/19 18:49:30 version 1.103, 2005/09/30 15:54:49
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.103  2005/09/30 15:54:49  lievre
      (Module): sump fixed, loop imx fixed, and simplifications.
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.102  2004/09/15 17:31:30  brouard
   first survey ("cross") where individuals from different ages are    Add the possibility to read data file including tab characters.
   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 1.101  2004/09/15 10:38:38  brouard
   second wave of interviews ("longitudinal") which measure each change    Fix on curr_time
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.100  2004/07/12 18:29:06  brouard
   model. More health states you consider, more time is necessary to reach the    Add version for Mac OS X. Just define UNIX in Makefile
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.99  2004/06/05 08:57:40  brouard
   probability to be observed in state j at the second wave    *** empty log message ***
   conditional to be observed in state i at the first wave. Therefore  
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Revision 1.98  2004/05/16 15:05:56  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    New version 0.97 . First attempt to estimate force of mortality
   complex model than "constant and age", you should modify the program    directly from the data i.e. without the need of knowing the health
   where the markup *Covariates have to be included here again* invites    state at each age, but using a Gompertz model: log u =a + b*age .
   you to do it.  More covariates you add, slower the    This is the basic analysis of mortality and should be done before any
   convergence.    other analysis, in order to test if the mortality estimated from the
     cross-longitudinal survey is different from the mortality estimated
   The advantage of this computer programme, compared to a simple    from other sources like vital statistic data.
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    The same imach parameter file can be used but the option for mle should be -3.
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      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.
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    The output is very simple: only an estimate of the intercept and of
   split into an exact number (nh*stepm) of unobserved intermediate    the slope with 95% confident intervals.
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Current limitations:
   matrix is simply the matrix product of nh*stepm elementary matrices    A) Even if you enter covariates, i.e. with the
   and the contribution of each individual to the likelihood is simply    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   hPijx.    B) There is no computation of Life Expectancy nor Life Table.
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.97  2004/02/20 13:25:42  lievre
   of the life expectancies. It also computes the prevalence limits.    Version 0.96d. Population forecasting command line is (temporarily)
      suppressed.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.96  2003/07/15 15:38:55  brouard
   This software have been partly granted by Euro-REVES, a concerted action    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   from the European Union.    rewritten within the same printf. Workaround: many printfs.
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.95  2003/07/08 07:54:34  brouard
   can be accessed at http://euroreves.ined.fr/imach .    * imach.c (Repository):
   **********************************************************************/    (Repository): Using imachwizard code to output a more meaningful covariance
      matrix (cov(a12,c31) instead of numbers.
 #include <math.h>  
 #include <stdio.h>    Revision 1.94  2003/06/27 13:00:02  brouard
 #include <stdlib.h>    Just cleaning
 #include <unistd.h>  
     Revision 1.93  2003/06/25 16:33:55  brouard
 #define MAXLINE 256    (Module): On windows (cygwin) function asctime_r doesn't
 #define GNUPLOTPROGRAM "gnuplot"    exist so I changed back to asctime which exists.
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    (Module): Version 0.96b
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.92  2003/06/25 16:30:45  brouard
 #define windows    (Module): On windows (cygwin) function asctime_r doesn't
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    exist so I changed back to asctime which exists.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.91  2003/06/25 15:30:29  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    * imach.c (Repository): Duplicated warning errors corrected.
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
 #define NINTERVMAX 8    is stamped in powell.  We created a new html file for the graphs
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    concerning matrix of covariance. It has extension -cov.htm.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.90  2003/06/24 12:34:15  brouard
 #define MAXN 20000    (Module): Some bugs corrected for windows. Also, when
 #define YEARM 12. /* Number of months per year */    mle=-1 a template is output in file "or"mypar.txt with the design
 #define AGESUP 130    of the covariance matrix to be input.
 #define AGEBASE 40  
 #ifdef windows    Revision 1.89  2003/06/24 12:30:52  brouard
 #define DIRSEPARATOR '\\'    (Module): Some bugs corrected for windows. Also, when
 #define ODIRSEPARATOR '/'    mle=-1 a template is output in file "or"mypar.txt with the design
 #else    of the covariance matrix to be input.
 #define DIRSEPARATOR '/'  
 #define ODIRSEPARATOR '\\'    Revision 1.88  2003/06/23 17:54:56  brouard
 #endif    * 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.
   
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";    Revision 1.87  2003/06/18 12:26:01  brouard
 int erreur; /* Error number */    Version 0.96
 int nvar;  
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.86  2003/06/17 20:04:08  brouard
 int npar=NPARMAX;    (Module): Change position of html and gnuplot routines and added
 int nlstate=2; /* Number of live states */    routine fileappend.
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.85  2003/06/17 13:12:43  brouard
 int popbased=0;    * imach.c (Repository): Check when date of death was earlier that
     current date of interview. It may happen when the death was just
 int *wav; /* Number of waves for this individuual 0 is possible */    prior to the death. In this case, dh was negative and likelihood
 int maxwav; /* Maxim number of waves */    was wrong (infinity). We still send an "Error" but patch by
 int jmin, jmax; /* min, max spacing between 2 waves */    assuming that the date of death was just one stepm after the
 int mle, weightopt;    interview.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Repository): Because some people have very long ID (first column)
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    we changed int to long in num[] and we added a new lvector for
 double jmean; /* Mean space between 2 waves */    memory allocation. But we also truncated to 8 characters (left
 double **oldm, **newm, **savm; /* Working pointers to matrices */    truncation)
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    (Repository): No more line truncation errors.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficlog;    Revision 1.84  2003/06/13 21:44:43  brouard
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    * imach.c (Repository): Replace "freqsummary" at a correct
 FILE *ficresprobmorprev;    place. It differs from routine "prevalence" which may be called
 FILE *fichtm; /* Html File */    many times. Probs is memory consuming and must be used with
 FILE *ficreseij;    parcimony.
 char filerese[FILENAMELENGTH];    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 FILE  *ficresvij;  
 char fileresv[FILENAMELENGTH];    Revision 1.83  2003/06/10 13:39:11  lievre
 FILE  *ficresvpl;    *** empty log message ***
 char fileresvpl[FILENAMELENGTH];  
 char title[MAXLINE];    Revision 1.82  2003/06/05 15:57:20  brouard
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    Add log in  imach.c and  fullversion number is now printed.
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  
   */
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  /*
 char filelog[FILENAMELENGTH]; /* Log file */     Interpolated Markov Chain
 char filerest[FILENAMELENGTH];  
 char fileregp[FILENAMELENGTH];    Short summary of the programme:
 char popfile[FILENAMELENGTH];    
     This program computes Healthy Life Expectancies from
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     first survey ("cross") where individuals from different ages are
 #define NR_END 1    interviewed on their health status or degree of disability (in the
 #define FREE_ARG char*    case of a health survey which is our main interest) -2- at least a
 #define FTOL 1.0e-10    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
 #define NRANSI    computed from the time spent in each health state according to a
 #define ITMAX 200    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
 #define TOL 2.0e-4    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
 #define CGOLD 0.3819660    conditional to be observed in state i at the first wave. Therefore
 #define ZEPS 1.0e-10    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    '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 GOLD 1.618034    where the markup *Covariates have to be included here again* invites
 #define GLIMIT 100.0    you to do it.  More covariates you add, slower the
 #define TINY 1.0e-20    convergence.
   
 static double maxarg1,maxarg2;    The advantage of this computer programme, compared to a simple
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    multinomial logistic model, is clear when the delay between waves is not
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    identical for each individual. Also, if a individual missed an
      intermediate interview, the information is lost, but taken into
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    account using an interpolation or extrapolation.  
 #define rint(a) floor(a+0.5)  
     hPijx is the probability to be observed in state i at age x+h
 static double sqrarg;    conditional to the observed state i at age x. The delay 'h' can be
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    split into an exact number (nh*stepm) of unobserved intermediate
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    states. This elementary transition (by month, quarter,
     semester or year) is modelled as a multinomial logistic.  The hPx
 int imx;    matrix is simply the matrix product of nh*stepm elementary matrices
 int stepm;    and the contribution of each individual to the likelihood is simply
 /* Stepm, step in month: minimum step interpolation*/    hPijx.
   
 int estepm;    Also this programme outputs the covariance matrix of the parameters but also
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    of the life expectancies. It also computes the stable prevalence. 
     
 int m,nb;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;             Institut national d'études démographiques, Paris.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    This software have been partly granted by Euro-REVES, a concerted action
 double **pmmij, ***probs, ***mobaverage;    from the European Union.
 double dateintmean=0;    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 double *weight;    can be accessed at http://euroreves.ined.fr/imach .
 int **s; /* Status */  
 double *agedc, **covar, idx;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    **********************************************************************/
 double ftolhess; /* Tolerance for computing hessian */  /*
     main
 /**************** split *************************/    read parameterfile
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    read datafile
 {    concatwav
    char *s;                             /* pointer */    freqsummary
    int  l1, l2;                         /* length counters */    if (mle >= 1)
       mlikeli
    l1 = strlen( path );                 /* length of path */    print results files
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    if mle==1 
    s= strrchr( path, DIRSEPARATOR );            /* find last / */       computes hessian
    if ( s == NULL ) {                   /* no directory, so use current */    read end of parameter file: agemin, agemax, bage, fage, estepm
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)        begin-prev-date,...
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/    open gnuplot file
 #if     defined(__bsd__)                /* get current working directory */    open html file
       extern char       *getwd( );    stable prevalence
      for age prevalim()
       if ( getwd( dirc ) == NULL ) {    h Pij x
 #else    variance of p varprob
       extern char       *getcwd( );    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Variance-covariance of DFLE
 #endif    prevalence()
          return( GLOCK_ERROR_GETCWD );     movingaverage()
       }    varevsij() 
       strcpy( name, path );             /* we've got it */    if popbased==1 varevsij(,popbased)
    } else {                             /* strip direcotry from path */    total life expectancies
       s++;                              /* after this, the filename */    Variance of stable prevalence
       l2 = strlen( s );                 /* length of filename */   end
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  */
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */  
    }   
    l1 = strlen( dirc );                 /* length of directory */  #include <math.h>
 #ifdef windows  #include <stdio.h>
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #include <stdlib.h>
 #else  #include <unistd.h>
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif  /* #include <sys/time.h> */
    s = strrchr( name, '.' );            /* find last / */  #include <time.h>
    s++;  #include "timeval.h"
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);  /* #include <libintl.h> */
    l2= strlen( s)+1;  /* #define _(String) gettext (String) */
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;  #define MAXLINE 256
    return( 0 );                         /* we're done */  #define GNUPLOTPROGRAM "gnuplot"
 }  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
   /*#define DEBUG*/
 /******************************************/  /*#define windows*/
   #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 void replace(char *s, char*t)  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 {  
   int i;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   int lg=20;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   i=0;  
   lg=strlen(t);  #define NINTERVMAX 8
   for(i=0; i<= lg; i++) {  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
     (s[i] = t[i]);  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
     if (t[i]== '\\') s[i]='/';  #define NCOVMAX 8 /* Maximum number of covariates */
   }  #define MAXN 20000
 }  #define YEARM 12. /* Number of months per year */
   #define AGESUP 130
 int nbocc(char *s, char occ)  #define AGEBASE 40
 {  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   int i,j=0;  #ifdef UNIX
   int lg=20;  #define DIRSEPARATOR '/'
   i=0;  #define ODIRSEPARATOR '\\'
   lg=strlen(s);  #else
   for(i=0; i<= lg; i++) {  #define DIRSEPARATOR '\\'
   if  (s[i] == occ ) j++;  #define ODIRSEPARATOR '/'
   }  #endif
   return j;  
 }  /* $Id$ */
   /* $State$ */
 void cutv(char *u,char *v, char*t, char occ)  
 {  char version[]="Imach version 0.97c, September 2004, INED-EUROREVES ";
   /* cuts string t into u and v where u is ended by char occ excluding it  char fullversion[]="$Revision$ $Date$"; 
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
      gives u="abcedf" and v="ghi2j" */  int nvar;
   int i,lg,j,p=0;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   i=0;  int npar=NPARMAX;
   for(j=0; j<=strlen(t)-1; j++) {  int nlstate=2; /* Number of live states */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  int ndeath=1; /* Number of dead states */
   }  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
   lg=strlen(t);  
   for(j=0; j<p; j++) {  int *wav; /* Number of waves for this individuual 0 is possible */
     (u[j] = t[j]);  int maxwav; /* Maxim number of waves */
   }  int jmin, jmax; /* min, max spacing between 2 waves */
      u[p]='\0';  int gipmx, gsw; /* Global variables on the number of contributions 
                      to the likelihood and the sum of weights (done by funcone)*/
    for(j=0; j<= lg; j++) {  int mle, weightopt;
     if (j>=(p+1))(v[j-p-1] = t[j]);  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   }  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 }  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
              * wave mi and wave mi+1 is not an exact multiple of stepm. */
 /********************** nrerror ********************/  double jmean; /* Mean space between 2 waves */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
 void nrerror(char error_text[])  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 {  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   fprintf(stderr,"ERREUR ...\n");  FILE *ficlog, *ficrespow;
   fprintf(stderr,"%s\n",error_text);  int globpr; /* Global variable for printing or not */
   exit(1);  double fretone; /* Only one call to likelihood */
 }  long ipmx; /* Number of contributions */
 /*********************** vector *******************/  double sw; /* Sum of weights */
 double *vector(int nl, int nh)  char filerespow[FILENAMELENGTH];
 {  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   double *v;  FILE *ficresilk;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   if (!v) nrerror("allocation failure in vector");  FILE *ficresprobmorprev;
   return v-nl+NR_END;  FILE *fichtm, *fichtmcov; /* Html File */
 }  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 /************************ free vector ******************/  FILE  *ficresvij;
 void free_vector(double*v, int nl, int nh)  char fileresv[FILENAMELENGTH];
 {  FILE  *ficresvpl;
   free((FREE_ARG)(v+nl-NR_END));  char fileresvpl[FILENAMELENGTH];
 }  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 /************************ivector *******************************/  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 int *ivector(long nl,long nh)  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 {  char command[FILENAMELENGTH];
   int *v;  int  outcmd=0;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   return v-nl+NR_END;  
 }  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
 /******************free ivector **************************/  char fileregp[FILENAMELENGTH];
 void free_ivector(int *v, long nl, long nh)  char popfile[FILENAMELENGTH];
 {  
   free((FREE_ARG)(v+nl-NR_END));  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 }  
   struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 /******************* imatrix *******************************/  struct timezone tzp;
 int **imatrix(long nrl, long nrh, long ncl, long nch)  extern int gettimeofday();
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  struct tm tmg, tm, tmf, *gmtime(), *localtime();
 {  long time_value;
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  extern long time();
   int **m;  char strcurr[80], strfor[80];
    
   /* allocate pointers to rows */  #define NR_END 1
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #define FREE_ARG char*
   if (!m) nrerror("allocation failure 1 in matrix()");  #define FTOL 1.0e-10
   m += NR_END;  
   m -= nrl;  #define NRANSI 
    #define ITMAX 200 
    
   /* allocate rows and set pointers to them */  #define TOL 2.0e-4 
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define CGOLD 0.3819660 
   m[nrl] += NR_END;  #define ZEPS 1.0e-10 
   m[nrl] -= ncl;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  #define GOLD 1.618034 
    #define GLIMIT 100.0 
   /* return pointer to array of pointers to rows */  #define TINY 1.0e-20 
   return m;  
 }  static double maxarg1,maxarg2;
   #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 /****************** free_imatrix *************************/  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 void free_imatrix(m,nrl,nrh,ncl,nch)    
       int **m;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       long nch,ncl,nrh,nrl;  #define rint(a) floor(a+0.5)
      /* free an int matrix allocated by imatrix() */  
 {  static double sqrarg;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   free((FREE_ARG) (m+nrl-NR_END));  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 }  int agegomp= AGEGOMP;
   
 /******************* matrix *******************************/  int imx; 
 double **matrix(long nrl, long nrh, long ncl, long nch)  int stepm=1;
 {  /* Stepm, step in month: minimum step interpolation*/
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;  int estepm;
   /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  int m,nb;
   m += NR_END;  long *num;
   m -= nrl;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  double **pmmij, ***probs;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  double *ageexmed,*agecens;
   m[nrl] += NR_END;  double dateintmean=0;
   m[nrl] -= ncl;  
   double *weight;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int **s; /* Status */
   return m;  double *agedc, **covar, idx;
 }  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   
 /*************************free matrix ************************/  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  double ftolhess; /* Tolerance for computing hessian */
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  /**************** split *************************/
   free((FREE_ARG)(m+nrl-NR_END));  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 }  {
     /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
 /******************* ma3x *******************************/       the name of the file (name), its extension only (ext) and its first part of the name (finame)
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    */ 
 {    char  *ss;                            /* pointer */
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    int   l1, l2;                         /* length counters */
   double ***m;  
     l1 = strlen(path );                   /* length of path */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   if (!m) nrerror("allocation failure 1 in matrix()");    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   m += NR_END;    if ( ss == NULL ) {                   /* no directory, so use current */
   m -= nrl;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));      /* get current working directory */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      /*    extern  char* getcwd ( char *buf , int len);*/
   m[nrl] += NR_END;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   m[nrl] -= ncl;        return( GLOCK_ERROR_GETCWD );
       }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;      strcpy( name, path );               /* we've got it */
     } else {                              /* strip direcotry from path */
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));      ss++;                               /* after this, the filename */
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");      l2 = strlen( ss );                  /* length of filename */
   m[nrl][ncl] += NR_END;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   m[nrl][ncl] -= nll;      strcpy( name, ss );         /* save file name */
   for (j=ncl+1; j<=nch; j++)      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     m[nrl][j]=m[nrl][j-1]+nlay;      dirc[l1-l2] = 0;                    /* add zero */
      }
   for (i=nrl+1; i<=nrh; i++) {    l1 = strlen( dirc );                  /* length of directory */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    /*#ifdef windows
     for (j=ncl+1; j<=nch; j++)    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
       m[i][j]=m[i][j-1]+nlay;  #else
   }    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   return m;  #endif
 }    */
     ss = strrchr( name, '.' );            /* find last / */
 /*************************free ma3x ************************/    if (ss >0){
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)      ss++;
 {      strcpy(ext,ss);                     /* save extension */
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));      l1= strlen( name);
   free((FREE_ARG)(m[nrl]+ncl-NR_END));      l2= strlen(ss)+1;
   free((FREE_ARG)(m+nrl-NR_END));      strncpy( finame, name, l1-l2);
 }      finame[l1-l2]= 0;
     }
 /***************** f1dim *************************/    return( 0 );                          /* we're done */
 extern int ncom;  }
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);  
    /******************************************/
 double f1dim(double x)  
 {  void replace_back_to_slash(char *s, char*t)
   int j;  {
   double f;    int i;
   double *xt;    int lg=0;
      i=0;
   xt=vector(1,ncom);    lg=strlen(t);
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    for(i=0; i<= lg; i++) {
   f=(*nrfunc)(xt);      (s[i] = t[i]);
   free_vector(xt,1,ncom);      if (t[i]== '\\') s[i]='/';
   return f;    }
 }  }
   
 /*****************brent *************************/  int nbocc(char *s, char occ)
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  {
 {    int i,j=0;
   int iter;    int lg=20;
   double a,b,d,etemp;    i=0;
   double fu,fv,fw,fx;    lg=strlen(s);
   double ftemp;    for(i=0; i<= lg; i++) {
   double p,q,r,tol1,tol2,u,v,w,x,xm;    if  (s[i] == occ ) j++;
   double e=0.0;    }
      return j;
   a=(ax < cx ? ax : cx);  }
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;  void cutv(char *u,char *v, char*t, char occ)
   fw=fv=fx=(*f)(x);  {
   for (iter=1;iter<=ITMAX;iter++) {    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
     xm=0.5*(a+b);       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);       gives u="abcedf" and v="ghi2j" */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    int i,lg,j,p=0;
     printf(".");fflush(stdout);    i=0;
     fprintf(ficlog,".");fflush(ficlog);    for(j=0; j<=strlen(t)-1; j++) {
 #ifdef DEBUG      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    }
     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)))) { */    lg=strlen(t);
 #endif    for(j=0; j<p; j++) {
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){      (u[j] = t[j]);
       *xmin=x;    }
       return fx;       u[p]='\0';
     }  
     ftemp=fu;     for(j=0; j<= lg; j++) {
     if (fabs(e) > tol1) {      if (j>=(p+1))(v[j-p-1] = t[j]);
       r=(x-w)*(fx-fv);    }
       q=(x-v)*(fx-fw);  }
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);  /********************** nrerror ********************/
       if (q > 0.0) p = -p;  
       q=fabs(q);  void nrerror(char error_text[])
       etemp=e;  {
       e=d;    fprintf(stderr,"ERREUR ...\n");
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    fprintf(stderr,"%s\n",error_text);
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    exit(EXIT_FAILURE);
       else {  }
         d=p/q;  /*********************** vector *******************/
         u=x+d;  double *vector(int nl, int nh)
         if (u-a < tol2 || b-u < tol2)  {
           d=SIGN(tol1,xm-x);    double *v;
       }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     } else {    if (!v) nrerror("allocation failure in vector");
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    return v-nl+NR_END;
     }  }
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);  /************************ free vector ******************/
     if (fu <= fx) {  void free_vector(double*v, int nl, int nh)
       if (u >= x) a=x; else b=x;  {
       SHFT(v,w,x,u)    free((FREE_ARG)(v+nl-NR_END));
         SHFT(fv,fw,fx,fu)  }
         } else {  
           if (u < x) a=u; else b=u;  /************************ivector *******************************/
           if (fu <= fw || w == x) {  int *ivector(long nl,long nh)
             v=w;  {
             w=u;    int *v;
             fv=fw;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
             fw=fu;    if (!v) nrerror("allocation failure in ivector");
           } else if (fu <= fv || v == x || v == w) {    return v-nl+NR_END;
             v=u;  }
             fv=fu;  
           }  /******************free ivector **************************/
         }  void free_ivector(int *v, long nl, long nh)
   }  {
   nrerror("Too many iterations in brent");    free((FREE_ARG)(v+nl-NR_END));
   *xmin=x;  }
   return fx;  
 }  /************************lvector *******************************/
   long *lvector(long nl,long nh)
 /****************** mnbrak ***********************/  {
     long *v;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
             double (*func)(double))    if (!v) nrerror("allocation failure in ivector");
 {    return v-nl+NR_END;
   double ulim,u,r,q, dum;  }
   double fu;  
    /******************free lvector **************************/
   *fa=(*func)(*ax);  void free_lvector(long *v, long nl, long nh)
   *fb=(*func)(*bx);  {
   if (*fb > *fa) {    free((FREE_ARG)(v+nl-NR_END));
     SHFT(dum,*ax,*bx,dum)  }
       SHFT(dum,*fb,*fa,dum)  
       }  /******************* imatrix *******************************/
   *cx=(*bx)+GOLD*(*bx-*ax);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   *fc=(*func)(*cx);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   while (*fb > *fc) {  { 
     r=(*bx-*ax)*(*fb-*fc);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     q=(*bx-*cx)*(*fb-*fa);    int **m; 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    /* allocate pointers to rows */ 
     ulim=(*bx)+GLIMIT*(*cx-*bx);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if ((*bx-u)*(u-*cx) > 0.0) {    if (!m) nrerror("allocation failure 1 in matrix()"); 
       fu=(*func)(u);    m += NR_END; 
     } else if ((*cx-u)*(u-ulim) > 0.0) {    m -= nrl; 
       fu=(*func)(u);    
       if (fu < *fc) {    
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    /* allocate rows and set pointers to them */ 
           SHFT(*fb,*fc,fu,(*func)(u))    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
           }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    m[nrl] += NR_END; 
       u=ulim;    m[nrl] -= ncl; 
       fu=(*func)(u);    
     } else {    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       u=(*cx)+GOLD*(*cx-*bx);    
       fu=(*func)(u);    /* return pointer to array of pointers to rows */ 
     }    return m; 
     SHFT(*ax,*bx,*cx,u)  } 
       SHFT(*fa,*fb,*fc,fu)  
       }  /****************** free_imatrix *************************/
 }  void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
 /*************** linmin ************************/        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
 int ncom;  { 
 double *pcom,*xicom;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 double (*nrfunc)(double []);    free((FREE_ARG) (m+nrl-NR_END)); 
    } 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {  /******************* matrix *******************************/
   double brent(double ax, double bx, double cx,  double **matrix(long nrl, long nrh, long ncl, long nch)
                double (*f)(double), double tol, double *xmin);  {
   double f1dim(double x);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    double **m;
               double *fc, double (*func)(double));  
   int j;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double xx,xmin,bx,ax;    if (!m) nrerror("allocation failure 1 in matrix()");
   double fx,fb,fa;    m += NR_END;
      m -= nrl;
   ncom=n;  
   pcom=vector(1,n);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   xicom=vector(1,n);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   nrfunc=func;    m[nrl] += NR_END;
   for (j=1;j<=n;j++) {    m[nrl] -= ncl;
     pcom[j]=p[j];  
     xicom[j]=xi[j];    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   }    return m;
   ax=0.0;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   xx=1.0;     */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  }
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  /*************************free matrix ************************/
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  {
 #endif    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   for (j=1;j<=n;j++) {    free((FREE_ARG)(m+nrl-NR_END));
     xi[j] *= xmin;  }
     p[j] += xi[j];  
   }  /******************* ma3x *******************************/
   free_vector(xicom,1,n);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   free_vector(pcom,1,n);  {
 }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
 /*************** powell ************************/  
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
             double (*func)(double []))    if (!m) nrerror("allocation failure 1 in matrix()");
 {    m += NR_END;
   void linmin(double p[], double xi[], int n, double *fret,    m -= nrl;
               double (*func)(double []));  
   int i,ibig,j;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double del,t,*pt,*ptt,*xit;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double fp,fptt;    m[nrl] += NR_END;
   double *xits;    m[nrl] -= ncl;
   pt=vector(1,n);  
   ptt=vector(1,n);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   xit=vector(1,n);  
   xits=vector(1,n);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   *fret=(*func)(p);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   for (j=1;j<=n;j++) pt[j]=p[j];    m[nrl][ncl] += NR_END;
   for (*iter=1;;++(*iter)) {    m[nrl][ncl] -= nll;
     fp=(*fret);    for (j=ncl+1; j<=nch; j++) 
     ibig=0;      m[nrl][j]=m[nrl][j-1]+nlay;
     del=0.0;    
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    for (i=nrl+1; i<=nrh; i++) {
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     for (i=1;i<=n;i++)      for (j=ncl+1; j<=nch; j++) 
       printf(" %d %.12f",i, p[i]);        m[i][j]=m[i][j-1]+nlay;
     fprintf(ficlog," %d %.12f",i, p[i]);    }
     printf("\n");    return m; 
     fprintf(ficlog,"\n");    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     for (i=1;i<=n;i++) {             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    */
       fptt=(*fret);  }
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);  /*************************free ma3x ************************/
       fprintf(ficlog,"fret=%lf \n",*fret);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 #endif  {
       printf("%d",i);fflush(stdout);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       fprintf(ficlog,"%d",i);fflush(ficlog);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       linmin(p,xit,n,fret,func);    free((FREE_ARG)(m+nrl-NR_END));
       if (fabs(fptt-(*fret)) > del) {  }
         del=fabs(fptt-(*fret));  
         ibig=i;  /*************** function subdirf ***********/
       }  char *subdirf(char fileres[])
 #ifdef DEBUG  {
       printf("%d %.12e",i,(*fret));    /* Caution optionfilefiname is hidden */
       fprintf(ficlog,"%d %.12e",i,(*fret));    strcpy(tmpout,optionfilefiname);
       for (j=1;j<=n;j++) {    strcat(tmpout,"/"); /* Add to the right */
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    strcat(tmpout,fileres);
         printf(" x(%d)=%.12e",j,xit[j]);    return tmpout;
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);  }
       }  
       for(j=1;j<=n;j++) {  /*************** function subdirf2 ***********/
         printf(" p=%.12e",p[j]);  char *subdirf2(char fileres[], char *preop)
         fprintf(ficlog," p=%.12e",p[j]);  {
       }    
       printf("\n");    /* Caution optionfilefiname is hidden */
       fprintf(ficlog,"\n");    strcpy(tmpout,optionfilefiname);
 #endif    strcat(tmpout,"/");
     }    strcat(tmpout,preop);
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    strcat(tmpout,fileres);
 #ifdef DEBUG    return tmpout;
       int k[2],l;  }
       k[0]=1;  
       k[1]=-1;  /*************** function subdirf3 ***********/
       printf("Max: %.12e",(*func)(p));  char *subdirf3(char fileres[], char *preop, char *preop2)
       fprintf(ficlog,"Max: %.12e",(*func)(p));  {
       for (j=1;j<=n;j++) {    
         printf(" %.12e",p[j]);    /* Caution optionfilefiname is hidden */
         fprintf(ficlog," %.12e",p[j]);    strcpy(tmpout,optionfilefiname);
       }    strcat(tmpout,"/");
       printf("\n");    strcat(tmpout,preop);
       fprintf(ficlog,"\n");    strcat(tmpout,preop2);
       for(l=0;l<=1;l++) {    strcat(tmpout,fileres);
         for (j=1;j<=n;j++) {    return tmpout;
           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]);  
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  /***************** f1dim *************************/
         }  extern int ncom; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  extern double *pcom,*xicom;
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  extern double (*nrfunc)(double []); 
       }   
 #endif  double f1dim(double x) 
   { 
     int j; 
       free_vector(xit,1,n);    double f;
       free_vector(xits,1,n);    double *xt; 
       free_vector(ptt,1,n);   
       free_vector(pt,1,n);    xt=vector(1,ncom); 
       return;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     }    f=(*nrfunc)(xt); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    free_vector(xt,1,ncom); 
     for (j=1;j<=n;j++) {    return f; 
       ptt[j]=2.0*p[j]-pt[j];  } 
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];  /*****************brent *************************/
     }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     fptt=(*func)(ptt);  { 
     if (fptt < fp) {    int iter; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    double a,b,d,etemp;
       if (t < 0.0) {    double fu,fv,fw,fx;
         linmin(p,xit,n,fret,func);    double ftemp;
         for (j=1;j<=n;j++) {    double p,q,r,tol1,tol2,u,v,w,x,xm; 
           xi[j][ibig]=xi[j][n];    double e=0.0; 
           xi[j][n]=xit[j];   
         }    a=(ax < cx ? ax : cx); 
 #ifdef DEBUG    b=(ax > cx ? ax : cx); 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    x=w=v=bx; 
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    fw=fv=fx=(*f)(x); 
         for(j=1;j<=n;j++){    for (iter=1;iter<=ITMAX;iter++) { 
           printf(" %.12e",xit[j]);      xm=0.5*(a+b); 
           fprintf(ficlog," %.12e",xit[j]);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         printf("\n");      printf(".");fflush(stdout);
         fprintf(ficlog,"\n");      fprintf(ficlog,".");fflush(ficlog);
 #endif  #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);
     }      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 }  #endif
       if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 /**** Prevalence limit ****************/        *xmin=x; 
         return fx; 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      } 
 {      ftemp=fu;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      if (fabs(e) > tol1) { 
      matrix by transitions matrix until convergence is reached */        r=(x-w)*(fx-fv); 
         q=(x-v)*(fx-fw); 
   int i, ii,j,k;        p=(x-v)*q-(x-w)*r; 
   double min, max, maxmin, maxmax,sumnew=0.;        q=2.0*(q-r); 
   double **matprod2();        if (q > 0.0) p = -p; 
   double **out, cov[NCOVMAX], **pmij();        q=fabs(q); 
   double **newm;        etemp=e; 
   double agefin, delaymax=50 ; /* Max number of years to converge */        e=d; 
         if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   for (ii=1;ii<=nlstate+ndeath;ii++)          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     for (j=1;j<=nlstate+ndeath;j++){        else { 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);          d=p/q; 
     }          u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
    cov[1]=1.;            d=SIGN(tol1,xm-x); 
          } 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      } else { 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     newm=savm;      } 
     /* Covariates have to be included here again */      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
      cov[2]=agefin;      fu=(*f)(u); 
        if (fu <= fx) { 
       for (k=1; k<=cptcovn;k++) {        if (u >= x) a=x; else b=x; 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        SHFT(v,w,x,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]]);*/          SHFT(fv,fw,fx,fu) 
       }          } else { 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];            if (u < x) a=u; else b=u; 
       for (k=1; k<=cptcovprod;k++)            if (fu <= fw || w == x) { 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];              v=w; 
               w=u; 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/              fv=fw; 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/              fw=fu; 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/            } else if (fu <= fv || v == x || v == w) { 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);              v=u; 
               fv=fu; 
     savm=oldm;            } 
     oldm=newm;          } 
     maxmax=0.;    } 
     for(j=1;j<=nlstate;j++){    nrerror("Too many iterations in brent"); 
       min=1.;    *xmin=x; 
       max=0.;    return fx; 
       for(i=1; i<=nlstate; i++) {  } 
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  /****************** mnbrak ***********************/
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
         min=FMIN(min,prlim[i][j]);              double (*func)(double)) 
       }  { 
       maxmin=max-min;    double ulim,u,r,q, dum;
       maxmax=FMAX(maxmax,maxmin);    double fu; 
     }   
     if(maxmax < ftolpl){    *fa=(*func)(*ax); 
       return prlim;    *fb=(*func)(*bx); 
     }    if (*fb > *fa) { 
   }      SHFT(dum,*ax,*bx,dum) 
 }        SHFT(dum,*fb,*fa,dum) 
         } 
 /*************** transition probabilities ***************/    *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    while (*fb > *fc) { 
 {      r=(*bx-*ax)*(*fb-*fc); 
   double s1, s2;      q=(*bx-*cx)*(*fb-*fa); 
   /*double t34;*/      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   int i,j,j1, nc, ii, jj;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
     for(i=1; i<= nlstate; i++){      if ((*bx-u)*(u-*cx) > 0.0) { 
     for(j=1; j<i;j++){        fu=(*func)(u); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         /*s2 += param[i][j][nc]*cov[nc];*/        fu=(*func)(u); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        if (fu < *fc) { 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       }            SHFT(*fb,*fc,fu,(*func)(u)) 
       ps[i][j]=s2;            } 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     }        u=ulim; 
     for(j=i+1; j<=nlstate+ndeath;j++){        fu=(*func)(u); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      } else { 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        u=(*cx)+GOLD*(*cx-*bx); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        fu=(*func)(u); 
       }      } 
       ps[i][j]=s2;      SHFT(*ax,*bx,*cx,u) 
     }        SHFT(*fa,*fb,*fc,fu) 
   }        } 
     /*ps[3][2]=1;*/  } 
   
   for(i=1; i<= nlstate; i++){  /*************** linmin ************************/
      s1=0;  
     for(j=1; j<i; j++)  int ncom; 
       s1+=exp(ps[i][j]);  double *pcom,*xicom;
     for(j=i+1; j<=nlstate+ndeath; j++)  double (*nrfunc)(double []); 
       s1+=exp(ps[i][j]);   
     ps[i][i]=1./(s1+1.);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     for(j=1; j<i; j++)  { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    double brent(double ax, double bx, double cx, 
     for(j=i+1; j<=nlstate+ndeath; j++)                 double (*f)(double), double tol, double *xmin); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    double f1dim(double x); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   } /* end i */                double *fc, double (*func)(double)); 
     int j; 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    double xx,xmin,bx,ax; 
     for(jj=1; jj<= nlstate+ndeath; jj++){    double fx,fb,fa;
       ps[ii][jj]=0;   
       ps[ii][ii]=1;    ncom=n; 
     }    pcom=vector(1,n); 
   }    xicom=vector(1,n); 
     nrfunc=func; 
     for (j=1;j<=n;j++) { 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      pcom[j]=p[j]; 
     for(jj=1; jj<= nlstate+ndeath; jj++){      xicom[j]=xi[j]; 
      printf("%lf ",ps[ii][jj]);    } 
    }    ax=0.0; 
     printf("\n ");    xx=1.0; 
     }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     printf("\n ");printf("%lf ",cov[2]);*/    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 /*  #ifdef DEBUG
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   goto end;*/    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     return ps;  #endif
 }    for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
 /**************** Product of 2 matrices ******************/      p[j] += xi[j]; 
     } 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    free_vector(xicom,1,n); 
 {    free_vector(pcom,1,n); 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  } 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized  char *asc_diff_time(long time_sec, char ascdiff[])
      before: only the contents of out is modified. The function returns  {
      a pointer to pointers identical to out */    long sec_left, days, hours, minutes;
   long i, j, k;    days = (time_sec) / (60*60*24);
   for(i=nrl; i<= nrh; i++)    sec_left = (time_sec) % (60*60*24);
     for(k=ncolol; k<=ncoloh; k++)    hours = (sec_left) / (60*60) ;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    sec_left = (sec_left) %(60*60);
         out[i][k] +=in[i][j]*b[j][k];    minutes = (sec_left) /60;
     sec_left = (sec_left) % (60);
   return out;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
 }    return ascdiff;
   }
   
 /************* Higher Matrix Product ***************/  /*************** powell ************************/
   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )              double (*func)(double [])) 
 {  { 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    void linmin(double p[], double xi[], int n, double *fret, 
      duration (i.e. until                double (*func)(double [])); 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    int i,ibig,j; 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    double del,t,*pt,*ptt,*xit;
      (typically every 2 years instead of every month which is too big).    double fp,fptt;
      Model is determined by parameters x and covariates have to be    double *xits;
      included manually here.    int niterf, itmp;
   
      */    pt=vector(1,n); 
     ptt=vector(1,n); 
   int i, j, d, h, k;    xit=vector(1,n); 
   double **out, cov[NCOVMAX];    xits=vector(1,n); 
   double **newm;    *fret=(*func)(p); 
     for (j=1;j<=n;j++) pt[j]=p[j]; 
   /* Hstepm could be zero and should return the unit matrix */    for (*iter=1;;++(*iter)) { 
   for (i=1;i<=nlstate+ndeath;i++)      fp=(*fret); 
     for (j=1;j<=nlstate+ndeath;j++){      ibig=0; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);      del=0.0; 
       po[i][j][0]=(i==j ? 1.0 : 0.0);      last_time=curr_time;
     }      (void) gettimeofday(&curr_time,&tzp);
   /* Even if hstepm = 1, at least one multiplication by 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(h=1; h <=nhstepm; h++){      /*    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(d=1; d <=hstepm; d++){      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       newm=savm;      */
       /* Covariates have to be included here again */     for (i=1;i<=n;i++) {
       cov[1]=1.;        printf(" %d %.12f",i, p[i]);
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        fprintf(ficlog," %d %.12lf",i, p[i]);
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        fprintf(ficrespow," %.12lf", p[i]);
       for (k=1; k<=cptcovage;k++)      }
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      printf("\n");
       for (k=1; k<=cptcovprod;k++)      fprintf(ficlog,"\n");
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      fprintf(ficrespow,"\n");fflush(ficrespow);
       if(*iter <=3){
         tm = *localtime(&curr_time.tv_sec);
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        strcpy(strcurr,asctime(&tm));
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  /*       asctime_r(&tm,strcurr); */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        forecast_time=curr_time; 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        itmp = strlen(strcurr);
       savm=oldm;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
       oldm=newm;          strcurr[itmp-1]='\0';
     }        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     for(i=1; i<=nlstate+ndeath; i++)        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       for(j=1;j<=nlstate+ndeath;j++) {        for(niterf=10;niterf<=30;niterf+=10){
         po[i][j][h]=newm[i][j];          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);          tmf = *localtime(&forecast_time.tv_sec);
          */  /*      asctime_r(&tmf,strfor); */
       }          strcpy(strfor,asctime(&tmf));
   } /* end h */          itmp = strlen(strfor);
   return po;          if(strfor[itmp-1]=='\n')
 }          strfor[itmp-1]='\0';
           printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(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);
 /*************** log-likelihood *************/        }
 double func( double *x)      }
 {      for (i=1;i<=n;i++) { 
   int i, ii, j, k, mi, d, kk;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        fptt=(*fret); 
   double **out;  #ifdef DEBUG
   double sw; /* Sum of weights */        printf("fret=%lf \n",*fret);
   double lli; /* Individual log likelihood */        fprintf(ficlog,"fret=%lf \n",*fret);
   long ipmx;  #endif
   /*extern weight */        printf("%d",i);fflush(stdout);
   /* We are differentiating ll according to initial status */        fprintf(ficlog,"%d",i);fflush(ficlog);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        linmin(p,xit,n,fret,func); 
   /*for(i=1;i<imx;i++)        if (fabs(fptt-(*fret)) > del) { 
     printf(" %d\n",s[4][i]);          del=fabs(fptt-(*fret)); 
   */          ibig=i; 
   cov[1]=1.;        } 
   #ifdef DEBUG
   for(k=1; k<=nlstate; k++) ll[k]=0.;        printf("%d %.12e",i,(*fret));
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        fprintf(ficlog,"%d %.12e",i,(*fret));
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        for (j=1;j<=n;j++) {
     for(mi=1; mi<= wav[i]-1; mi++){          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       for (ii=1;ii<=nlstate+ndeath;ii++)          printf(" x(%d)=%.12e",j,xit[j]);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       for(d=0; d<dh[mi][i]; d++){        }
         newm=savm;        for(j=1;j<=n;j++) {
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          printf(" p=%.12e",p[j]);
         for (kk=1; kk<=cptcovage;kk++) {          fprintf(ficlog," p=%.12e",p[j]);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        }
         }        printf("\n");
                fprintf(ficlog,"\n");
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  #endif
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      } 
         savm=oldm;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
         oldm=newm;  #ifdef DEBUG
                int k[2],l;
                k[0]=1;
       } /* end mult */        k[1]=-1;
              printf("Max: %.12e",(*func)(p));
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        fprintf(ficlog,"Max: %.12e",(*func)(p));
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        for (j=1;j<=n;j++) {
       ipmx +=1;          printf(" %.12e",p[j]);
       sw += weight[i];          fprintf(ficlog," %.12e",p[j]);
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        }
     } /* end of wave */        printf("\n");
   } /* end of individual */        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];          for (j=1;j<=n;j++) {
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   return -l;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 }          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 /*********** Maximum Likelihood Estimation ***************/        }
   #endif
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {  
   int i,j, iter;        free_vector(xit,1,n); 
   double **xi,*delti;        free_vector(xits,1,n); 
   double fret;        free_vector(ptt,1,n); 
   xi=matrix(1,npar,1,npar);        free_vector(pt,1,n); 
   for (i=1;i<=npar;i++)        return; 
     for (j=1;j<=npar;j++)      } 
       xi[i][j]=(i==j ? 1.0 : 0.0);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   printf("Powell\n");  fprintf(ficlog,"Powell\n");      for (j=1;j<=n;j++) { 
   powell(p,xi,npar,ftol,&iter,&fret,func);        ptt[j]=2.0*p[j]-pt[j]; 
         xit[j]=p[j]-pt[j]; 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        pt[j]=p[j]; 
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      } 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      fptt=(*func)(ptt); 
       if (fptt < fp) { 
 }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         if (t < 0.0) { 
 /**** Computes Hessian and covariance matrix ***/          linmin(p,xit,n,fret,func); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          for (j=1;j<=n;j++) { 
 {            xi[j][ibig]=xi[j][n]; 
   double  **a,**y,*x,pd;            xi[j][n]=xit[j]; 
   double **hess;          }
   int i, j,jk;  #ifdef DEBUG
   int *indx;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   double hessii(double p[], double delta, int theta, double delti[]);          for(j=1;j<=n;j++){
   double hessij(double p[], double delti[], int i, int j);            printf(" %.12e",xit[j]);
   void lubksb(double **a, int npar, int *indx, double b[]) ;            fprintf(ficlog," %.12e",xit[j]);
   void ludcmp(double **a, int npar, int *indx, double *d) ;          }
           printf("\n");
   hess=matrix(1,npar,1,npar);          fprintf(ficlog,"\n");
   #endif
   printf("\nCalculation of the hessian matrix. Wait...\n");        }
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");      } 
   for (i=1;i<=npar;i++){    } 
     printf("%d",i);fflush(stdout);  } 
     fprintf(ficlog,"%d",i);fflush(ficlog);  
     hess[i][i]=hessii(p,ftolhess,i,delti);  /**** Prevalence limit (stable prevalence)  ****************/
     /*printf(" %f ",p[i]);*/  
     /*printf(" %lf ",hess[i][i]);*/  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   }  {
      /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   for (i=1;i<=npar;i++) {       matrix by transitions matrix until convergence is reached */
     for (j=1;j<=npar;j++)  {  
       if (j>i) {    int i, ii,j,k;
         printf(".%d%d",i,j);fflush(stdout);    double min, max, maxmin, maxmax,sumnew=0.;
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);    double **matprod2();
         hess[i][j]=hessij(p,delti,i,j);    double **out, cov[NCOVMAX], **pmij();
         hess[j][i]=hess[i][j];        double **newm;
         /*printf(" %lf ",hess[i][j]);*/    double agefin, delaymax=50 ; /* Max number of years to converge */
       }  
     }    for (ii=1;ii<=nlstate+ndeath;ii++)
   }      for (j=1;j<=nlstate+ndeath;j++){
   printf("\n");        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficlog,"\n");      }
   
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");     cov[1]=1.;
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");   
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   a=matrix(1,npar,1,npar);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   y=matrix(1,npar,1,npar);      newm=savm;
   x=vector(1,npar);      /* Covariates have to be included here again */
   indx=ivector(1,npar);       cov[2]=agefin;
   for (i=1;i<=npar;i++)    
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        for (k=1; k<=cptcovn;k++) {
   ludcmp(a,npar,indx,&pd);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
   for (j=1;j<=npar;j++) {        }
     for (i=1;i<=npar;i++) x[i]=0;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     x[j]=1;        for (k=1; k<=cptcovprod;k++)
     lubksb(a,npar,indx,x);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     for (i=1;i<=npar;i++){  
       matcov[i][j]=x[i];        /*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]);*/
       out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   printf("\n#Hessian matrix#\n");  
   fprintf(ficlog,"\n#Hessian matrix#\n");      savm=oldm;
   for (i=1;i<=npar;i++) {      oldm=newm;
     for (j=1;j<=npar;j++) {      maxmax=0.;
       printf("%.3e ",hess[i][j]);      for(j=1;j<=nlstate;j++){
       fprintf(ficlog,"%.3e ",hess[i][j]);        min=1.;
     }        max=0.;
     printf("\n");        for(i=1; i<=nlstate; i++) {
     fprintf(ficlog,"\n");          sumnew=0;
   }          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           prlim[i][j]= newm[i][j]/(1-sumnew);
   /* Recompute Inverse */          max=FMAX(max,prlim[i][j]);
   for (i=1;i<=npar;i++)          min=FMIN(min,prlim[i][j]);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        }
   ludcmp(a,npar,indx,&pd);        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
   /*  printf("\n#Hessian matrix recomputed#\n");      }
       if(maxmax < ftolpl){
   for (j=1;j<=npar;j++) {        return prlim;
     for (i=1;i<=npar;i++) x[i]=0;      }
     x[j]=1;    }
     lubksb(a,npar,indx,x);  }
     for (i=1;i<=npar;i++){  
       y[i][j]=x[i];  /*************** transition probabilities ***************/ 
       printf("%.3e ",y[i][j]);  
       fprintf(ficlog,"%.3e ",y[i][j]);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     }  {
     printf("\n");    double s1, s2;
     fprintf(ficlog,"\n");    /*double t34;*/
   }    int i,j,j1, nc, ii, jj;
   */  
       for(i=1; i<= nlstate; i++){
   free_matrix(a,1,npar,1,npar);        for(j=1; j<i;j++){
   free_matrix(y,1,npar,1,npar);          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   free_vector(x,1,npar);            /*s2 += param[i][j][nc]*cov[nc];*/
   free_ivector(indx,1,npar);            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   free_matrix(hess,1,npar,1,npar);  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
           }
           ps[i][j]=s2;
 }  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
         }
 /*************** hessian matrix ****************/        for(j=i+1; j<=nlstate+ndeath;j++){
 double hessii( double x[], double delta, int theta, double delti[])          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];
   int i;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
   int l=1, lmax=20;          }
   double k1,k2;          ps[i][j]=s2;
   double p2[NPARMAX+1];        }
   double res;      }
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      /*ps[3][2]=1;*/
   double fx;      
   int k=0,kmax=10;      for(i=1; i<= nlstate; i++){
   double l1;        s1=0;
         for(j=1; j<i; j++)
   fx=func(x);          s1+=exp(ps[i][j]);
   for (i=1;i<=npar;i++) p2[i]=x[i];        for(j=i+1; j<=nlstate+ndeath; j++)
   for(l=0 ; l <=lmax; l++){          s1+=exp(ps[i][j]);
     l1=pow(10,l);        ps[i][i]=1./(s1+1.);
     delts=delt;        for(j=1; j<i; j++)
     for(k=1 ; k <kmax; k=k+1){          ps[i][j]= exp(ps[i][j])*ps[i][i];
       delt = delta*(l1*k);        for(j=i+1; j<=nlstate+ndeath; j++)
       p2[theta]=x[theta] +delt;          ps[i][j]= exp(ps[i][j])*ps[i][i];
       k1=func(p2)-fx;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       p2[theta]=x[theta]-delt;      } /* end i */
       k2=func(p2)-fx;      
       /*res= (k1-2.0*fx+k2)/delt/delt; */      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        for(jj=1; jj<= nlstate+ndeath; jj++){
                ps[ii][jj]=0;
 #ifdef DEBUG          ps[ii][ii]=1;
       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.)){  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
         k=kmax;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
       }  /*         printf("ddd %lf ",ps[ii][jj]); */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  /*       } */
         k=kmax; l=lmax*10.;  /*       printf("\n "); */
       }  /*        } */
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  /*        printf("\n ");printf("%lf ",cov[2]); */
         delts=delt;         /*
       }        for(i=1; i<= npar; i++) printf("%f ",x[i]);
     }        goto end;*/
   }      return ps;
   delti[theta]=delts;  }
   return res;  
    /**************** Product of 2 matrices ******************/
 }  
   double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
 double hessij( double x[], double delti[], int thetai,int thetaj)  {
 {    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   int i;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   int l=1, l1, lmax=20;    /* in, b, out are matrice of pointers which should have been initialized 
   double k1,k2,k3,k4,res,fx;       before: only the contents of out is modified. The function returns
   double p2[NPARMAX+1];       a pointer to pointers identical to out */
   int k;    long i, j, k;
     for(i=nrl; i<= nrh; i++)
   fx=func(x);      for(k=ncolol; k<=ncoloh; k++)
   for (k=1; k<=2; k++) {        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     for (i=1;i<=npar;i++) p2[i]=x[i];          out[i][k] +=in[i][j]*b[j][k];
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    return out;
     k1=func(p2)-fx;  }
    
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  /************* Higher Matrix Product ***************/
     k2=func(p2)-fx;  
    double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     p2[thetai]=x[thetai]-delti[thetai]/k;  {
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    /* Computes the transition matrix starting at age 'age' over 
     k3=func(p2)-fx;       'nhstepm*hstepm*stepm' months (i.e. until
         age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     p2[thetai]=x[thetai]-delti[thetai]/k;       nhstepm*hstepm matrices. 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     k4=func(p2)-fx;       (typically every 2 years instead of every month which is too big 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */       for the memory).
 #ifdef DEBUG       Model is determined by parameters x and covariates have to be 
     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);       included manually here. 
     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       */
   }  
   return res;    int i, j, d, h, k;
 }    double **out, cov[NCOVMAX];
     double **newm;
 /************** Inverse of matrix **************/  
 void ludcmp(double **a, int n, int *indx, double *d)    /* Hstepm could be zero and should return the unit matrix */
 {    for (i=1;i<=nlstate+ndeath;i++)
   int i,imax,j,k;      for (j=1;j<=nlstate+ndeath;j++){
   double big,dum,sum,temp;        oldm[i][j]=(i==j ? 1.0 : 0.0);
   double *vv;        po[i][j][0]=(i==j ? 1.0 : 0.0);
        }
   vv=vector(1,n);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   *d=1.0;    for(h=1; h <=nhstepm; h++){
   for (i=1;i<=n;i++) {      for(d=1; d <=hstepm; d++){
     big=0.0;        newm=savm;
     for (j=1;j<=n;j++)        /* Covariates have to be included here again */
       if ((temp=fabs(a[i][j])) > big) big=temp;        cov[1]=1.;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     vv[i]=1.0/big;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   }        for (k=1; k<=cptcovage;k++)
   for (j=1;j<=n;j++) {          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for (i=1;i<j;i++) {        for (k=1; k<=cptcovprod;k++)
       sum=a[i][j];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;  
     }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     big=0.0;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     for (i=j;i<=n;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<j;k++)        savm=oldm;
         sum -= a[i][k]*a[k][j];        oldm=newm;
       a[i][j]=sum;      }
       if ( (dum=vv[i]*fabs(sum)) >= big) {      for(i=1; i<=nlstate+ndeath; i++)
         big=dum;        for(j=1;j<=nlstate+ndeath;j++) {
         imax=i;          po[i][j][h]=newm[i][j];
       }          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     }           */
     if (j != imax) {        }
       for (k=1;k<=n;k++) {    } /* end h */
         dum=a[imax][k];    return po;
         a[imax][k]=a[j][k];  }
         a[j][k]=dum;  
       }  
       *d = -(*d);  /*************** log-likelihood *************/
       vv[imax]=vv[j];  double func( double *x)
     }  {
     indx[j]=imax;    int i, ii, j, k, mi, d, kk;
     if (a[j][j] == 0.0) a[j][j]=TINY;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     if (j != n) {    double **out;
       dum=1.0/(a[j][j]);    double sw; /* Sum of weights */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    double lli; /* Individual log likelihood */
     }    int s1, s2;
   }    double bbh, survp;
   free_vector(vv,1,n);  /* Doesn't work */    long ipmx;
 ;    /*extern weight */
 }    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 void lubksb(double **a, int n, int *indx, double b[])    /*for(i=1;i<imx;i++) 
 {      printf(" %d\n",s[4][i]);
   int i,ii=0,ip,j;    */
   double sum;    cov[1]=1.;
    
   for (i=1;i<=n;i++) {    for(k=1; k<=nlstate; k++) ll[k]=0.;
     ip=indx[i];  
     sum=b[ip];    if(mle==1){
     b[ip]=b[i];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     if (ii)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        for(mi=1; mi<= wav[i]-1; mi++){
     else if (sum) ii=i;          for (ii=1;ii<=nlstate+ndeath;ii++)
     b[i]=sum;            for (j=1;j<=nlstate+ndeath;j++){
   }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (i=n;i>=1;i--) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     sum=b[i];            }
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          for(d=0; d<dh[mi][i]; d++){
     b[i]=sum/a[i][i];            newm=savm;
   }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 /************ 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)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 {  /* Some frequencies */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;            oldm=newm;
   int first;          } /* end mult */
   double ***freq; /* Frequencies */        
   double *pp;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   double pos, k2, dateintsum=0,k2cpt=0;          /* But now since version 0.9 we anticipate for bias at large stepm.
   FILE *ficresp;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   char fileresp[FILENAMELENGTH];           * (in months) between two waves is not a multiple of stepm, we rounded to 
             * the nearest (and in case of equal distance, to the lowest) interval but now
   pp=vector(1,nlstate);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   strcpy(fileresp,"p");           * probability in order to take into account the bias as a fraction of the way
   strcat(fileresp,fileres);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   if((ficresp=fopen(fileresp,"w"))==NULL) {           * -stepm/2 to stepm/2 .
     printf("Problem with prevalence resultfile: %s\n", fileresp);           * For stepm=1 the results are the same as for previous versions of Imach.
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);           * For stepm > 1 the results are less biased than in previous versions. 
     exit(0);           */
   }          s1=s[mw[mi][i]][i];
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          s2=s[mw[mi+1][i]][i];
   j1=0;          bbh=(double)bh[mi][i]/(double)stepm; 
            /* bias bh is positive if real duration
   j=cptcoveff;           * is higher than the multiple of stepm and negative otherwise.
   if (cptcovn<1) {j=1;ncodemax[1]=1;}           */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   first=1;          if( s2 > nlstate){ 
             /* i.e. if s2 is a death state and if the date of death is known then the contribution
   for(k1=1; k1<=j;k1++){               to the likelihood is the probability to die between last step unit time and current 
     for(i1=1; i1<=ncodemax[k1];i1++){               step unit time, which is also equal to probability to die before dh 
       j1++;               minus probability to die before dh-stepm . 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);               In version up to 0.92 likelihood was computed
         scanf("%d", i);*/          as if date of death was unknown. Death was treated as any other
       for (i=-1; i<=nlstate+ndeath; i++)            health state: the date of the interview describes the actual state
         for (jk=-1; jk<=nlstate+ndeath; jk++)            and not the date of a change in health state. The former idea was
           for(m=agemin; m <= agemax+3; m++)          to consider that at each interview the state was recorded
             freq[i][jk][m]=0;          (healthy, disable or death) and IMaCh was corrected; but when we
                introduced the exact date of death then we should have modified
       dateintsum=0;          the contribution of an exact death to the likelihood. This new
       k2cpt=0;          contribution is smaller and very dependent of the step unit
       for (i=1; i<=imx; i++) {          stepm. It is no more the probability to die between last interview
         bool=1;          and month of death but the probability to survive from last
         if  (cptcovn>0) {          interview up to one month before death multiplied by the
           for (z1=1; z1<=cptcoveff; z1++)          probability to die within a month. Thanks to Chris
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          Jackson for correcting this bug.  Former versions increased
               bool=0;          mortality artificially. The bad side is that we add another loop
         }          which slows down the processing. The difference can be up to 10%
         if (bool==1) {          lower mortality.
           for(m=firstpass; m<=lastpass; m++){            */
             k2=anint[m][i]+(mint[m][i]/12.);            lli=log(out[s1][s2] - savm[s1][s2]);
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          }else{
               if(agev[m][i]==0) agev[m][i]=agemax+1;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
               if(agev[m][i]==1) agev[m][i]=agemax+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 */
               if (m<lastpass) {          } 
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          /*if(lli ==000.0)*/
               }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
                        ipmx +=1;
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          sw += weight[i];
                 dateintsum=dateintsum+k2;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                 k2cpt++;        } /* end of wave */
               }      } /* end of individual */
             }    }  else if(mle==2){
           }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       }        for(mi=1; mi<= wav[i]-1; mi++){
                  for (ii=1;ii<=nlstate+ndeath;ii++)
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       if  (cptcovn>0) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficresp, "\n#********** Variable ");            }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for(d=0; d<=dh[mi][i]; d++){
         fprintf(ficresp, "**********\n#");            newm=savm;
       }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(i=1; i<=nlstate;i++)            for (kk=1; kk<=cptcovage;kk++) {
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       fprintf(ficresp, "\n");            }
                  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(i=(int)agemin; i <= (int)agemax+3; i++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if(i==(int)agemax+3){            savm=oldm;
           fprintf(ficlog,"Total");            oldm=newm;
         }else{          } /* end mult */
           if(first==1){        
             first=0;          s1=s[mw[mi][i]][i];
             printf("See log file for details...\n");          s2=s[mw[mi+1][i]][i];
           }          bbh=(double)bh[mi][i]/(double)stepm; 
           fprintf(ficlog,"Age %d", i);          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 */
         }          ipmx +=1;
         for(jk=1; jk <=nlstate ; jk++){          sw += weight[i];
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             pp[jk] += freq[jk][m][i];        } /* end of wave */
         }      } /* end of individual */
         for(jk=1; jk <=nlstate ; jk++){    }  else if(mle==3){  /* exponential inter-extrapolation */
           for(m=-1, pos=0; m <=0 ; m++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             pos += freq[jk][m][i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           if(pp[jk]>=1.e-10){        for(mi=1; mi<= wav[i]-1; mi++){
             if(first==1){          for (ii=1;ii<=nlstate+ndeath;ii++)
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            for (j=1;j<=nlstate+ndeath;j++){
             }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }else{            }
             if(first==1)          for(d=0; d<dh[mi][i]; d++){
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            newm=savm;
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           }            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
         for(jk=1; jk <=nlstate ; jk++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             pp[jk] += freq[jk][m][i];            savm=oldm;
         }            oldm=newm;
           } /* end mult */
         for(jk=1,pos=0; jk <=nlstate ; jk++)        
           pos += pp[jk];          s1=s[mw[mi][i]][i];
         for(jk=1; jk <=nlstate ; jk++){          s2=s[mw[mi+1][i]][i];
           if(pos>=1.e-5){          bbh=(double)bh[mi][i]/(double)stepm; 
             if(first==1)          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 */
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          ipmx +=1;
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          sw += weight[i];
           }else{          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             if(first==1)        } /* end of wave */
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      } /* end of individual */
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
           }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           if( i <= (int) agemax){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             if(pos>=1.e-5){        for(mi=1; mi<= wav[i]-1; mi++){
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          for (ii=1;ii<=nlstate+ndeath;ii++)
               probs[i][jk][j1]= pp[jk]/pos;            for (j=1;j<=nlstate+ndeath;j++){
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             else            }
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          for(d=0; d<dh[mi][i]; d++){
           }            newm=savm;
         }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                    for (kk=1; kk<=cptcovage;kk++) {
         for(jk=-1; jk <=nlstate+ndeath; jk++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           for(m=-1; m <=nlstate+ndeath; m++)            }
             if(freq[jk][m][i] !=0 ) {          
             if(first==1)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);            savm=oldm;
             }            oldm=newm;
         if(i <= (int) agemax)          } /* end mult */
           fprintf(ficresp,"\n");        
         if(first==1)          s1=s[mw[mi][i]][i];
           printf("Others in log...\n");          s2=s[mw[mi+1][i]][i];
         fprintf(ficlog,"\n");          if( s2 > nlstate){ 
       }            lli=log(out[s1][s2] - savm[s1][s2]);
     }          }else{
   }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   dateintmean=dateintsum/k2cpt;          }
            ipmx +=1;
   fclose(ficresp);          sw += weight[i];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   free_vector(pp,1,nlstate);  /*      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 */
   /* End of Freq */      } /* end of individual */
 }    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 /************ Prevalence ********************/        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 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(mi=1; mi<= wav[i]-1; mi++){
 {  /* Some frequencies */          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double ***freq; /* Frequencies */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double *pp;            }
   double pos, k2;          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   pp=vector(1,nlstate);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            }
   j1=0;          
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   j=cptcoveff;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            savm=oldm;
              oldm=newm;
   for(k1=1; k1<=j;k1++){          } /* end mult */
     for(i1=1; i1<=ncodemax[k1];i1++){        
       j1++;          s1=s[mw[mi][i]][i];
                s2=s[mw[mi+1][i]][i];
       for (i=-1; i<=nlstate+ndeath; i++)            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         for (jk=-1; jk<=nlstate+ndeath; jk++)            ipmx +=1;
           for(m=agemin; m <= agemax+3; m++)          sw += weight[i];
             freq[i][jk][m]=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
       for (i=1; i<=imx; i++) {        } /* end of wave */
         bool=1;      } /* end of individual */
         if  (cptcovn>0) {    } /* End of if */
           for (z1=1; z1<=cptcoveff; z1++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
               bool=0;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         }    return -l;
         if (bool==1) {  }
           for(m=firstpass; m<=lastpass; m++){  
             k2=anint[m][i]+(mint[m][i]/12.);  /*************** log-likelihood *************/
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  double funcone( double *x)
               if(agev[m][i]==0) agev[m][i]=agemax+1;  {
               if(agev[m][i]==1) agev[m][i]=agemax+2;    /* Same as likeli but slower because of a lot of printf and if */
               if (m<lastpass) {    int i, ii, j, k, mi, d, kk;
                 if (calagedate>0)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    double **out;
                 else    double lli; /* Individual log likelihood */
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    double llt;
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];    int s1, s2;
               }    double bbh, survp;
             }    /*extern weight */
           }    /* We are differentiating ll according to initial status */
         }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       }    /*for(i=1;i<imx;i++) 
       for(i=(int)agemin; i <= (int)agemax+3; i++){      printf(" %d\n",s[4][i]);
         for(jk=1; jk <=nlstate ; jk++){    */
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    cov[1]=1.;
             pp[jk] += freq[jk][m][i];  
         }    for(k=1; k<=nlstate; k++) ll[k]=0.;
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pos=0; m <=0 ; m++)    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             pos += freq[jk][m][i];      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }      for(mi=1; mi<= wav[i]-1; mi++){
                for (ii=1;ii<=nlstate+ndeath;ii++)
         for(jk=1; jk <=nlstate ; jk++){          for (j=1;j<=nlstate+ndeath;j++){
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             pp[jk] += freq[jk][m][i];            savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }          }
                for(d=0; d<dh[mi][i]; d++){
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          newm=savm;
                  cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for(jk=1; jk <=nlstate ; jk++){              for (kk=1; kk<=cptcovage;kk++) {
           if( i <= (int) agemax){            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             if(pos>=1.e-5){          }
               probs[i][jk][j1]= pp[jk]/pos;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             }                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           }          savm=oldm;
         }/* end jk */          oldm=newm;
       }/* end i */        } /* end mult */
     } /* end i1 */        
   } /* end k1 */        s1=s[mw[mi][i]][i];
         s2=s[mw[mi+1][i]][i];
          bbh=(double)bh[mi][i]/(double)stepm; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        /* bias is positive if real duration
   free_vector(pp,1,nlstate);         * is higher than the multiple of stepm and negative otherwise.
           */
 }  /* End of Freq */        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
 /************* Waves Concatenation ***************/        } else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 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 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 */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        } else if(mle==3){  /* exponential inter-extrapolation */
      Death is a valid wave (if date is known).          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 */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        } else if (mle==4){  /* mle=4 no inter-extrapolation */
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          lli=log(out[s1][s2]); /* Original formula */
      and mw[mi+1][i]. dh depends on stepm.        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
      */          lli=log(out[s1][s2]); /* Original formula */
         } /* End of if */
   int i, mi, m;        ipmx +=1;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        sw += weight[i];
      double sum=0., jmean=0.;*/        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int first;  /*       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]); */
   int j, k=0,jk, ju, jl;        if(globpr){
   double sum=0.;          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
   first=0;   %10.6f %10.6f %10.6f ", \
   jmin=1e+5;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   jmax=-1;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   jmean=0.;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   for(i=1; i<=imx; i++){            llt +=ll[k]*gipmx/gsw;
     mi=0;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     m=firstpass;          }
     while(s[m][i] <= nlstate){          fprintf(ficresilk," %10.6f\n", -llt);
       if(s[m][i]>=1)        }
         mw[++mi][i]=m;      } /* end of wave */
       if(m >=lastpass)    } /* end of individual */
         break;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       else    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         m++;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     }/* end while */    if(globpr==0){ /* First time we count the contributions and weights */
     if (s[m][i] > nlstate){      gipmx=ipmx;
       mi++;     /* Death is another wave */      gsw=sw;
       /* if(mi==0)  never been interviewed correctly before death */    }
          /* Only death is a correct wave */    return -l;
       mw[mi][i]=m;  }
     }  
   
     wav[i]=mi;  /*************** function likelione ***********/
     if(mi==0){  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
       if(first==0){  {
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);    /* This routine should help understanding what is done with 
         first=1;       the selection of individuals/waves and
       }       to check the exact contribution to the likelihood.
       if(first==1){       Plotting could be done.
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);     */
       }    int k;
     } /* end mi==0 */  
   }    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
   for(i=1; i<=imx; i++){      strcat(fileresilk,fileres);
     for(mi=1; mi<wav[i];mi++){      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       if (stepm <=0)        printf("Problem with resultfile: %s\n", fileresilk);
         dh[mi][i]=1;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       else{      }
         if (s[mw[mi+1][i]][i] > nlstate) {      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");
           if (agedc[i] < 2*AGESUP) {      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      /*  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(j==0) j=1;  /* Survives at least one month after exam */      for(k=1; k<=nlstate; k++) 
           k=k+1;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
           if (j >= jmax) jmax=j;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
           if (j <= jmin) jmin=j;    }
           sum=sum+j;  
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    *fretone=(*funcone)(p);
           }    if(*globpri !=0){
         }      fclose(ficresilk);
         else{      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      fflush(fichtm); 
           k=k+1;    } 
           if (j >= jmax) jmax=j;    return;
           else if (j <= jmin)jmin=j;  }
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  
           sum=sum+j;  
         }  /*********** Maximum Likelihood Estimation ***************/
         jk= j/stepm;  
         jl= j -jk*stepm;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
         ju= j -(jk+1)*stepm;  {
         if(jl <= -ju)    int i,j, iter;
           dh[mi][i]=jk;    double **xi;
         else    double fret;
           dh[mi][i]=jk+1;    double fretone; /* Only one call to likelihood */
         if(dh[mi][i]==0)    /*  char filerespow[FILENAMELENGTH];*/
           dh[mi][i]=1; /* At least one step */    xi=matrix(1,npar,1,npar);
       }    for (i=1;i<=npar;i++)
     }      for (j=1;j<=npar;j++)
   }        xi[i][j]=(i==j ? 1.0 : 0.0);
   jmean=sum/k;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    strcpy(filerespow,"pow"); 
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    strcat(filerespow,fileres);
  }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
 /*********** Tricode ****************************/      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
 void tricode(int *Tvar, int **nbcode, int imx)    }
 {    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   int Ndum[20],ij=1, k, j, i;    for (i=1;i<=nlstate;i++)
   int cptcode=0;      for(j=1;j<=nlstate+ndeath;j++)
   cptcoveff=0;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
      fprintf(ficrespow,"\n");
   for (k=0; k<19; k++) Ndum[k]=0;  
   for (k=1; k<=7; k++) ncodemax[k]=0;    powell(p,xi,npar,ftol,&iter,&fret,func);
   
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    fclose(ficrespow);
     for (i=1; i<=imx; i++) {    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       ij=(int)(covar[Tvar[j]][i]);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       Ndum[ij]++;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  
       if (ij > cptcode) cptcode=ij;  }
     }  
   /**** Computes Hessian and covariance matrix ***/
     for (i=0; i<=cptcode; i++) {  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       if(Ndum[i]!=0) ncodemax[j]++;  {
     }    double  **a,**y,*x,pd;
     ij=1;    double **hess;
     int i, j,jk;
     int *indx;
     for (i=1; i<=ncodemax[j]; i++) {  
       for (k=0; k<=19; k++) {    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
         if (Ndum[k] != 0) {    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
           nbcode[Tvar[j]][ij]=k;    void lubksb(double **a, int npar, int *indx, double b[]) ;
              void ludcmp(double **a, int npar, int *indx, double *d) ;
           ij++;    double gompertz(double p[]);
         }    hess=matrix(1,npar,1,npar);
         if (ij > ncodemax[j]) break;  
       }      printf("\nCalculation of the hessian matrix. Wait...\n");
     }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   }      for (i=1;i<=npar;i++){
       printf("%d",i);fflush(stdout);
  for (k=0; k<19; k++) Ndum[k]=0;      fprintf(ficlog,"%d",i);fflush(ficlog);
      
  for (i=1; i<=ncovmodel-2; i++) {       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
    ij=Tvar[i];      
    Ndum[ij]++;      /*  printf(" %f ",p[i]);
  }          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }
  ij=1;    
  for (i=1; i<=10; i++) {    for (i=1;i<=npar;i++) {
    if((Ndum[i]!=0) && (i<=ncovcol)){      for (j=1;j<=npar;j++)  {
      Tvaraff[ij]=i;        if (j>i) { 
      ij++;          printf(".%d%d",i,j);fflush(stdout);
    }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
  }          hess[i][j]=hessij(p,delti,i,j,func,npar);
            
  cptcoveff=ij-1;          hess[j][i]=hess[i][j];    
 }          /*printf(" %lf ",hess[i][j]);*/
         }
 /*********** Health Expectancies ****************/      }
     }
 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 )    printf("\n");
     fprintf(ficlog,"\n");
 {  
   /* Health expectancies */    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   double age, agelim, hf;    
   double ***p3mat,***varhe;    a=matrix(1,npar,1,npar);
   double **dnewm,**doldm;    y=matrix(1,npar,1,npar);
   double *xp;    x=vector(1,npar);
   double **gp, **gm;    indx=ivector(1,npar);
   double ***gradg, ***trgradg;    for (i=1;i<=npar;i++)
   int theta;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     ludcmp(a,npar,indx,&pd);
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);  
   xp=vector(1,npar);    for (j=1;j<=npar;j++) {
   dnewm=matrix(1,nlstate*2,1,npar);      for (i=1;i<=npar;i++) x[i]=0;
   doldm=matrix(1,nlstate*2,1,nlstate*2);      x[j]=1;
        lubksb(a,npar,indx,x);
   fprintf(ficreseij,"# Health expectancies\n");      for (i=1;i<=npar;i++){ 
   fprintf(ficreseij,"# Age");        matcov[i][j]=x[i];
   for(i=1; i<=nlstate;i++)      }
     for(j=1; j<=nlstate;j++)    }
       fprintf(ficreseij," %1d-%1d (SE)",i,j);  
   fprintf(ficreseij,"\n");    printf("\n#Hessian matrix#\n");
     fprintf(ficlog,"\n#Hessian matrix#\n");
   if(estepm < stepm){    for (i=1;i<=npar;i++) { 
     printf ("Problem %d lower than %d\n",estepm, stepm);      for (j=1;j<=npar;j++) { 
   }        printf("%.3e ",hess[i][j]);
   else  hstepm=estepm;          fprintf(ficlog,"%.3e ",hess[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      printf("\n");
    * if stepm=24 months pijx are given only every 2 years and by summing them      fprintf(ficlog,"\n");
    * we are calculating an estimate of the Life Expectancy assuming a linear    }
    * progression inbetween and thus overestimating or underestimating according  
    * to the curvature of the survival function. If, for the same date, we    /* Recompute Inverse */
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    for (i=1;i<=npar;i++)
    * to compare the new estimate of Life expectancy with the same linear      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
    * hypothesis. A more precise result, taking into account a more precise    ludcmp(a,npar,indx,&pd);
    * curvature will be obtained if estepm is as small as stepm. */  
     /*  printf("\n#Hessian matrix recomputed#\n");
   /* For example we decided to compute the life expectancy with the smallest unit */  
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    for (j=1;j<=npar;j++) {
      nhstepm is the number of hstepm from age to agelim      for (i=1;i<=npar;i++) x[i]=0;
      nstepm is the number of stepm from age to agelin.      x[j]=1;
      Look at hpijx to understand the reason of that which relies in memory size      lubksb(a,npar,indx,x);
      and note for a fixed period like estepm months */      for (i=1;i<=npar;i++){ 
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        y[i][j]=x[i];
      survival function given by stepm (the optimization length). Unfortunately it        printf("%.3e ",y[i][j]);
      means that if the survival funtion is printed only each two years of age and if        fprintf(ficlog,"%.3e ",y[i][j]);
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      }
      results. So we changed our mind and took the option of the best precision.      printf("\n");
   */      fprintf(ficlog,"\n");
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    }
     */
   agelim=AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    free_matrix(a,1,npar,1,npar);
     /* nhstepm age range expressed in number of stepm */    free_matrix(y,1,npar,1,npar);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    free_vector(x,1,npar);
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    free_ivector(indx,1,npar);
     /* if (stepm >= YEARM) hstepm=1;*/    free_matrix(hess,1,npar,1,npar);
     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*2);  }
     gp=matrix(0,nhstepm,1,nlstate*2);  
     gm=matrix(0,nhstepm,1,nlstate*2);  /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  {
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    int i;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      int l=1, lmax=20;
      double k1,k2;
     double p2[NPARMAX+1];
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    double res;
     double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     /* Computing Variances of health expectancies */    double fx;
     int k=0,kmax=10;
      for(theta=1; theta <=npar; theta++){    double l1;
       for(i=1; i<=npar; i++){  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    fx=func(x);
       }    for (i=1;i<=npar;i++) p2[i]=x[i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      for(l=0 ; l <=lmax; l++){
        l1=pow(10,l);
       cptj=0;      delts=delt;
       for(j=1; j<= nlstate; j++){      for(k=1 ; k <kmax; k=k+1){
         for(i=1; i<=nlstate; i++){        delt = delta*(l1*k);
           cptj=cptj+1;        p2[theta]=x[theta] +delt;
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){        k1=func(p2)-fx;
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        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 */
              
        #ifdef DEBUG
       for(i=1; i<=npar; i++)        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        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);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    #endif
              /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       cptj=0;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       for(j=1; j<= nlstate; j++){          k=kmax;
         for(i=1;i<=nlstate;i++){        }
           cptj=cptj+1;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){          k=kmax; l=lmax*10.;
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        }
           }        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         }          delts=delt;
       }        }
       for(j=1; j<= nlstate*2; j++)      }
         for(h=0; h<=nhstepm-1; h++){    }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    delti[theta]=delts;
         }    return res; 
      }    
      }
 /* End theta */  
   double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);  {
     int i;
      for(h=0; h<=nhstepm-1; h++)    int l=1, l1, lmax=20;
       for(j=1; j<=nlstate*2;j++)    double k1,k2,k3,k4,res,fx;
         for(theta=1; theta <=npar; theta++)    double p2[NPARMAX+1];
           trgradg[h][j][theta]=gradg[h][theta][j];    int k;
        
     fx=func(x);
      for(i=1;i<=nlstate*2;i++)    for (k=1; k<=2; k++) {
       for(j=1;j<=nlstate*2;j++)      for (i=1;i<=npar;i++) p2[i]=x[i];
         varhe[i][j][(int)age] =0.;      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
      printf("%d|",(int)age);fflush(stdout);      k1=func(p2)-fx;
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);    
      for(h=0;h<=nhstepm-1;h++){      p2[thetai]=x[thetai]+delti[thetai]/k;
       for(k=0;k<=nhstepm-1;k++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);      k2=func(p2)-fx;
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);    
         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] += doldm[i][j]*hf*hf;      k3=func(p2)-fx;
       }    
     }      p2[thetai]=x[thetai]-delti[thetai]/k;
     /* Computing expectancies */      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     for(i=1; i<=nlstate;i++)      k4=func(p2)-fx;
       for(j=1; j<=nlstate;j++)      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){  #ifdef DEBUG
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      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);
 /* 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]);*/  #endif
     }
         }    return res;
   }
     fprintf(ficreseij,"%3.0f",age );  
     cptj=0;  /************** Inverse of matrix **************/
     for(i=1; i<=nlstate;i++)  void ludcmp(double **a, int n, int *indx, double *d) 
       for(j=1; j<=nlstate;j++){  { 
         cptj++;    int i,imax,j,k; 
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );    double big,dum,sum,temp; 
       }    double *vv; 
     fprintf(ficreseij,"\n");   
        vv=vector(1,n); 
     free_matrix(gm,0,nhstepm,1,nlstate*2);    *d=1.0; 
     free_matrix(gp,0,nhstepm,1,nlstate*2);    for (i=1;i<=n;i++) { 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);      big=0.0; 
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);      for (j=1;j<=n;j++) 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if ((temp=fabs(a[i][j])) > big) big=temp; 
   }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   printf("\n");      vv[i]=1.0/big; 
   fprintf(ficlog,"\n");    } 
     for (j=1;j<=n;j++) { 
   free_vector(xp,1,npar);      for (i=1;i<j;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<i;k++) sum -= a[i][k]*a[k][j]; 
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);        a[i][j]=sum; 
 }      } 
       big=0.0; 
 /************ Variance ******************/      for (i=j;i<=n;i++) { 
 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)        sum=a[i][j]; 
 {        for (k=1;k<j;k++) 
   /* Variance of health expectancies */          sum -= a[i][k]*a[k][j]; 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        a[i][j]=sum; 
   /* double **newm;*/        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   double **dnewm,**doldm;          big=dum; 
   double **dnewmp,**doldmp;          imax=i; 
   int i, j, nhstepm, hstepm, h, nstepm ;        } 
   int k, cptcode;      } 
   double *xp;      if (j != imax) { 
   double **gp, **gm;  /* for var eij */        for (k=1;k<=n;k++) { 
   double ***gradg, ***trgradg; /*for var eij */          dum=a[imax][k]; 
   double **gradgp, **trgradgp; /* for var p point j */          a[imax][k]=a[j][k]; 
   double *gpp, *gmp; /* for var p point j */          a[j][k]=dum; 
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */        } 
   double ***p3mat;        *d = -(*d); 
   double age,agelim, hf;        vv[imax]=vv[j]; 
   int theta;      } 
   char digit[4];      indx[j]=imax; 
   char digitp[16];      if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
   char fileresprobmorprev[FILENAMELENGTH];        dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   if(popbased==1)      } 
     strcpy(digitp,"-populbased-");    } 
   else    free_vector(vv,1,n);  /* Doesn't work */
     strcpy(digitp,"-stablbased-");  ;
   } 
   strcpy(fileresprobmorprev,"prmorprev");  
   sprintf(digit,"%-d",ij);  void lubksb(double **a, int n, int *indx, double b[]) 
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/  { 
   strcat(fileresprobmorprev,digit); /* Tvar to be done */    int i,ii=0,ip,j; 
   strcat(fileresprobmorprev,digitp); /* Popbased or not */    double sum; 
   strcat(fileresprobmorprev,fileres);   
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {    for (i=1;i<=n;i++) { 
     printf("Problem with resultfile: %s\n", fileresprobmorprev);      ip=indx[i]; 
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);      sum=b[ip]; 
   }      b[ip]=b[i]; 
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);      if (ii) 
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);        for (j=ii;j<=i-1;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");      else if (sum) ii=i; 
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);      b[i]=sum; 
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){    } 
     fprintf(ficresprobmorprev," p.%-d SE",j);    for (i=n;i>=1;i--) { 
     for(i=1; i<=nlstate;i++)      sum=b[i]; 
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   }        b[i]=sum/a[i][i]; 
   fprintf(ficresprobmorprev,"\n");    } 
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {  } 
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);  
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);  /************ Frequencies ********************/
     exit(0);  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 */
   else{    
     fprintf(ficgp,"\n# Routine varevsij");    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   }    int first;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {    double ***freq; /* Frequencies */
     printf("Problem with html file: %s\n", optionfilehtm);    double *pp, **prop;
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     exit(0);    FILE *ficresp;
   }    char fileresp[FILENAMELENGTH];
   else{    
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");    pp=vector(1,nlstate);
   }    prop=matrix(1,nlstate,iagemin,iagemax+3);
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    strcpy(fileresp,"p");
     strcat(fileresp,fileres);
   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");    if((ficresp=fopen(fileresp,"w"))==NULL) {
   fprintf(ficresvij,"# Age");      printf("Problem with prevalence resultfile: %s\n", fileresp);
   for(i=1; i<=nlstate;i++)      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     for(j=1; j<=nlstate;j++)      exit(0);
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    }
   fprintf(ficresvij,"\n");    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
   xp=vector(1,npar);    
   dnewm=matrix(1,nlstate,1,npar);    j=cptcoveff;
   doldm=matrix(1,nlstate,1,nlstate);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);  
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    first=1;
   
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);    for(k1=1; k1<=j;k1++){
   gpp=vector(nlstate+1,nlstate+ndeath);      for(i1=1; i1<=ncodemax[k1];i1++){
   gmp=vector(nlstate+1,nlstate+ndeath);        j1++;
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
            scanf("%d", i);*/
   if(estepm < stepm){        for (i=-1; i<=nlstate+ndeath; i++)  
     printf ("Problem %d lower than %d\n",estepm, stepm);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   }            for(m=iagemin; m <= iagemax+3; m++)
   else  hstepm=estepm;                freq[i][jk][m]=0;
   /* For example we decided to compute the life expectancy with the smallest unit */  
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      for (i=1; i<=nlstate; i++)  
      nhstepm is the number of hstepm from age to agelim        for(m=iagemin; m <= iagemax+3; m++)
      nstepm is the number of stepm from age to agelin.          prop[i][m]=0;
      Look at hpijx to understand the reason of that which relies in memory size        
      and note for a fixed period like k years */        dateintsum=0;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        k2cpt=0;
      survival function given by stepm (the optimization length). Unfortunately it        for (i=1; i<=imx; i++) {
      means that if the survival funtion is printed only each two years of age and if          bool=1;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          if  (cptcovn>0) {
      results. So we changed our mind and took the option of the best precision.            for (z1=1; z1<=cptcoveff; z1++) 
   */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */                bool=0;
   agelim = AGESUP;          }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          if (bool==1){
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            for(m=firstpass; m<=lastpass; m++){
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */              k2=anint[m][i]+(mint[m][i]/12.);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     gp=matrix(0,nhstepm,1,nlstate);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     gm=matrix(0,nhstepm,1,nlstate);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                 if (m<lastpass) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     for(theta=1; theta <=npar; theta++){                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       for(i=1; i<=npar; i++){ /* Computes gradient */                }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                
       }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                    dateintsum=dateintsum+k2;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);                  k2cpt++;
                 }
       if (popbased==1) {                /*}*/
         for(i=1; i<=nlstate;i++)            }
           prlim[i][i]=probs[(int)age][i][ij];          }
       }        }
           
       for(j=1; j<= nlstate; j++){        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        if  (cptcovn>0) {
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          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#");
       /* This for computing forces of mortality (h=1)as a weighted average */        }
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){        for(i=1; i<=nlstate;i++) 
         for(i=1; i<= nlstate; i++)          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
           gpp[j] += prlim[i][i]*p3mat[i][j][1];        fprintf(ficresp, "\n");
       }            
       /* end force of mortality */        for(i=iagemin; i <= iagemax+3; i++){
           if(i==iagemax+3){
       for(i=1; i<=npar; i++) /* Computes gradient */            fprintf(ficlog,"Total");
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          }else{
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              if(first==1){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              first=0;
                printf("See log file for details...\n");
       if (popbased==1) {            }
         for(i=1; i<=nlstate;i++)            fprintf(ficlog,"Age %d", i);
           prlim[i][i]=probs[(int)age][i][ij];          }
       }          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       for(j=1; j<= nlstate; j++){              pp[jk] += freq[jk][m][i]; 
         for(h=0; h<=nhstepm; h++){          }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            for(m=-1, pos=0; m <=0 ; m++)
         }              pos += freq[jk][m][i];
       }            if(pp[jk]>=1.e-10){
       /* This for computing force of mortality (h=1)as a weighted average */              if(first==1){
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         for(i=1; i<= nlstate; i++)              }
           gmp[j] += prlim[i][i]*p3mat[i][j][1];              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       }                }else{
       /* end force of mortality */              if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       for(j=1; j<= nlstate; j++) /* vareij */              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         for(h=0; h<=nhstepm; h++){            }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          }
         }  
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */          for(jk=1; jk <=nlstate ; jk++){
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       }              pp[jk] += freq[jk][m][i];
           }       
     } /* End theta */          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */            posprop += prop[jk][i];
           }
     for(h=0; h<=nhstepm; h++) /* veij */          for(jk=1; jk <=nlstate ; jk++){
       for(j=1; j<=nlstate;j++)            if(pos>=1.e-5){
         for(theta=1; theta <=npar; theta++)              if(first==1)
           trgradg[h][j][theta]=gradg[h][theta][j];                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */            }else{
       for(theta=1; theta <=npar; theta++)              if(first==1)
         trgradgp[j][theta]=gradgp[theta][j];                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            }
     for(i=1;i<=nlstate;i++)            if( i <= iagemax){
       for(j=1;j<=nlstate;j++)              if(pos>=1.e-5){
         vareij[i][j][(int)age] =0.;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
     for(h=0;h<=nhstepm;h++){                /*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(k=0;k<=nhstepm;k++){              }
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);              else
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
         for(i=1;i<=nlstate;i++)            }
           for(j=1;j<=nlstate;j++)          }
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          
       }          for(jk=-1; jk <=nlstate+ndeath; jk++)
     }            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
     /* pptj */              if(first==1)
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     for(j=nlstate+1;j<=nlstate+ndeath;j++)              }
       for(i=nlstate+1;i<=nlstate+ndeath;i++)          if(i <= iagemax)
         varppt[j][i]=doldmp[j][i];            fprintf(ficresp,"\n");
     /* end ppptj */          if(first==1)
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);              printf("Others in log...\n");
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);          fprintf(ficlog,"\n");
          }
     if (popbased==1) {      }
       for(i=1; i<=nlstate;i++)    }
         prlim[i][i]=probs[(int)age][i][ij];    dateintmean=dateintsum/k2cpt; 
     }   
        fclose(ficresp);
     /* This for computing force of mortality (h=1)as a weighted average */    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){    free_vector(pp,1,nlstate);
       for(i=1; i<= nlstate; i++)    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
         gmp[j] += prlim[i][i]*p3mat[i][j][1];    /* End of Freq */
     }      }
     /* end force of mortality */  
   /************ Prevalence ********************/
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);  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(j=nlstate+1; j<=(nlstate+ndeath);j++){  {  
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       for(i=1; i<=nlstate;i++){       in each health status at the date of interview (if between dateprev1 and dateprev2).
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);       We still use firstpass and lastpass as another selection.
       }    */
     }   
     fprintf(ficresprobmorprev,"\n");    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     double ***freq; /* Frequencies */
     fprintf(ficresvij,"%.0f ",age );    double *pp, **prop;
     for(i=1; i<=nlstate;i++)    double pos,posprop; 
       for(j=1; j<=nlstate;j++){    double  y2; /* in fractional years */
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    int iagemin, iagemax;
       }  
     fprintf(ficresvij,"\n");    iagemin= (int) agemin;
     free_matrix(gp,0,nhstepm,1,nlstate);    iagemax= (int) agemax;
     free_matrix(gm,0,nhstepm,1,nlstate);    /*pp=vector(1,nlstate);*/
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    j1=0;
   } /* End age */    
   free_vector(gpp,nlstate+1,nlstate+ndeath);    j=cptcoveff;
   free_vector(gmp,nlstate+1,nlstate+ndeath);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);    
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/    for(k1=1; k1<=j;k1++){
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");      for(i1=1; i1<=ncodemax[k1];i1++){
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */        j1++;
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");        
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);        for (i=1; i<=nlstate; i++)  
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);          for(m=iagemin; m <= iagemax+3; m++)
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);            prop[i][m]=0.0;
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);       
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);        for (i=1; i<=imx; i++) { /* Each individual */
   /*  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);          bool=1;
 */          if  (cptcovn>0) {
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   free_vector(xp,1,npar);                bool=0;
   free_matrix(doldm,1,nlstate,1,nlstate);          } 
   free_matrix(dnewm,1,nlstate,1,npar);          if (bool==1) { 
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   fclose(ficresprobmorprev);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   fclose(ficgp);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   fclose(fichtm);                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                 if (s[m][i]>0 && s[m][i]<=nlstate) { 
 }                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];
 /************ Variance of prevlim ******************/                  prop[s[m][i]][iagemax+3] += weight[i]; 
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)                } 
 {              }
   /* Variance of prevalence limit */            } /* end selection of waves */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          }
   double **newm;        }
   double **dnewm,**doldm;        for(i=iagemin; i <= iagemax+3; i++){  
   int i, j, nhstepm, hstepm;          
   int k, cptcode;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   double *xp;            posprop += prop[jk][i]; 
   double *gp, *gm;          } 
   double **gradg, **trgradg;  
   double age,agelim;          for(jk=1; jk <=nlstate ; jk++){     
   int theta;            if( i <=  iagemax){ 
                  if(posprop>=1.e-5){ 
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");                probs[i][jk][j1]= prop[jk][i]/posprop;
   fprintf(ficresvpl,"# Age");              } 
   for(i=1; i<=nlstate;i++)            } 
       fprintf(ficresvpl," %1d-%1d",i,i);          }/* end jk */ 
   fprintf(ficresvpl,"\n");        }/* end i */ 
       } /* end i1 */
   xp=vector(1,npar);    } /* end k1 */
   dnewm=matrix(1,nlstate,1,npar);    
   doldm=matrix(1,nlstate,1,nlstate);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
      /*free_vector(pp,1,nlstate);*/
   hstepm=1*YEARM; /* Every year of age */    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  }  /* End of prevalence */
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  /************* Waves Concatenation ***************/
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
     if (stepm >= YEARM) hstepm=1;  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)
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  {
     gradg=matrix(1,npar,1,nlstate);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     gp=vector(1,nlstate);       Death is a valid wave (if date is known).
     gm=vector(1,nlstate);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
        dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     for(theta=1; theta <=npar; theta++){       and mw[mi+1][i]. dh depends on stepm.
       for(i=1; i<=npar; i++){ /* Computes gradient */       */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }    int i, mi, m;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       for(i=1;i<=nlstate;i++)       double sum=0., jmean=0.;*/
         gp[i] = prlim[i][i];    int first;
        int j, k=0,jk, ju, jl;
       for(i=1; i<=npar; i++) /* Computes gradient */    double sum=0.;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    first=0;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    jmin=1e+5;
       for(i=1;i<=nlstate;i++)    jmax=-1;
         gm[i] = prlim[i][i];    jmean=0.;
     for(i=1; i<=imx; i++){
       for(i=1;i<=nlstate;i++)      mi=0;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      m=firstpass;
     } /* End theta */      while(s[m][i] <= nlstate){
         if(s[m][i]>=1)
     trgradg =matrix(1,nlstate,1,npar);          mw[++mi][i]=m;
         if(m >=lastpass)
     for(j=1; j<=nlstate;j++)          break;
       for(theta=1; theta <=npar; theta++)        else
         trgradg[j][theta]=gradg[theta][j];          m++;
       }/* end while */
     for(i=1;i<=nlstate;i++)      if (s[m][i] > nlstate){
       varpl[i][(int)age] =0.;        mi++;     /* Death is another wave */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        /* if(mi==0)  never been interviewed correctly before death */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);           /* Only death is a correct wave */
     for(i=1;i<=nlstate;i++)        mw[mi][i]=m;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      }
   
     fprintf(ficresvpl,"%.0f ",age );      wav[i]=mi;
     for(i=1; i<=nlstate;i++)      if(mi==0){
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        nbwarn++;
     fprintf(ficresvpl,"\n");        if(first==0){
     free_vector(gp,1,nlstate);          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     free_vector(gm,1,nlstate);          first=1;
     free_matrix(gradg,1,npar,1,nlstate);        }
     free_matrix(trgradg,1,nlstate,1,npar);        if(first==1){
   } /* End age */          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
         }
   free_vector(xp,1,npar);      } /* end mi==0 */
   free_matrix(doldm,1,nlstate,1,npar);    } /* End individuals */
   free_matrix(dnewm,1,nlstate,1,nlstate);  
     for(i=1; i<=imx; i++){
 }      for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
 /************ Variance of one-step probabilities  ******************/          dh[mi][i]=1;
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)        else{
 {          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   int i, j=0,  i1, k1, l1, t, tj;            if (agedc[i] < 2*AGESUP) {
   int k2, l2, j1,  z1;              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   int k=0,l, cptcode;              if(j==0) j=1;  /* Survives at least one month after exam */
   int first=1, first1;              else if(j<0){
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;                nberr++;
   double **dnewm,**doldm;                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]);
   double *xp;                j=1; /* Temporary Dangerous patch */
   double *gp, *gm;                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 **gradg, **trgradg;                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 **mu;                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 age,agelim, cov[NCOVMAX];              }
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */              k=k+1;
   int theta;              if (j >= jmax) jmax=j;
   char fileresprob[FILENAMELENGTH];              if (j <= jmin) jmin=j;
   char fileresprobcov[FILENAMELENGTH];              sum=sum+j;
   char fileresprobcor[FILENAMELENGTH];              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   double ***varpij;            }
           }
   strcpy(fileresprob,"prob");          else{
   strcat(fileresprob,fileres);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     printf("Problem with resultfile: %s\n", fileresprob);            k=k+1;
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);            if (j >= jmax) jmax=j;
   }            else if (j <= jmin)jmin=j;
   strcpy(fileresprobcov,"probcov");            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   strcat(fileresprobcov,fileres);            /*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]);*/
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {            if(j<0){
     printf("Problem with resultfile: %s\n", fileresprobcov);              nberr++;
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   }              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   strcpy(fileresprobcor,"probcor");            }
   strcat(fileresprobcor,fileres);            sum=sum+j;
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {          }
     printf("Problem with resultfile: %s\n", fileresprobcor);          jk= j/stepm;
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);          jl= j -jk*stepm;
   }          ju= j -(jk+1)*stepm;
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);            if(jl==0){
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);              dh[mi][i]=jk;
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);              bh[mi][i]=0;
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);            }else{ /* We want a negative bias in order to only have interpolation ie
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);                    * at the price of an extra matrix product in likelihood */
                dh[mi][i]=jk+1;
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");              bh[mi][i]=ju;
   fprintf(ficresprob,"# Age");            }
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");          }else{
   fprintf(ficresprobcov,"# Age");            if(jl <= -ju){
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");              dh[mi][i]=jk;
   fprintf(ficresprobcov,"# Age");              bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
                                    */
   for(i=1; i<=nlstate;i++)            }
     for(j=1; j<=(nlstate+ndeath);j++){            else{
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);              dh[mi][i]=jk+1;
       fprintf(ficresprobcov," p%1d-%1d ",i,j);              bh[mi][i]=ju;
       fprintf(ficresprobcor," p%1d-%1d ",i,j);            }
     }              if(dh[mi][i]==0){
   fprintf(ficresprob,"\n");              dh[mi][i]=1; /* At least one step */
   fprintf(ficresprobcov,"\n");              bh[mi][i]=ju; /* At least one step */
   fprintf(ficresprobcor,"\n");              /*  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);*/
   xp=vector(1,npar);            }
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);          } /* end if mle */
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));        }
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);      } /* end wave */
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);    }
   first=1;    jmean=sum/k;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);   }
     exit(0);  
   }  /*********** Tricode ****************************/
   else{  void tricode(int *Tvar, int **nbcode, int imx)
     fprintf(ficgp,"\n# Routine varprob");  {
   }    
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {    int Ndum[20],ij=1, k, j, i, maxncov=19;
     printf("Problem with html file: %s\n", optionfilehtm);    int cptcode=0;
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);    cptcoveff=0; 
     exit(0);   
   }    for (k=0; k<maxncov; k++) Ndum[k]=0;
   else{    for (k=1; k<=7; k++) ncodemax[k]=0;
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");  
     fprintf(fichtm,"\n");    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");                                 modality*/ 
     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");        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     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");        Ndum[ij]++; /*store the modality */
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   }        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                                          Tvar[j]. If V=sex and male is 0 and 
                                           female is 1, then  cptcode=1.*/
   cov[1]=1;      }
   tj=cptcoveff;  
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}      for (i=0; i<=cptcode; i++) {
   j1=0;        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 */
   for(t=1; t<=tj;t++){      }
     for(i1=1; i1<=ncodemax[t];i1++){  
       j1++;      ij=1; 
            for (i=1; i<=ncodemax[j]; i++) {
       if  (cptcovn>0) {        for (k=0; k<= maxncov; k++) {
         fprintf(ficresprob, "\n#********** Variable ");          if (Ndum[k] != 0) {
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            nbcode[Tvar[j]][ij]=k; 
         fprintf(ficresprob, "**********\n#");            /* 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; */
         fprintf(ficresprobcov, "\n#********** Variable ");            
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            ij++;
         fprintf(ficresprobcov, "**********\n#");          }
                  if (ij > ncodemax[j]) break; 
         fprintf(ficgp, "\n#********** Variable ");        }  
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      } 
         fprintf(ficgp, "**********\n#");    }  
          
           for (k=0; k< maxncov; k++) Ndum[k]=0;
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");  
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);   for (i=1; i<=ncovmodel-2; i++) { 
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");     /* 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(ficresprobcor, "\n#********** Variable ");         Ndum[ij]++;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);   }
         fprintf(ficgp, "**********\n#");      
       }   ij=1;
         for (i=1; i<= maxncov; i++) {
       for (age=bage; age<=fage; age ++){     if((Ndum[i]!=0) && (i<=ncovcol)){
         cov[2]=age;       Tvaraff[ij]=i; /*For printing */
         for (k=1; k<=cptcovn;k++) {       ij++;
           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];   
         for (k=1; k<=cptcovprod;k++)   cptcoveff=ij-1; /*Number of simple covariates*/
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  }
          
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));  /*********** Health Expectancies ****************/
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);  
         gp=vector(1,(nlstate)*(nlstate+ndeath));  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 )
         gm=vector(1,(nlstate)*(nlstate+ndeath));  
      {
         for(theta=1; theta <=npar; theta++){    /* Health expectancies */
           for(i=1; i<=npar; i++)    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    double age, agelim, hf;
              double ***p3mat,***varhe;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    double **dnewm,**doldm;
              double *xp;
           k=0;    double **gp, **gm;
           for(i=1; i<= (nlstate); i++){    double ***gradg, ***trgradg;
             for(j=1; j<=(nlstate+ndeath);j++){    int theta;
               k=k+1;  
               gp[k]=pmmij[i][j];    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
             }    xp=vector(1,npar);
           }    dnewm=matrix(1,nlstate*nlstate,1,npar);
              doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
           for(i=1; i<=npar; i++)    
             xp[i] = x[i] - (i==theta ?delti[theta]:0);    fprintf(ficreseij,"# Health expectancies\n");
        fprintf(ficreseij,"# Age");
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    for(i=1; i<=nlstate;i++)
           k=0;      for(j=1; j<=nlstate;j++)
           for(i=1; i<=(nlstate); i++){        fprintf(ficreseij," %1d-%1d (SE)",i,j);
             for(j=1; j<=(nlstate+ndeath);j++){    fprintf(ficreseij,"\n");
               k=k+1;  
               gm[k]=pmmij[i][j];    if(estepm < stepm){
             }      printf ("Problem %d lower than %d\n",estepm, stepm);
           }    }
          else  hstepm=estepm;   
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)    /* We compute the life expectancy from trapezoids spaced every estepm months
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];       * 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(j=1; j<=(nlstate)*(nlstate+ndeath);j++)     * progression in between and thus overestimating or underestimating according
           for(theta=1; theta <=npar; theta++)     * to the curvature of the survival function. If, for the same date, we 
             trgradg[j][theta]=gradg[theta][j];     * 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 
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);     * hypothesis. A more precise result, taking into account a more precise
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);     * curvature will be obtained if estepm is as small as stepm. */
          
         pmij(pmmij,cov,ncovmodel,x,nlstate);    /* For example we decided to compute the life expectancy with the smallest unit */
            /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         k=0;       nhstepm is the number of hstepm from age to agelim 
         for(i=1; i<=(nlstate); i++){       nstepm is the number of stepm from age to agelin. 
           for(j=1; j<=(nlstate+ndeath);j++){       Look at hpijx to understand the reason of that which relies in memory size
             k=k+1;       and note for a fixed period like estepm months */
             mu[k][(int) age]=pmmij[i][j];    /* 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
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)       results. So we changed our mind and took the option of the best precision.
             varpij[i][j][(int)age] = doldm[i][j];    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         /*printf("\n%d ",(int)age);  
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    agelim=AGESUP;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      /* 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 */ 
         fprintf(ficresprob,"\n%d ",(int)age);      /* if (stepm >= YEARM) hstepm=1;*/
         fprintf(ficresprobcov,"\n%d ",(int)age);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         fprintf(ficresprobcor,"\n%d ",(int)age);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)      gp=matrix(0,nhstepm,1,nlstate*nlstate);
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));      gm=matrix(0,nhstepm,1,nlstate*nlstate);
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){  
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
         }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
         i=0;   
         for (k=1; k<=(nlstate);k++){  
           for (l=1; l<=(nlstate+ndeath);l++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
             i=i++;  
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);      /* Computing  Variances of health expectancies */
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);  
             for (j=1; j<=i;j++){       for(theta=1; theta <=npar; theta++){
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);        for(i=1; i<=npar; i++){ 
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             }        }
           }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         }/* end of loop for state */    
       } /* end of loop for age */        cptj=0;
         for(j=1; j<= nlstate; j++){
       /* Confidence intervalle of pij  */          for(i=1; i<=nlstate; i++){
       /*            cptj=cptj+1;
       fprintf(ficgp,"\nset noparametric;unset label");            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");            }
       fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);          }
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);        }
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);       
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);       
       */        for(i=1; i<=npar; i++) 
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       first1=1;        
       for (k2=1; k2<=(nlstate);k2++){        cptj=0;
         for (l2=1; l2<=(nlstate+ndeath);l2++){        for(j=1; j<= nlstate; j++){
           if(l2==k2) continue;          for(i=1;i<=nlstate;i++){
           j=(k2-1)*(nlstate+ndeath)+l2;            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;            }
               if(i<=j) continue;          }
               for (age=bage; age<=fage; age ++){        }
                 if ((int)age %5==0){        for(j=1; j<= nlstate*nlstate; j++)
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;          for(h=0; h<=nhstepm-1; h++){
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;          }
                   mu1=mu[i][(int) age]/stepm*YEARM ;       } 
                   mu2=mu[j][(int) age]/stepm*YEARM;     
                   c12=cv12/sqrt(v1*v2);  /* End theta */
                   /* Computing eigen value of matrix of covariance */  
                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;  
                   /* Eigen vectors */       for(h=0; h<=nhstepm-1; h++)
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));        for(j=1; j<=nlstate*nlstate;j++)
                   /*v21=sqrt(1.-v11*v11); *//* error */          for(theta=1; theta <=npar; theta++)
                   v21=(lc1-v1)/cv12*v11;            trgradg[h][j][theta]=gradg[h][theta][j];
                   v12=-v21;       
                   v22=v11;  
                   tnalp=v21/v11;       for(i=1;i<=nlstate*nlstate;i++)
                   if(first1==1){        for(j=1;j<=nlstate*nlstate;j++)
                     first1=0;          varhe[i][j][(int)age] =0.;
                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);  
                   }       printf("%d|",(int)age);fflush(stdout);
                   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);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                   /*printf(fignu*/       for(h=0;h<=nhstepm-1;h++){
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */        for(k=0;k<=nhstepm-1;k++){
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
                   if(first==1){          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
                     first=0;          for(i=1;i<=nlstate*nlstate;i++)
                     fprintf(ficgp,"\nset parametric;unset label");            for(j=1;j<=nlstate*nlstate;j++)
                     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);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");        }
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);      }
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);      /* Computing expectancies */
                     fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);      for(i=1; i<=nlstate;i++)
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);        for(j=1; j<=nlstate;j++)
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);          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, k1,l1,k2,l2);            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)) not",\            
                             mu1,std,v11,sqrt(lc1),v12,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]);*/
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));  
                   }else{          }
                     first=0;  
                     fprintf(fichtm," %d (%.3f),",(int) age, c12);      fprintf(ficreseij,"%3.0f",age );
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);      cptj=0;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);      for(i=1; i<=nlstate;i++)
                     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",\        for(j=1; j<=nlstate;j++){
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\          cptj++;
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
                   }/* if first */        }
                 } /* age mod 5 */      fprintf(ficreseij,"\n");
               } /* end loop age */     
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
               first=1;      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
             } /*l12 */      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
           } /* k12 */      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
         } /*l1 */      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }/* k1 */    }
     } /* loop covariates */    printf("\n");
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);    fprintf(ficlog,"\n");
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    free_vector(xp,1,npar);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }  }
   free_vector(xp,1,npar);  
   fclose(ficresprob);  /************ Variance ******************/
   fclose(ficresprobcov);  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)
   fclose(ficresprobcor);  {
   fclose(ficgp);    /* Variance of health expectancies */
   fclose(fichtm);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
 }    /* double **newm;*/
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
 /******************* Printing html file ***********/    int i, j, nhstepm, hstepm, h, nstepm ;
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    int k, cptcode;
                   int lastpass, int stepm, int weightopt, char model[],\    double *xp;
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\    double **gp, **gm;  /* for var eij */
                   int popforecast, int estepm ,\    double ***gradg, ***trgradg; /*for var eij */
                   double jprev1, double mprev1,double anprev1, \    double **gradgp, **trgradgp; /* for var p point j */
                   double jprev2, double mprev2,double anprev2){    double *gpp, *gmp; /* for var p point j */
   int jj1, k1, i1, cpt;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   /*char optionfilehtm[FILENAMELENGTH];*/    double ***p3mat;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {    double age,agelim, hf;
     printf("Problem with %s \n",optionfilehtm), exit(0);    double ***mobaverage;
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);    int theta;
   }    char digit[4];
     char digitp[25];
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n  
  - 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    char fileresprobmorprev[FILENAMELENGTH];
  - 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(popbased==1){
  - Life expectancies by age and initial health status (estepm=%2d months):      if(mobilav!=0)
    <a href=\"e%s\">e%s</a> <br>\n</li>", \        strcpy(digitp,"-populbased-mobilav-");
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);      else strcpy(digitp,"-populbased-nomobil-");
     }
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");    else 
       strcpy(digitp,"-stablbased-");
  m=cptcoveff;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  jj1=0;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
  for(k1=1; k1<=m;k1++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
    for(i1=1; i1<=ncodemax[k1];i1++){        printf(" Error in movingaverage mobilav=%d\n",mobilav);
      jj1++;      }
      if (cptcovn > 0) {    }
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  
        for (cpt=1; cpt<=cptcoveff;cpt++)    strcpy(fileresprobmorprev,"prmorprev"); 
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    sprintf(digit,"%-d",ij);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
      }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
      /* Pij */    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
      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>    strcat(fileresprobmorprev,fileres);
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
      /* Quasi-incidences */      printf("Problem with resultfile: %s\n", fileresprobmorprev);
      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>      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    }
        /* Stable prevalence in each health state */    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
        for(cpt=1; cpt<nlstate;cpt++){    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    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);
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
        }    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
      for(cpt=1; cpt<=nlstate;cpt++) {      fprintf(ficresprobmorprev," p.%-d SE",j);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>      for(i=1; i<=nlstate;i++)
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
      }    }  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    fprintf(ficresprobmorprev,"\n");
 health expectancies in states (1) and (2): e%s%d.png<br>    fprintf(ficgp,"\n# Routine varevsij");
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),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");
    } /* end i1 */    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
  }/* End k1 */  /*   } */
  fprintf(fichtm,"</ul>");    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     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><li><h4> Result files (second order: variances)</h4>\n    fprintf(ficresvij,"# Age");
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n    for(i=1; i<=nlstate;i++)
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n      for(j=1; j<=nlstate;j++)
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n    fprintf(ficresvij,"\n");
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n  
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n    xp=vector(1,npar);
  - 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);    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
  if(popforecast==1) fprintf(fichtm,"\n    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n  
         <br>",fileres,fileres,fileres,fileres);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
  else    gpp=vector(nlstate+1,nlstate+ndeath);
    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);    gmp=vector(nlstate+1,nlstate+ndeath);
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
  m=cptcoveff;    if(estepm < stepm){
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
  jj1=0;    else  hstepm=estepm;   
  for(k1=1; k1<=m;k1++){    /* For example we decided to compute the life expectancy with the smallest unit */
    for(i1=1; i1<=ncodemax[k1];i1++){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      jj1++;       nhstepm is the number of hstepm from age to agelim 
      if (cptcovn > 0) {       nstepm is the number of stepm from age to agelin. 
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");       Look at hpijx to understand the reason of that which relies in memory size
        for (cpt=1; cpt<=cptcoveff;cpt++)       and note for a fixed period like k years */
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");       survival function given by stepm (the optimization length). Unfortunately it
      }       means that if the survival funtion is printed every two years of age and if
      for(cpt=1; cpt<=nlstate;cpt++) {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident       results. So we changed our mind and took the option of the best precision.
 interval) in state (%d): v%s%d%d.png <br>    */
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      }    agelim = AGESUP;
    } /* end i1 */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
  }/* End k1 */      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
  fprintf(fichtm,"</ul>");      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 fclose(fichtm);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
 /******************* Gnuplot file **************/      gm=matrix(0,nhstepm,1,nlstate);
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  
   
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      for(theta=1; theta <=npar; theta++){
   int ng;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     printf("Problem with file %s",optionfilegnuplot);        }
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
 #ifdef windows        if (popbased==1) {
     fprintf(ficgp,"cd \"%s\" \n",pathc);          if(mobilav ==0){
 #endif            for(i=1; i<=nlstate;i++)
 m=pow(2,cptcoveff);              prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
  /* 1eme*/            for(i=1; i<=nlstate;i++)
   for (cpt=1; cpt<= nlstate ; cpt ++) {              prlim[i][i]=mobaverage[(int)age][i][ij];
    for (k1=1; k1<= m ; k1 ++) {          }
         }
 #ifdef windows    
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        for(j=1; j<= nlstate; j++){
      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);          for(h=0; h<=nhstepm; h++){
 #endif            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
 #ifdef unix              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          }
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);        }
 #endif        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
 for (i=1; i<= nlstate ; i ++) {           as a weighted average of prlim.
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        */
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
 }          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     for (i=1; i<= nlstate ; i ++) {        }    
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        /* end probability of death */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
      for (i=1; i<= nlstate ; i ++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   else fprintf(ficgp," \%%*lf (\%%*lf)");   
 }          if (popbased==1) {
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          if(mobilav ==0){
 #ifdef unix            for(i=1; i<=nlstate;i++)
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");              prlim[i][i]=probs[(int)age][i][ij];
 #endif          }else{ /* mobilav */ 
    }            for(i=1; i<=nlstate;i++)
   }              prlim[i][i]=mobaverage[(int)age][i][ij];
   /*2 eme*/          }
         }
   for (k1=1; k1<= m ; k1 ++) {  
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);        for(j=1; j<= nlstate; j++){
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);          for(h=0; h<=nhstepm; h++){
                for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     for (i=1; i<= nlstate+1 ; i ++) {              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
       k=2*i;          }
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        }
       for (j=1; j<= nlstate+1 ; j ++) {        /* This for computing probability of death (h=1 means
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");           computed over hstepm matrices product = hstepm*stepm months) 
   else fprintf(ficgp," \%%*lf (\%%*lf)");           as a weighted average of prlim.
 }          */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
       for (j=1; j<= nlstate+1 ; j ++) {        }    
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        /* end probability of death */
         else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }          for(j=1; j<= nlstate; j++) /* vareij */
       fprintf(ficgp,"\" t\"\" w l 0,");          for(h=0; h<=nhstepm; h++){
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       for (j=1; j<= nlstate+1 ; j ++) {          }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
 }            gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        }
       else fprintf(ficgp,"\" t\"\" w l 0,");  
     }      } /* End theta */
   }  
        trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   /*3eme*/  
       for(h=0; h<=nhstepm; h++) /* veij */
   for (k1=1; k1<= m ; k1 ++) {        for(j=1; j<=nlstate;j++)
     for (cpt=1; cpt<= nlstate ; cpt ++) {          for(theta=1; theta <=npar; theta++)
       k=2+nlstate*(2*cpt-2);            trgradg[h][j][theta]=gradg[h][theta][j];
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        for(theta=1; theta <=npar; theta++)
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          trgradgp[j][theta]=gradgp[theta][j];
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 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] =0.;
       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);      for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
       }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     }          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   }          for(i=1;i<=nlstate;i++)
              for(j=1;j<=nlstate;j++)
   /* CV preval stat */              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     for (k1=1; k1<= m ; k1 ++) {        }
     for (cpt=1; cpt<nlstate ; cpt ++) {      }
       k=3;    
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      /* pptj */
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for (i=1; i< nlstate ; i ++)      for(j=nlstate+1;j<=nlstate+ndeath;j++)
         fprintf(ficgp,"+$%d",k+i+1);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          varppt[j][i]=doldmp[j][i];
            /* end ppptj */
       l=3+(nlstate+ndeath)*cpt;      /*  x centered again */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       for (i=1; i< nlstate ; i ++) {      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
         l=3+(nlstate+ndeath)*cpt;   
         fprintf(ficgp,"+$%d",l+i+1);      if (popbased==1) {
       }        if(mobilav ==0){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            for(i=1; i<=nlstate;i++)
     }            prlim[i][i]=probs[(int)age][i][ij];
   }          }else{ /* mobilav */ 
            for(i=1; i<=nlstate;i++)
   /* proba elementaires */            prlim[i][i]=mobaverage[(int)age][i][ij];
    for(i=1,jk=1; i <=nlstate; i++){        }
     for(k=1; k <=(nlstate+ndeath); k++){      }
       if (k != i) {               
         for(j=1; j <=ncovmodel; j++){      /* This for computing probability of death (h=1 means
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           jk++;         as a weighted average of prlim.
           fprintf(ficgp,"\n");      */
         }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
       }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     }          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
    }      }    
       /* end probability of death */
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/  
      for(jk=1; jk <=m; jk++) {      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
        if (ng==2)        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");        for(i=1; i<=nlstate;i++){
        else          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
          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);      } 
        i=1;      fprintf(ficresprobmorprev,"\n");
        for(k2=1; k2<=nlstate; k2++) {  
          k3=i;      fprintf(ficresvij,"%.0f ",age );
          for(k=1; k<=(nlstate+ndeath); k++) {      for(i=1; i<=nlstate;i++)
            if (k != k2){        for(j=1; j<=nlstate;j++){
              if(ng==2)          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);        }
              else      fprintf(ficresvij,"\n");
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      free_matrix(gp,0,nhstepm,1,nlstate);
              ij=1;      free_matrix(gm,0,nhstepm,1,nlstate);
              for(j=3; j <=ncovmodel; j++) {      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                  ij++;    } /* End age */
                }    free_vector(gpp,nlstate+1,nlstate+ndeath);
                else    free_vector(gmp,nlstate+1,nlstate+ndeath);
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
              }    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
              fprintf(ficgp,")/(1");    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(k1=1; k1 <=nlstate; k1++){      fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
                ij=1;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
                for(j=3; j <=ncovmodel; j++){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
                    ij++;    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));
                  else    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,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /*  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,")");  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
              }    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);  
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    free_vector(xp,1,npar);
              i=i+ncovmodel;    free_matrix(doldm,1,nlstate,1,nlstate);
            }    free_matrix(dnewm,1,nlstate,1,npar);
          } /* end k */    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        } /* end k2 */    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
      } /* end jk */    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    } /* end ng */    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    fclose(ficgp);    fclose(ficresprobmorprev);
 }  /* end gnuplot */    fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
 /*************** Moving average **************/  
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){  /************ 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)
   int i, cpt, cptcod;  {
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    /* Variance of prevalence limit */
       for (i=1; i<=nlstate;i++)    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    double **newm;
           mobaverage[(int)agedeb][i][cptcod]=0.;    double **dnewm,**doldm;
        int i, j, nhstepm, hstepm;
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    int k, cptcode;
       for (i=1; i<=nlstate;i++){    double *xp;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    double *gp, *gm;
           for (cpt=0;cpt<=4;cpt++){    double **gradg, **trgradg;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    double age,agelim;
           }    int theta;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;     
         }    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
       }    fprintf(ficresvpl,"# Age");
     }    for(i=1; i<=nlstate;i++)
            fprintf(ficresvpl," %1d-%1d",i,i);
 }    fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
 /************** Forecasting ******************/    dnewm=matrix(1,nlstate,1,npar);
 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){    doldm=matrix(1,nlstate,1,nlstate);
      
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    hstepm=1*YEARM; /* Every year of age */
   int *popage;    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    agelim = AGESUP;
   double *popeffectif,*popcount;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   double ***p3mat;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   char fileresf[FILENAMELENGTH];      if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
  agelim=AGESUP;      gradg=matrix(1,npar,1,nlstate);
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  
        for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ /* Computes gradient */
   strcpy(fileresf,"f");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   strcat(fileresf,fileres);        }
   if((ficresf=fopen(fileresf,"w"))==NULL) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     printf("Problem with forecast resultfile: %s\n", fileresf);        for(i=1;i<=nlstate;i++)
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);          gp[i] = prlim[i][i];
   }      
   printf("Computing forecasting: result on file '%s' \n", fileresf);        for(i=1; i<=npar; i++) /* Computes gradient */
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(i=1;i<=nlstate;i++)
     movingaverage(agedeb, fage, ageminpar, mobaverage);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   }      } /* End theta */
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;      trgradg =matrix(1,nlstate,1,npar);
   if (stepm<=12) stepsize=1;  
        for(j=1; j<=nlstate;j++)
   agelim=AGESUP;        for(theta=1; theta <=npar; theta++)
            trgradg[j][theta]=gradg[theta][j];
   hstepm=1;  
   hstepm=hstepm/stepm;      for(i=1;i<=nlstate;i++)
   yp1=modf(dateintmean,&yp);        varpl[i][(int)age] =0.;
   anprojmean=yp;      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   yp2=modf((yp1*12),&yp);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   mprojmean=yp;      for(i=1;i<=nlstate;i++)
   yp1=modf((yp2*30.5),&yp);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   jprojmean=yp;  
   if(jprojmean==0) jprojmean=1;      fprintf(ficresvpl,"%.0f ",age );
   if(mprojmean==0) jprojmean=1;      for(i=1; i<=nlstate;i++)
          fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      fprintf(ficresvpl,"\n");
        free_vector(gp,1,nlstate);
   for(cptcov=1;cptcov<=i2;cptcov++){      free_vector(gm,1,nlstate);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      free_matrix(gradg,1,npar,1,nlstate);
       k=k+1;      free_matrix(trgradg,1,nlstate,1,npar);
       fprintf(ficresf,"\n#******");    } /* End age */
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_vector(xp,1,npar);
       }    free_matrix(doldm,1,nlstate,1,npar);
       fprintf(ficresf,"******\n");    free_matrix(dnewm,1,nlstate,1,nlstate);
       fprintf(ficresf,"# StartingAge FinalAge");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  }
        
        /************ Variance of one-step probabilities  ******************/
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {  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,"\n");  {
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    int k=0,l, cptcode;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    int first=1, first1;
           nhstepm = nhstepm/hstepm;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
              double **dnewm,**doldm;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double *xp;
           oldm=oldms;savm=savms;    double *gp, *gm;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double **gradg, **trgradg;
            double **mu;
           for (h=0; h<=nhstepm; h++){    double age,agelim, cov[NCOVMAX];
             if (h==(int) (calagedate+YEARM*cpt)) {    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    int theta;
             }    char fileresprob[FILENAMELENGTH];
             for(j=1; j<=nlstate+ndeath;j++) {    char fileresprobcov[FILENAMELENGTH];
               kk1=0.;kk2=0;    char fileresprobcor[FILENAMELENGTH];
               for(i=1; i<=nlstate;i++) {                
                 if (mobilav==1)    double ***varpij;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {    strcpy(fileresprob,"prob"); 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    strcat(fileresprob,fileres);
                 }    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
                      printf("Problem with resultfile: %s\n", fileresprob);
               }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
               if (h==(int)(calagedate+12*cpt)){    }
                 fprintf(ficresf," %.3f", kk1);    strcpy(fileresprobcov,"probcov"); 
                            strcat(fileresprobcov,fileres);
               }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
             }      printf("Problem with resultfile: %s\n", fileresprobcov);
           }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
         }    strcpy(fileresprobcor,"probcor"); 
       }    strcat(fileresprobcor,fileres);
     }    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprobcor);
              fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   fclose(ficresf);    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);
 /************** Forecasting ******************/    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
 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("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);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    
   int *popage;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    fprintf(ficresprob,"# Age");
   double *popeffectif,*popcount;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   double ***p3mat,***tabpop,***tabpopprev;    fprintf(ficresprobcov,"# Age");
   char filerespop[FILENAMELENGTH];    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# Age");
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   agelim=AGESUP;    for(i=1; i<=nlstate;i++)
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;      for(j=1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
          fprintf(ficresprobcor," p%1d-%1d ",i,j);
        }  
   strcpy(filerespop,"pop");   /* fprintf(ficresprob,"\n");
   strcat(filerespop,fileres);    fprintf(ficresprobcov,"\n");
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    fprintf(ficresprobcor,"\n");
     printf("Problem with forecast resultfile: %s\n", filerespop);   */
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);   xp=vector(1,npar);
   }    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   printf("Computing forecasting: result on file '%s' \n", filerespop);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    first=1;
     fprintf(ficgp,"\n# Routine varprob");
   if (mobilav==1) {    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(fichtm,"\n");
     movingaverage(agedeb, fage, ageminpar, mobaverage);  
   }    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
   stepsize=(int) (stepm+YEARM-1)/YEARM;    file %s<br>\n",optionfilehtmcov);
   if (stepm<=12) stepsize=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.\
   agelim=AGESUP;   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
      fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   hstepm=1;  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   hstepm=hstepm/stepm;  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>\
   if (popforecast==1) {   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
     if((ficpop=fopen(popfile,"r"))==NULL) {   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
       printf("Problem with population file : %s\n",popfile);exit(0);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);  
     }    cov[1]=1;
     popage=ivector(0,AGESUP);    tj=cptcoveff;
     popeffectif=vector(0,AGESUP);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     popcount=vector(0,AGESUP);    j1=0;
        for(t=1; t<=tj;t++){
     i=1;        for(i1=1; i1<=ncodemax[t];i1++){ 
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        j1++;
            if  (cptcovn>0) {
     imx=i;          fprintf(ficresprob, "\n#********** Variable "); 
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
   for(cptcov=1;cptcov<=i2;cptcov++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          fprintf(ficresprobcov, "**********\n#\n");
       k=k+1;          
       fprintf(ficrespop,"\n#******");          fprintf(ficgp, "\n#********** Variable "); 
       for(j=1;j<=cptcoveff;j++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficgp, "**********\n#\n");
       }          
       fprintf(ficrespop,"******\n");          
       fprintf(ficrespop,"# Age");          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       if (popforecast==1)  fprintf(ficrespop," [Population]");          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
                
       for (cpt=0; cpt<=0;cpt++) {          fprintf(ficresprobcor, "\n#********** Variable ");    
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                  fprintf(ficresprobcor, "**********\n#");    
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        
           nhstepm = nhstepm/hstepm;        for (age=bage; age<=fage; age ++){ 
                    cov[2]=age;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (k=1; k<=cptcovn;k++) {
           oldm=oldms;savm=savms;            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            }
                  for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (h=0; h<=nhstepm; h++){          for (k=1; k<=cptcovprod;k++)
             if (h==(int) (calagedate+YEARM*cpt)) {            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          
             }          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
             for(j=1; j<=nlstate+ndeath;j++) {          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
               kk1=0.;kk2=0;          gp=vector(1,(nlstate)*(nlstate+ndeath));
               for(i=1; i<=nlstate;i++) {                        gm=vector(1,(nlstate)*(nlstate+ndeath));
                 if (mobilav==1)      
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          for(theta=1; theta <=npar; theta++){
                 else {            for(i=1; i<=npar; i++)
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
                 }            
               }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
               if (h==(int)(calagedate+12*cpt)){            
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;            k=0;
                   /*fprintf(ficrespop," %.3f", kk1);            for(i=1; i<= (nlstate); i++){
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/              for(j=1; j<=(nlstate+ndeath);j++){
               }                k=k+1;
             }                gp[k]=pmmij[i][j];
             for(i=1; i<=nlstate;i++){              }
               kk1=0.;            }
                 for(j=1; j<=nlstate;j++){            
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];            for(i=1; i<=npar; i++)
                 }              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      
             }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)            for(i=1; i<=(nlstate); i++){
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);              for(j=1; j<=(nlstate+ndeath);j++){
           }                k=k+1;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                gm[k]=pmmij[i][j];
         }              }
       }            }
         
   /******/            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            for(theta=1; theta <=npar; theta++)
           nhstepm = nhstepm/hstepm;              trgradg[j][theta]=gradg[theta][j];
                    
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           oldm=oldms;savm=savms;          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           for (h=0; h<=nhstepm; h++){          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
             if (h==(int) (calagedate+YEARM*cpt)) {          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
             }  
             for(j=1; j<=nlstate+ndeath;j++) {          pmij(pmmij,cov,ncovmodel,x,nlstate);
               kk1=0.;kk2=0;          
               for(i=1; i<=nlstate;i++) {                        k=0;
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              for(i=1; i<=(nlstate); i++){
               }            for(j=1; j<=(nlstate+ndeath);j++){
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);              k=k+1;
             }              mu[k][(int) age]=pmmij[i][j];
           }            }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
         }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
       }            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
    }              varpij[i][j][(int)age] = doldm[i][j];
   }  
            /*printf("\n%d ",(int)age);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            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]));
   if (popforecast==1) {            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     free_ivector(popage,0,AGESUP);            }*/
     free_vector(popeffectif,0,AGESUP);  
     free_vector(popcount,0,AGESUP);          fprintf(ficresprob,"\n%d ",(int)age);
   }          fprintf(ficresprobcov,"\n%d ",(int)age);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          fprintf(ficresprobcor,"\n%d ",(int)age);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   fclose(ficrespop);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
 }            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
 /***********************************************/            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
 /**************** Main Program *****************/            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
 /***********************************************/          }
           i=0;
 int main(int argc, char *argv[])          for (k=1; k<=(nlstate);k++){
 {            for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   double agedeb, agefin,hf;              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;              for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   double fret;                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   double **xi,tmp,delta;              }
             }
   double dum; /* Dummy variable */          }/* end of loop for state */
   double ***p3mat;        } /* end of loop for age */
   int *indx;  
   char line[MAXLINE], linepar[MAXLINE];        /* Confidence intervalle of pij  */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];        /*
   int firstobs=1, lastobs=10;          fprintf(ficgp,"\nset noparametric;unset label");
   int sdeb, sfin; /* Status at beginning and end */          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   int c,  h , cpt,l;          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   int ju,jl, mi;          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);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   int mobilav=0,popforecast=0;          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   int hstepm, nhstepm;        */
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;  
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   double bage, fage, age, agelim, agebase;        first1=1;
   double ftolpl=FTOL;        for (k2=1; k2<=(nlstate);k2++){
   double **prlim;          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   double *severity;            if(l2==k2) continue;
   double ***param; /* Matrix of parameters */            j=(k2-1)*(nlstate+ndeath)+l2;
   double  *p;            for (k1=1; k1<=(nlstate);k1++){
   double **matcov; /* Matrix of covariance */              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   double ***delti3; /* Scale */                if(l1==k1) continue;
   double *delti; /* Scale */                i=(k1-1)*(nlstate+ndeath)+l1;
   double ***eij, ***vareij;                if(i<=j) continue;
   double **varpl; /* Variances of prevalence limits by age */                for (age=bage; age<=fage; age ++){ 
   double *epj, vepp;                  if ((int)age %5==0){
   double kk1, kk2;                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                      cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
   char *alph[]={"a","a","b","c","d","e"}, str[4];                    mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
   char z[1]="c", occ;                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
 #include <sys/time.h>                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
 #include <time.h>                    /* Eigen vectors */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                      /*v21=sqrt(1.-v11*v11); *//* error */
   /* long total_usecs;                    v21=(lc1-v1)/cv12*v11;
   struct timeval start_time, end_time;                    v12=-v21;
                      v22=v11;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */                    tnalp=v21/v11;
   getcwd(pathcd, size);                    if(first1==1){
                       first1=0;
   printf("\n%s",version);                      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);
   if(argc <=1){                    }
     printf("\nEnter the parameter file name: ");                    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);
     scanf("%s",pathtot);                    /*printf(fignu*/
   }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   else{                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     strcpy(pathtot,argv[1]);                    if(first==1){
   }                      first=0;
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/                      fprintf(ficgp,"\nset parametric;unset label");
   /*cygwin_split_path(pathtot,path,optionfile);                      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("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   /* cutv(path,optionfile,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\">\
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
   chdir(path);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   replace(pathc,path);                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
 /*-------- arguments in the command line --------*/                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   /* Log file */                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   strcat(filelog, 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",\
   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);                    }else{
     goto end;                      first=0;
   }                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
   fprintf(ficlog,"Log filename:%s\n",filelog);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   fprintf(ficlog,"\n%s",version);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   fprintf(ficlog,"\nEnter the parameter file name: ");                      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",\
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   fflush(ficlog);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
   /* */                  } /* age mod 5 */
   strcpy(fileres,"r");                } /* end loop age */
   strcat(fileres, optionfilefiname);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   strcat(fileres,".txt");    /* Other files have txt extension */                first=1;
               } /*l12 */
   /*---------arguments file --------*/            } /* k12 */
           } /*l1 */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        }/* k1 */
     printf("Problem with optionfile %s\n",optionfile);      } /* loop covariates */
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);    }
     goto end;    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   }    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
   strcpy(filereso,"o");    fclose(ficresprob);
   strcat(filereso,fileres);    fclose(ficresprobcov);
   if((ficparo=fopen(filereso,"w"))==NULL) {    fclose(ficresprobcor);
     printf("Problem with Output resultfile: %s\n", filereso);    fflush(ficgp);
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);    fflush(fichtmcov);
     goto end;  }
   }  
   
   /* Reads comments: lines beginning with '#' */  /******************* Printing html file ***********/
   while((c=getc(ficpar))=='#' && c!= EOF){  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     ungetc(c,ficpar);                    int lastpass, int stepm, int weightopt, char model[],\
     fgets(line, MAXLINE, ficpar);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     puts(line);                    int popforecast, int estepm ,\
     fputs(line,ficparo);                    double jprev1, double mprev1,double anprev1, \
   }                    double jprev2, double mprev2,double anprev2){
   ungetc(c,ficpar);    int jj1, k1, i1, cpt;
   
   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);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
   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);   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
   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);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
 while((c=getc(ficpar))=='#' && c!= EOF){     fprintf(fichtm,"\
     ungetc(c,ficpar);   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
     fgets(line, MAXLINE, ficpar);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
     puts(line);     fprintf(fichtm,"\
     fputs(line,ficparo);   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
   }             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
   ungetc(c,ficpar);     fprintf(fichtm,"\
     - Life expectancies by age and initial health status (estepm=%2d months): \
         <a href=\"%s\">%s</a> <br>\n</li>",
   covar=matrix(0,NCOVMAX,1,n);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   cptcovn=0;  
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
   ncovmodel=2+cptcovn;   m=cptcoveff;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    
   /* Read guess parameters */   jj1=0;
   /* Reads comments: lines beginning with '#' */   for(k1=1; k1<=m;k1++){
   while((c=getc(ficpar))=='#' && c!= EOF){     for(i1=1; i1<=ncodemax[k1];i1++){
     ungetc(c,ficpar);       jj1++;
     fgets(line, MAXLINE, ficpar);       if (cptcovn > 0) {
     puts(line);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     fputs(line,ficparo);         for (cpt=1; cpt<=cptcoveff;cpt++) 
   }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   ungetc(c,ficpar);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         }
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);       /* Pij */
     for(i=1; i <=nlstate; i++)       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> \
     for(j=1; j <=nlstate+ndeath-1; j++){  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
       fscanf(ficpar,"%1d%1d",&i1,&j1);       /* Quasi-incidences */
       fprintf(ficparo,"%1d%1d",i1,j1);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
       if(mle==1)   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
         printf("%1d%1d",i,j);  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
       fprintf(ficlog,"%1d%1d",i,j);         /* Stable prevalence in each health state */
       for(k=1; k<=ncovmodel;k++){         for(cpt=1; cpt<nlstate;cpt++){
         fscanf(ficpar," %lf",&param[i][j][k]);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
         if(mle==1){  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
           printf(" %lf",param[i][j][k]);         }
           fprintf(ficlog," %lf",param[i][j][k]);       for(cpt=1; cpt<=nlstate;cpt++) {
         }          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
         else  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
           fprintf(ficlog," %lf",param[i][j][k]);       }
         fprintf(ficparo," %lf",param[i][j][k]);     } /* end i1 */
       }   }/* End k1 */
       fscanf(ficpar,"\n");   fprintf(fichtm,"</ul>");
       if(mle==1)  
         printf("\n");  
       fprintf(ficlog,"\n");   fprintf(fichtm,"\
       fprintf(ficparo,"\n");  \n<br><li><h4> Result files (second order: variances)</h4>\n\
     }   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
    
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
   p=param[1][1];   fprintf(fichtm,"\
     - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   /* Reads comments: lines beginning with '#' */           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);   fprintf(fichtm,"\
     fgets(line, MAXLINE, ficpar);   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
     puts(line);           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
     fputs(line,ficparo);   fprintf(fichtm,"\
   }   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
   ungetc(c,ficpar);           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
   for(i=1; i <=nlstate; i++){   fprintf(fichtm,"\
     for(j=1; j <=nlstate+ndeath-1; j++){   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
       fscanf(ficpar,"%1d%1d",&i1,&j1);           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);  /*  if(popforecast==1) fprintf(fichtm,"\n */
       for(k=1; k<=ncovmodel;k++){  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
         fscanf(ficpar,"%le",&delti3[i][j][k]);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
         printf(" %le",delti3[i][j][k]);  /*      <br>",fileres,fileres,fileres,fileres); */
         fprintf(ficparo," %le",delti3[i][j][k]);  /*  else  */
       }  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
       fscanf(ficpar,"\n");   fflush(fichtm);
       printf("\n");   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
       fprintf(ficparo,"\n");  
     }   m=cptcoveff;
   }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   delti=delti3[1][1];  
     jj1=0;
   /* Reads comments: lines beginning with '#' */   for(k1=1; k1<=m;k1++){
   while((c=getc(ficpar))=='#' && c!= EOF){     for(i1=1; i1<=ncodemax[k1];i1++){
     ungetc(c,ficpar);       jj1++;
     fgets(line, MAXLINE, ficpar);       if (cptcovn > 0) {
     puts(line);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     fputs(line,ficparo);         for (cpt=1; cpt<=cptcoveff;cpt++) 
   }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   ungetc(c,ficpar);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         }
   matcov=matrix(1,npar,1,npar);       for(cpt=1; cpt<=nlstate;cpt++) {
   for(i=1; i <=npar; i++){         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
     fscanf(ficpar,"%s",&str);  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
     if(mle==1)  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
       printf("%s",str);       }
     fprintf(ficlog,"%s",str);       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
     fprintf(ficparo,"%s",str);  health expectancies in states (1) and (2): %s%d.png<br>\
     for(j=1; j <=i; j++){  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
       fscanf(ficpar," %le",&matcov[i][j]);     } /* end i1 */
       if(mle==1){   }/* End k1 */
         printf(" %.5le",matcov[i][j]);   fprintf(fichtm,"</ul>");
         fprintf(ficlog," %.5le",matcov[i][j]);   fflush(fichtm);
       }  }
       else  
         fprintf(ficlog," %.5le",matcov[i][j]);  /******************* Gnuplot file **************/
       fprintf(ficparo," %.5le",matcov[i][j]);  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
     }  
     fscanf(ficpar,"\n");    char dirfileres[132],optfileres[132];
     if(mle==1)    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
       printf("\n");    int ng;
     fprintf(ficlog,"\n");  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
     fprintf(ficparo,"\n");  /*     printf("Problem with file %s",optionfilegnuplot); */
   }  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   for(i=1; i <=npar; i++)  /*   } */
     for(j=i+1;j<=npar;j++)  
       matcov[i][j]=matcov[j][i];    /*#ifdef windows */
        fprintf(ficgp,"cd \"%s\" \n",pathc);
   if(mle==1)      /*#endif */
     printf("\n");    m=pow(2,cptcoveff);
   fprintf(ficlog,"\n");  
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     /*-------- Rewriting paramater file ----------*/   /* 1eme*/
      strcpy(rfileres,"r");    /* "Rparameterfile */    for (cpt=1; cpt<= nlstate ; cpt ++) {
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/     for (k1=1; k1<= m ; k1 ++) {
      strcat(rfileres,".");    /* */       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
     if((ficres =fopen(rfileres,"w"))==NULL) {       fprintf(ficgp,"set xlabel \"Age\" \n\
       printf("Problem writing new parameter file: %s\n", fileres);goto end;  set ylabel \"Probability\" \n\
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;  set ter png small\n\
     }  set size 0.65,0.65\n\
     fprintf(ficres,"#%s\n",version);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
      
     /*-------- data file ----------*/       for (i=1; i<= nlstate ; i ++) {
     if((fic=fopen(datafile,"r"))==NULL)    {         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       printf("Problem with datafile: %s\n", datafile);goto end;         else fprintf(ficgp," \%%*lf (\%%*lf)");
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);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 ++) {
     n= lastobs;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     severity = vector(1,maxwav);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     outcome=imatrix(1,maxwav+1,1,n);       } 
     num=ivector(1,n);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
     moisnais=vector(1,n);       for (i=1; i<= nlstate ; i ++) {
     annais=vector(1,n);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     moisdc=vector(1,n);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     andc=vector(1,n);       }  
     agedc=vector(1,n);       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
     cod=ivector(1,n);     }
     weight=vector(1,n);    }
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    /*2 eme*/
     mint=matrix(1,maxwav,1,n);    
     anint=matrix(1,maxwav,1,n);    for (k1=1; k1<= m ; k1 ++) { 
     s=imatrix(1,maxwav+1,1,n);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
     adl=imatrix(1,maxwav+1,1,n);          fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
     tab=ivector(1,NCOVMAX);      
     ncodemax=ivector(1,8);      for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
     i=1;        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     while (fgets(line, MAXLINE, fic) != NULL)    {        for (j=1; j<= nlstate+1 ; j ++) {
       if ((i >= firstobs) && (i <=lastobs)) {          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
                  else fprintf(ficgp," \%%*lf (\%%*lf)");
         for (j=maxwav;j>=1;j--){        }   
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
           strcpy(line,stra);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        for (j=1; j<= nlstate+1 ; j ++) {
         }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
                  else fprintf(ficgp," \%%*lf (\%%*lf)");
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        }   
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        for (j=1; j<= nlstate+1 ; j ++) {
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        }   
         for (j=ncovcol;j>=1;j--){        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        else fprintf(ficgp,"\" t\"\" w l 0,");
         }      }
         num[i]=atol(stra);    }
            
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    /*3eme*/
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/    
     for (k1=1; k1<= m ; k1 ++) { 
         i=i+1;      for (cpt=1; cpt<= nlstate ; cpt ++) {
       }        k=2+nlstate*(2*cpt-2);
     }        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
     /* printf("ii=%d", ij);        fprintf(ficgp,"set ter png small\n\
        scanf("%d",i);*/  set size 0.65,0.65\n\
   imx=i-1; /* Number of individuals */  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   /* for (i=1; i<=imx; i++){          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     }*/          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
    /*  for (i=1; i<=imx; i++){          
      if (s[4][i]==9)  s[4][i]=-1;        */
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/        for (i=1; i< nlstate ; i ++) {
            fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,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);    /* CV preval stable (period) */
   Tage=ivector(1,15);          for (k1=1; k1<= m ; k1 ++) { 
          for (cpt=1; cpt<=nlstate ; cpt ++) {
   if (strlen(model) >1){        k=3;
     j=0, j1=0, k1=1, k2=1;        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
     j=nbocc(model,'+');        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
     j1=nbocc(model,'*');  set ter png small\nset size 0.65,0.65\n\
     cptcovn=j+1;  unset log y\n\
     cptcovprod=j1;  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
            
     strcpy(modelsav,model);        for (i=1; i< nlstate ; i ++)
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          fprintf(ficgp,"+$%d",k+i+1);
       printf("Error. Non available option model=%s ",model);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
       fprintf(ficlog,"Error. Non available option model=%s ",model);        
       goto end;        l=3+(nlstate+ndeath)*cpt;
     }        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
            for (i=1; i< nlstate ; i ++) {
     for(i=(j+1); i>=1;i--){          l=3+(nlstate+ndeath)*cpt;
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */          fprintf(ficgp,"+$%d",l+i+1);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */        }
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       /*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 */    /* proba elementaires */
           cptcovprod--;    for(i=1,jk=1; i <=nlstate; i++){
           cutv(strb,stre,strd,'V');      for(k=1; k <=(nlstate+ndeath); k++){
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/        if (k != i) {
           cptcovage++;          for(j=1; j <=ncovmodel; j++){
             Tage[cptcovage]=i;            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             /*printf("stre=%s ", stre);*/            jk++; 
         }            fprintf(ficgp,"\n");
         else if (strcmp(strd,"age")==0) { /* or age*Vn */          }
           cptcovprod--;        }
           cutv(strb,stre,strc,'V');      }
           Tvar[i]=atoi(stre);     }
           cptcovage++;  
           Tage[cptcovage]=i;     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
         }       for(jk=1; jk <=m; jk++) {
         else {  /* Age is not in the model */         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/         if (ng==2)
           Tvar[i]=ncovcol+k1;           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */         else
           Tprod[k1]=i;           fprintf(ficgp,"\nset title \"Probability\"\n");
           Tvard[k1][1]=atoi(strc); /* m*/         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
           Tvard[k1][2]=atoi(stre); /* n */         i=1;
           Tvar[cptcovn+k2]=Tvard[k1][1];         for(k2=1; k2<=nlstate; k2++) {
           Tvar[cptcovn+k2+1]=Tvard[k1][2];           k3=i;
           for (k=1; k<=lastobs;k++)           for(k=1; k<=(nlstate+ndeath); k++) {
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];             if (k != k2){
           k1++;               if(ng==2)
           k2=k2+2;                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
         }               else
       }                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
       else { /* no more sum */               ij=1;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/               for(j=3; j <=ncovmodel; j++) {
        /*  scanf("%d",i);*/                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
       cutv(strd,strc,strb,'V');                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       Tvar[i]=atoi(strc);                   ij++;
       }                 }
       strcpy(modelsav,stra);                   else
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
         scanf("%d",i);*/               }
     } /* end of loop + */               fprintf(ficgp,")/(1");
   } /* end model */               
                 for(k1=1; k1 <=nlstate; k1++){   
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
   printf("cptcovprod=%d ", cptcovprod);                 ij=1;
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);                 for(j=3; j <=ncovmodel; j++){
   scanf("%d ",i);*/                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     fclose(fic);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
     /*  if(mle==1){*/                   }
     if (weightopt != 1) { /* Maximisation without weights*/                   else
       for(i=1;i<=n;i++) weight[i]=1.0;                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     }                 }
     /*-calculation of age at interview from date of interview and age at death -*/                 fprintf(ficgp,")");
     agev=matrix(1,maxwav,1,imx);               }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
     for (i=1; i<=imx; i++) {               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
       for(m=2; (m<= maxwav); m++) {               i=i+ncovmodel;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){             }
          anint[m][i]=9999;           } /* end k */
          s[m][i]=-1;         } /* end k2 */
        }       } /* end jk */
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;     } /* end ng */
       }     fflush(ficgp); 
     }  }  /* end gnuplot */
   
     for (i=1; i<=imx; i++)  {  
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  /*************** Moving average **************/
       for(m=1; (m<= maxwav); m++){  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
         if(s[m][i] >0){  
           if (s[m][i] >= nlstate+1) {    int i, cpt, cptcod;
             if(agedc[i]>0)    int modcovmax =1;
               if(moisdc[i]!=99 && andc[i]!=9999)    int mobilavrange, mob;
                 agev[m][i]=agedc[i];    double age;
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/  
            else {    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
               if (andc[i]!=9999){                             a covariate has 2 modalities */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
               }      if(mobilav==1) mobilavrange=5; /* default */
             }      else mobilavrange=mobilav;
           }      for (age=bage; age<=fage; age++)
           else if(s[m][i] !=9){ /* Should no more exist */        for (i=1; i<=nlstate;i++)
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          for (cptcod=1;cptcod<=modcovmax;cptcod++)
             if(mint[m][i]==99 || anint[m][i]==9999)            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
               agev[m][i]=1;      /* We keep the original values on the extreme ages bage, fage and for 
             else if(agev[m][i] <agemin){         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
               agemin=agev[m][i];         we use a 5 terms etc. until the borders are no more concerned. 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      */ 
             }      for (mob=3;mob <=mobilavrange;mob=mob+2){
             else if(agev[m][i] >agemax){        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
               agemax=agev[m][i];          for (i=1; i<=nlstate;i++){
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/            for (cptcod=1;cptcod<=modcovmax;cptcod++){
             }              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
             /*agev[m][i]=anint[m][i]-annais[i];*/                for (cpt=1;cpt<=(mob-1)/2;cpt++){
             /*   agev[m][i] = age[i]+2*m;*/                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
           }                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
           else { /* =9 */                }
             agev[m][i]=1;              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             s[m][i]=-1;            }
           }          }
         }        }/* end age */
         else /*= 0 Unknown */      }/* end mob */
           agev[m][i]=1;    }else return -1;
       }    return 0;
      }/* End movingaverage */
     }  
     for (i=1; i<=imx; i++)  {  
       for(m=1; (m<= maxwav); m++){  /************** Forecasting ******************/
         if (s[m][i] > (nlstate+ndeath)) {  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){
           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);      /* proj1, year, month, day of starting projection 
           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);         agemin, agemax range of age
           goto end;       dateprev1 dateprev2 range of dates during which prevalence is computed
         }       anproj2 year of en of projection (same day and month as proj1).
       }    */
     }    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    double agec; /* generic age */
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     free_vector(severity,1,maxwav);    double ***p3mat;
     free_imatrix(outcome,1,maxwav+1,1,n);    double ***mobaverage;
     free_vector(moisnais,1,n);    char fileresf[FILENAMELENGTH];
     free_vector(annais,1,n);  
     /* free_matrix(mint,1,maxwav,1,n);    agelim=AGESUP;
        free_matrix(anint,1,maxwav,1,n);*/    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     free_vector(moisdc,1,n);   
     free_vector(andc,1,n);    strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
        if((ficresf=fopen(fileresf,"w"))==NULL) {
     wav=ivector(1,imx);      printf("Problem with forecast resultfile: %s\n", fileresf);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    }
        printf("Computing forecasting: result on file '%s' \n", fileresf);
     /* Concatenates waves */    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
       Tcode=ivector(1,100);    if (mobilav!=0) {
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       ncodemax[1]=1;      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
              printf(" Error in movingaverage mobilav=%d\n",mobilav);
    codtab=imatrix(1,100,1,10);      }
    h=0;    }
    m=pow(2,cptcoveff);  
      stepsize=(int) (stepm+YEARM-1)/YEARM;
    for(k=1;k<=cptcoveff; k++){    if (stepm<=12) stepsize=1;
      for(i=1; i <=(m/pow(2,k));i++){    if(estepm < stepm){
        for(j=1; j <= ncodemax[k]; j++){      printf ("Problem %d lower than %d\n",estepm, stepm);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    }
            h++;    else  hstepm=estepm;   
            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]);*/    hstepm=hstepm/stepm; 
          }    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
        }                                 fractional in yp1 */
      }    anprojmean=yp;
    }    yp2=modf((yp1*12),&yp);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    mprojmean=yp;
       codtab[1][2]=1;codtab[2][2]=2; */    yp1=modf((yp2*30.5),&yp);
    /* for(i=1; i <=m ;i++){    jprojmean=yp;
       for(k=1; k <=cptcovn; k++){    if(jprojmean==0) jprojmean=1;
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    if(mprojmean==0) jprojmean=1;
       }  
       printf("\n");    i1=cptcoveff;
       }    if (cptcovn < 1){i1=1;}
       scanf("%d",i);*/    
        fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
    /* Calculates basic frequencies. Computes observed prevalence at single age    
        and prints on file fileres'p'. */    fprintf(ficresf,"#****** Routine prevforecast **\n");
   
      /*            if (h==(int)(YEARM*yearp)){ */
        for(cptcov=1, k=0;cptcov<=i1;cptcov++){
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        k=k+1;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficresf,"\n#******");
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(j=1;j<=cptcoveff;j++) {
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          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]]);
              }
     /* 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,"# Covariate valuofcovar yearproj age");
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
     if(mle==1){            fprintf(ficresf," p%d%d",i,j);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          fprintf(ficresf," p.%d",j);
     }        }
            for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
     /*--------- results files --------------*/          fprintf(ficresf,"\n");
     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(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
    
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
    jk=1;            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            nhstepm = nhstepm/hstepm; 
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            oldm=oldms;savm=savms;
    for(i=1,jk=1; i <=nlstate; i++){            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
      for(k=1; k <=(nlstate+ndeath); k++){          
        if (k != i)            for (h=0; h<=nhstepm; h++){
          {              if (h*hstepm/YEARM*stepm ==yearp) {
            printf("%d%d ",i,k);                fprintf(ficresf,"\n");
            fprintf(ficlog,"%d%d ",i,k);                for(j=1;j<=cptcoveff;j++) 
            fprintf(ficres,"%1d%1d ",i,k);                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
            for(j=1; j <=ncovmodel; j++){                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
              printf("%f ",p[jk]);              } 
              fprintf(ficlog,"%f ",p[jk]);              for(j=1; j<=nlstate+ndeath;j++) {
              fprintf(ficres,"%f ",p[jk]);                ppij=0.;
              jk++;                for(i=1; i<=nlstate;i++) {
            }                  if (mobilav==1) 
            printf("\n");                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
            fprintf(ficlog,"\n");                  else {
            fprintf(ficres,"\n");                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
          }                  }
      }                  if (h*hstepm/YEARM*stepm== yearp) {
    }                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
    if(mle==1){                  }
      /* Computing hessian and covariance matrix */                } /* end i */
      ftolhess=ftol; /* Usually correct */                if (h*hstepm/YEARM*stepm==yearp) {
      hesscov(matcov, p, npar, delti, ftolhess, func);                  fprintf(ficresf," %.3f", ppij);
    }                }
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");              }/* end j */
    printf("# Scales (for hessian or gradient estimation)\n");            } /* end h */
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    for(i=1,jk=1; i <=nlstate; i++){          } /* end agec */
      for(j=1; j <=nlstate+ndeath; j++){        } /* end yearp */
        if (j!=i) {      } /* end cptcod */
          fprintf(ficres,"%1d%1d",i,j);    } /* end  cptcov */
          printf("%1d%1d",i,j);         
          fprintf(ficlog,"%1d%1d",i,j);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
          for(k=1; k<=ncovmodel;k++){  
            printf(" %.5e",delti[jk]);    fclose(ficresf);
            fprintf(ficlog," %.5e",delti[jk]);  }
            fprintf(ficres," %.5e",delti[jk]);  
            jk++;  /************** Forecasting *****not tested NB*************/
          }  populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
          printf("\n");    
          fprintf(ficlog,"\n");    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
          fprintf(ficres,"\n");    int *popage;
        }    double calagedatem, agelim, kk1, kk2;
      }    double *popeffectif,*popcount;
    }    double ***p3mat,***tabpop,***tabpopprev;
        double ***mobaverage;
    k=1;    char filerespop[FILENAMELENGTH];
    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)    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      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");    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    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");    agelim=AGESUP;
    for(i=1;i<=npar;i++){    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
      /*  if (k>nlstate) k=1;    
          i1=(i-1)/(ncovmodel*nlstate)+1;    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    
          printf("%s%d%d",alph[k],i1,tab[i]);*/    
      fprintf(ficres,"%3d",i);    strcpy(filerespop,"pop"); 
      if(mle==1)    strcat(filerespop,fileres);
        printf("%3d",i);    if((ficrespop=fopen(filerespop,"w"))==NULL) {
      fprintf(ficlog,"%3d",i);      printf("Problem with forecast resultfile: %s\n", filerespop);
      for(j=1; j<=i;j++){      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
        fprintf(ficres," %.5e",matcov[i][j]);    }
        if(mle==1)    printf("Computing forecasting: result on file '%s' \n", filerespop);
          printf(" %.5e",matcov[i][j]);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
        fprintf(ficlog," %.5e",matcov[i][j]);  
      }    if (cptcoveff==0) ncodemax[cptcoveff]=1;
      fprintf(ficres,"\n");  
      if(mle==1)    if (mobilav!=0) {
        printf("\n");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      fprintf(ficlog,"\n");      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
      k++;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
    }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
          }
    while((c=getc(ficpar))=='#' && c!= EOF){    }
      ungetc(c,ficpar);  
      fgets(line, MAXLINE, ficpar);    stepsize=(int) (stepm+YEARM-1)/YEARM;
      puts(line);    if (stepm<=12) stepsize=1;
      fputs(line,ficparo);    
    }    agelim=AGESUP;
    ungetc(c,ficpar);    
    estepm=0;    hstepm=1;
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);    hstepm=hstepm/stepm; 
    if (estepm==0 || estepm < stepm) estepm=stepm;    
    if (fage <= 2) {    if (popforecast==1) {
      bage = ageminpar;      if((ficpop=fopen(popfile,"r"))==NULL) {
      fage = agemaxpar;        printf("Problem with population file : %s\n",popfile);exit(0);
    }        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
          } 
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      popage=ivector(0,AGESUP);
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      popeffectif=vector(0,AGESUP);
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      popcount=vector(0,AGESUP);
          
    while((c=getc(ficpar))=='#' && c!= EOF){      i=1;   
      ungetc(c,ficpar);      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      fgets(line, MAXLINE, ficpar);     
      puts(line);      imx=i;
      fputs(line,ficparo);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
    }    }
    ungetc(c,ficpar);  
      for(cptcov=1,k=0;cptcov<=i2;cptcov++){
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        k=k+1;
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        fprintf(ficrespop,"\n#******");
            for(j=1;j<=cptcoveff;j++) {
    while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
      ungetc(c,ficpar);        }
      fgets(line, MAXLINE, ficpar);        fprintf(ficrespop,"******\n");
      puts(line);        fprintf(ficrespop,"# Age");
      fputs(line,ficparo);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
    }        if (popforecast==1)  fprintf(ficrespop," [Population]");
    ungetc(c,ficpar);        
          for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   fscanf(ficpar,"pop_based=%d\n",&popbased);            nhstepm = nhstepm/hstepm; 
   fprintf(ficparo,"pop_based=%d\n",popbased);              
   fprintf(ficres,"pop_based=%d\n",popbased);              p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              oldm=oldms;savm=savms;
   while((c=getc(ficpar))=='#' && c!= EOF){            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     ungetc(c,ficpar);          
     fgets(line, MAXLINE, ficpar);            for (h=0; h<=nhstepm; h++){
     puts(line);              if (h==(int) (calagedatem+YEARM*cpt)) {
     fputs(line,ficparo);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   }              } 
   ungetc(c,ficpar);              for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
   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);                for(i=1; i<=nlstate;i++) {              
 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);                  if (mobilav==1) 
 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);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
 while((c=getc(ficpar))=='#' && c!= EOF){                  }
     ungetc(c,ficpar);                }
     fgets(line, MAXLINE, ficpar);                if (h==(int)(calagedatem+12*cpt)){
     puts(line);                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
     fputs(line,ficparo);                    /*fprintf(ficrespop," %.3f", kk1);
   }                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+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);              for(i=1; i<=nlstate;i++){
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                kk1=0.;
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                  for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                  }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
 /*------------ gnuplot -------------*/              }
   strcpy(optionfilegnuplot,optionfilefiname);  
   strcat(optionfilegnuplot,".gp");              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
     printf("Problem with file %s",optionfilegnuplot);            }
   }            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fclose(ficgp);          }
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);        }
 /*--------- index.htm --------*/   
     /******/
   strcpy(optionfilehtm,optionfile);  
   strcat(optionfilehtm,".htm");        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
     printf("Problem with %s \n",optionfilehtm), exit(0);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   }            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n            
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 \n            oldm=oldms;savm=savms;
 Total number of observations=%d <br>\n            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n            for (h=0; h<=nhstepm; h++){
 <hr  size=\"2\" color=\"#EC5E5E\">              if (h==(int) (calagedatem+YEARM*cpt)) {
  <ul><li><h4>Parameter files</h4>\n                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
  - 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              for(j=1; j<=nlstate+ndeath;j++) {
  - 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);                kk1=0.;kk2=0;
   fclose(fichtm);                for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);                }
                  if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
 /*------------ free_vector  -------------*/              }
  chdir(path);            }
              free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  free_ivector(wav,1,imx);          }
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        }
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);       } 
  free_ivector(num,1,n);    }
  free_vector(agedc,1,n);   
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  fclose(ficparo);  
  fclose(ficres);    if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
   /*--------------- Prevalence limit --------------*/      free_vector(popcount,0,AGESUP);
      }
   strcpy(filerespl,"pl");    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcat(filerespl,fileres);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    fclose(ficrespop);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  } /* End of popforecast */
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;  
   }  int fileappend(FILE *fichier, char *optionfich)
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  {
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);    if((fichier=fopen(optionfich,"a"))==NULL) {
   fprintf(ficrespl,"#Prevalence limit\n");      printf("Problem with file: %s\n", optionfich);
   fprintf(ficrespl,"#Age ");      fprintf(ficlog,"Problem with file: %s\n", optionfich);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      return (0);
   fprintf(ficrespl,"\n");    }
      fflush(fichier);
   prlim=matrix(1,nlstate,1,nlstate);    return (1);
   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 */  /**************** function prwizard **********************/
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   k=0;  {
   agebase=ageminpar;  
   agelim=agemaxpar;    /* Wizard to print covariance matrix template */
   ftolpl=1.e-10;  
   i1=cptcoveff;    char ca[32], cb[32], cc[32];
   if (cptcovn < 1){i1=1;}    int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
         k=k+1;    fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    for(i=1; i <=nlstate; i++){
         fprintf(ficrespl,"\n#******");      jj=0;
         printf("\n#******");      for(j=1; j <=nlstate+ndeath; j++){
         fprintf(ficlog,"\n#******");        if(j==i) continue;
         for(j=1;j<=cptcoveff;j++) {        jj++;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        /*ca[0]= k+'a'-1;ca[1]='\0';*/
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        printf("%1d%1d",i,j);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficparo,"%1d%1d",i,j);
         }        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.");
                  fprintf(ficparo," 0.");
         for (age=agebase; age<=agelim; age++){        }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        printf("\n");
           fprintf(ficrespl,"%.0f",age );        fprintf(ficparo,"\n");
           for(i=1; i<=nlstate;i++)      }
           fprintf(ficrespl," %.5f", prlim[i][i]);    }
           fprintf(ficrespl,"\n");    printf("# Scales (for hessian or gradient estimation)\n");
         }    fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
       }    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     }    for(i=1; i <=nlstate; i++){
   fclose(ficrespl);      jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
   /*------------- h Pij x at various ages ------------*/        if(j==i) continue;
          jj++;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        fprintf(ficparo,"%1d%1d",i,j);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        printf("%1d%1d",i,j);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        fflush(stdout);
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;        for(k=1; k<=ncovmodel;k++){
   }          /*      printf(" %le",delti3[i][j][k]); */
   printf("Computing pij: result on file '%s' \n", filerespij);          /*      fprintf(ficparo," %le",delti3[i][j][k]); */
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);          printf(" 0.");
            fprintf(ficparo," 0.");
   stepsize=(int) (stepm+YEARM-1)/YEARM;        }
   /*if (stepm<=24) stepsize=2;*/        numlinepar++;
         printf("\n");
   agelim=AGESUP;        fprintf(ficparo,"\n");
   hstepm=stepsize*YEARM; /* Every year of age */      }
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    }
     printf("# Covariance matrix\n");
   /* hstepm=1;   aff par mois*/  /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   k=0;  /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   for(cptcov=1;cptcov<=i1;cptcov++){  /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       k=k+1;  /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
         fprintf(ficrespij,"\n#****** ");  /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
         for(j=1;j<=cptcoveff;j++)  /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fflush(stdout);
         fprintf(ficrespij,"******\n");    fprintf(ficparo,"# Covariance matrix\n");
            /* # 121 Var(a12)\n\ */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    /* # 122 Cov(b12,a12) Var(b12)\n\ */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    /* #   ...\n\ */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
           /*      nhstepm=nhstepm*YEARM; aff par mois*/    for(itimes=1;itimes<=2;itimes++){
       jj=0;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(i=1; i <=nlstate; i++){
           oldm=oldms;savm=savms;        for(j=1; j <=nlstate+ndeath; j++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            if(j==i) continue;
           fprintf(ficrespij,"# Age");          for(k=1; k<=ncovmodel;k++){
           for(i=1; i<=nlstate;i++)            jj++;
             for(j=1; j<=nlstate+ndeath;j++)            ca[0]= k+'a'-1;ca[1]='\0';
               fprintf(ficrespij," %1d-%1d",i,j);            if(itimes==1){
           fprintf(ficrespij,"\n");              printf("#%1d%1d%d",i,j,k);
            for (h=0; h<=nhstepm; h++){              fprintf(ficparo,"#%1d%1d%d",i,j,k);
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );            }else{
             for(i=1; i<=nlstate;i++)              printf("%1d%1d%d",i,j,k);
               for(j=1; j<=nlstate+ndeath;j++)              fprintf(ficparo,"%1d%1d%d",i,j,k);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);              /*  printf(" %.5le",matcov[i][j]); */
             fprintf(ficrespij,"\n");            }
              }            ll=0;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(li=1;li <=nlstate; li++){
           fprintf(ficrespij,"\n");              for(lj=1;lj <=nlstate+ndeath; lj++){
         }                if(lj==li) continue;
     }                for(lk=1;lk<=ncovmodel;lk++){
   }                  ll++;
                   if(ll<=jj){
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);                    cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
   fclose(ficrespij);                      if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
   /*---------- 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{
   else{                      if(itimes==1){
     erreur=108;                        printf(" Var(%s%1d%1d)",ca,i,j);
     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);                        fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
     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);                      }else{
   }                        printf(" 0.");
                          fprintf(ficparo," 0.");
                       }
   /*---------- Health expectancies and variances ------------*/                    }
                   }
   strcpy(filerest,"t");                } /* end lk */
   strcat(filerest,fileres);              } /* end lj */
   if((ficrest=fopen(filerest,"w"))==NULL) {            } /* end li */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;            printf("\n");
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;            fprintf(ficparo,"\n");
   }            numlinepar++;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          } /* end k*/
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);        } /*end j */
       } /* end i */
     } /* end itimes */
   strcpy(filerese,"e");  
   strcat(filerese,fileres);  } /* end of prwizard */
   if((ficreseij=fopen(filerese,"w"))==NULL) {  /******************* Gompertz Likelihood ******************************/
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  double gompertz(double x[])
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  { 
   }    double A,B,L=0.0,sump=0.,num=0.;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    int i,n=0; /* n is the size of the sample */
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);    for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
   strcpy(fileresv,"v");      /*    sump=sump+1;*/
   strcat(fileresv,fileres);      num=num+1;
   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);   
   }    /* for (i=0; i<=imx; i++) 
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);       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]);*/
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  
   calagedate=-1;    for (i=1;i<=imx ; i++)
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      {
         if (cens[i]==1 & wav[i]>1)
   k=0;          A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
   for(cptcov=1;cptcov<=i1;cptcov++){        
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        if (cens[i]==0 & wav[i]>1)
       k=k+1;          A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
       fprintf(ficrest,"\n#****** ");               +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
       for(j=1;j<=cptcoveff;j++)        
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        if (wav[i]>1 & agecens[i]>15) {
       fprintf(ficrest,"******\n");          L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
       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");   /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
       fprintf(ficresvij,"\n#****** ");    return -2*L*num/sump;
       for(j=1;j<=cptcoveff;j++)  }
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficresvij,"******\n");  /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                    int lastpass, int stepm, int weightopt, char model[],\
       oldm=oldms;savm=savms;                    int imx,  double p[],double **matcov){
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      int i;
    
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
       oldm=oldms;savm=savms;    fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);    for (i=1;i<=2;i++) 
       if(popbased==1){      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]));
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);    fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
        }    fprintf(fichtm,"</ul>");
     fflush(fichtm);
    }
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  /******************* Gnuplot file **************/
       fprintf(ficrest,"\n");  void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
       epj=vector(1,nlstate+1);    char dirfileres[132],optfileres[132];
       for(age=bage; age <=fage ;age++){    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    int ng;
         if (popbased==1) {  
           for(i=1; i<=nlstate;i++)  
             prlim[i][i]=probs[(int)age][i][k];    /*#ifdef windows */
         }    fprintf(ficgp,"cd \"%s\" \n",pathc);
              /*#endif */
         fprintf(ficrest," %4.0f",age);  
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    strcpy(dirfileres,optionfilefiname);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    strcpy(optfileres,"vpl");
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    fprintf(ficgp,"set out \"graphmort.png\"\n "); 
           }    fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
           epj[nlstate+1] +=epj[j];    fprintf(ficgp, "set ter png small\n set log y\n"); 
         }    fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
         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");  /**************** Main Program *****************/
       }  /***********************************************/
     }  
   }  int main(int argc, char *argv[])
 free_matrix(mint,1,maxwav,1,n);  {
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     free_vector(weight,1,n);    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
   fclose(ficreseij);    int jj, ll, li, lj, lk, imk;
   fclose(ficresvij);    int numlinepar=0; /* Current linenumber of parameter file */
   fclose(ficrest);    int itimes;
   fclose(ficpar);    int NDIM=2;
   free_vector(epj,1,nlstate+1);  
      char ca[32], cb[32], cc[32];
   /*------- Variance limit prevalence------*/      /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
   strcpy(fileresvpl,"vpl");    double agedeb, agefin,hf;
   strcat(fileresvpl,fileres);    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    double fret;
     exit(0);    double **xi,tmp,delta;
   }  
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    double dum; /* Dummy variable */
     double ***p3mat;
   k=0;    double ***mobaverage;
   for(cptcov=1;cptcov<=i1;cptcov++){    int *indx;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    char line[MAXLINE], linepar[MAXLINE];
       k=k+1;    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
       fprintf(ficresvpl,"\n#****** ");    char pathr[MAXLINE], pathimach[MAXLINE]; 
       for(j=1;j<=cptcoveff;j++)    int firstobs=1, lastobs=10;
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int sdeb, sfin; /* Status at beginning and end */
       fprintf(ficresvpl,"******\n");    int c,  h , cpt,l;
          int ju,jl, mi;
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
       oldm=oldms;savm=savms;    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     }    int mobilav=0,popforecast=0;
  }    int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
   fclose(ficresvpl);    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
   /*---------- End : free ----------------*/    double bage, fage, age, agelim, agebase;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    double ftolpl=FTOL;
      double **prlim;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    double *severity;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    double ***param; /* Matrix of parameters */
      double  *p;
      double **matcov; /* Matrix of covariance */
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    double ***delti3; /* Scale */
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    double *delti; /* Scale */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    double ***eij, ***vareij;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    double **varpl; /* Variances of prevalence limits by age */
      double *epj, vepp;
   free_matrix(matcov,1,npar,1,npar);    double kk1, kk2;
   free_vector(delti,1,npar);    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   free_matrix(agev,1,maxwav,1,imx);    double **ximort;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   fprintf(fichtm,"\n</body>");  
   fclose(fichtm);    char z[1]="c", occ;
   fclose(ficgp);  
      char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
   if(erreur >0){    char *stratrunc;
     printf("End of Imach with error or warning %d\n",erreur);    int lstra;
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);  
   }else{    long total_usecs;
    printf("End of Imach\n");   
    fprintf(ficlog,"End of Imach\n");  /*   setlocale (LC_ALL, ""); */
   }  /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   printf("See log file on %s\n",filelog);  /*   textdomain (PACKAGE); */
   fclose(ficlog);  /*   setlocale (LC_CTYPE, ""); */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  /*   setlocale (LC_MESSAGES, ""); */
    
   /* 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);*/    /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
   /*printf("Total time was %d uSec.\n", total_usecs);*/    (void) gettimeofday(&start_time,&tzp);
   /*------ End -----------*/    curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
  end:    strcpy(strstart,asctime(&tm));
 #ifdef windows  
   /* chdir(pathcd);*/  /*  printf("Localtime (at start)=%s",strstart); */
 #endif  /*  tp.tv_sec = tp.tv_sec +86400; */
  /*system("wgnuplot graph.plt");*/  /*  tm = *localtime(&start_time.tv_sec); */
  /*system("../gp37mgw/wgnuplot graph.plt");*/  /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
  /*system("cd ../gp37mgw");*/  /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  /*   tmg.tm_hour=tmg.tm_hour + 1; */
  strcpy(plotcmd,GNUPLOTPROGRAM);  /*   tp.tv_sec = mktime(&tmg); */
  strcat(plotcmd," ");  /*   strt=asctime(&tmg); */
  strcat(plotcmd,optionfilegnuplot);  /*   printf("Time(after) =%s",strstart);  */
  system(plotcmd);  /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
 #ifdef windows  *  tm = *localtime(&time_value);
   while (z[0] != 'q') {  *  strstart=asctime(&tm);
     /* chdir(path); */  *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");  */
     scanf("%s",z);  
     if (z[0] == 'c') system("./imach");    nberr=0; /* Number of errors and warnings */
     else if (z[0] == 'e') system(optionfilehtm);    nbwarn=0;
     else if (z[0] == 'g') system(plotcmd);    getcwd(pathcd, size);
     else if (z[0] == 'q') exit(0);  
   }    printf("\n%s\n%s",version,fullversion);
 #endif    if(argc <=1){
 }      printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(argv[0],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=0; line[j] != '\n';j++){  /* Untabifies line */
           if(line[j] == '\t')
             line[j] = ' ';
         }
         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.1.52  
changed lines
  Added in v.1.103


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