Diff for /imach/src/imach.c between versions 1.32 and 1.104

version 1.32, 2002/03/11 14:17:15 version 1.104, 2005/09/30 16:11:43
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.104  2005/09/30 16:11:43  lievre
      (Module): sump fixed, loop imx fixed, and simplifications.
   This program computes Healthy Life Expectancies from    (Module): If the status is missing at the last wave but we know
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    that the person is alive, then we can code his/her status as -2
   first survey ("cross") where individuals from different ages are    (instead of missing=-1 in earlier versions) and his/her
   interviewed on their health status or degree of disability (in the    contributions to the likelihood is 1 - Prob of dying from last
   case of a health survey which is our main interest) -2- at least a    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   second wave of interviews ("longitudinal") which measure each change    the healthy state at last known wave). Version is 0.98
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.103  2005/09/30 15:54:49  lievre
   model. More health states you consider, more time is necessary to reach the    (Module): sump fixed, loop imx fixed, and simplifications.
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.102  2004/09/15 17:31:30  brouard
   probabibility to be observed in state j at the second wave    Add the possibility to read data file including tab characters.
   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 1.101  2004/09/15 10:38:38  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    Fix on curr_time
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.100  2004/07/12 18:29:06  brouard
   you to do it.  More covariates you add, slower the    Add version for Mac OS X. Just define UNIX in Makefile
   convergence.  
     Revision 1.99  2004/06/05 08:57:40  brouard
   The advantage of this computer programme, compared to a simple    *** empty log message ***
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.98  2004/05/16 15:05:56  brouard
   intermediate interview, the information is lost, but taken into    New version 0.97 . First attempt to estimate force of mortality
   account using an interpolation or extrapolation.      directly from the data i.e. without the need of knowing the health
     state at each age, but using a Gompertz model: log u =a + b*age .
   hPijx is the probability to be observed in state i at age x+h    This is the basic analysis of mortality and should be done before any
   conditional to the observed state i at age x. The delay 'h' can be    other analysis, in order to test if the mortality estimated from the
   split into an exact number (nh*stepm) of unobserved intermediate    cross-longitudinal survey is different from the mortality estimated
   states. This elementary transition (by month or quarter trimester,    from other sources like vital statistic data.
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    The same imach parameter file can be used but the option for mle should be -3.
   and the contribution of each individual to the likelihood is simply  
   hPijx.    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.
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    The output is very simple: only an estimate of the intercept and of
      the slope with 95% confident intervals.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Current limitations:
   This software have been partly granted by Euro-REVES, a concerted action    A) Even if you enter covariates, i.e. with the
   from the European Union.    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   It is copyrighted identically to a GNU software product, ie programme and    B) There is no computation of Life Expectancy nor Life Table.
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Revision 1.97  2004/02/20 13:25:42  lievre
   **********************************************************************/    Version 0.96d. Population forecasting command line is (temporarily)
      suppressed.
 #include <math.h>  
 #include <stdio.h>    Revision 1.96  2003/07/15 15:38:55  brouard
 #include <stdlib.h>    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #include <unistd.h>    rewritten within the same printf. Workaround: many printfs.
   
 #define MAXLINE 256    Revision 1.95  2003/07/08 07:54:34  brouard
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    * imach.c (Repository):
 #define FILENAMELENGTH 80    (Repository): Using imachwizard code to output a more meaningful covariance
 /*#define DEBUG*/    matrix (cov(a12,c31) instead of numbers.
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.94  2003/06/27 13:00:02  brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Just cleaning
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.93  2003/06/25 16:33:55  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 #define NINTERVMAX 8    (Module): Version 0.96b
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.92  2003/06/25 16:30:45  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    (Module): On windows (cygwin) function asctime_r doesn't
 #define MAXN 20000    exist so I changed back to asctime which exists.
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.91  2003/06/25 15:30:29  brouard
 #define AGEBASE 40    * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
 int erreur; /* Error number */    is stamped in powell.  We created a new html file for the graphs
 int nvar;    concerning matrix of covariance. It has extension -cov.htm.
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.90  2003/06/24 12:34:15  brouard
 int nlstate=2; /* Number of live states */    (Module): Some bugs corrected for windows. Also, when
 int ndeath=1; /* Number of dead states */    mle=-1 a template is output in file "or"mypar.txt with the design
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    of the covariance matrix to be input.
 int popbased=0;  
     Revision 1.89  2003/06/24 12:30:52  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    (Module): Some bugs corrected for windows. Also, when
 int maxwav; /* Maxim number of waves */    mle=-1 a template is output in file "or"mypar.txt with the design
 int jmin, jmax; /* min, max spacing between 2 waves */    of the covariance matrix to be input.
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.88  2003/06/23 17:54:56  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.87  2003/06/18 12:26:01  brouard
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Version 0.96
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficgp,*ficresprob,*ficpop;    Revision 1.86  2003/06/17 20:04:08  brouard
 FILE *ficreseij;    (Module): Change position of html and gnuplot routines and added
   char filerese[FILENAMELENGTH];    routine fileappend.
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    Revision 1.85  2003/06/17 13:12:43  brouard
  FILE  *ficresvpl;    * imach.c (Repository): Check when date of death was earlier that
   char fileresvpl[FILENAMELENGTH];    current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
 #define NR_END 1    was wrong (infinity). We still send an "Error" but patch by
 #define FREE_ARG char*    assuming that the date of death was just one stepm after the
 #define FTOL 1.0e-10    interview.
     (Repository): Because some people have very long ID (first column)
 #define NRANSI    we changed int to long in num[] and we added a new lvector for
 #define ITMAX 200    memory allocation. But we also truncated to 8 characters (left
     truncation)
 #define TOL 2.0e-4    (Repository): No more line truncation errors.
   
 #define CGOLD 0.3819660    Revision 1.84  2003/06/13 21:44:43  brouard
 #define ZEPS 1.0e-10    * imach.c (Repository): Replace "freqsummary" at a correct
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
 #define GOLD 1.618034    parcimony.
 #define GLIMIT 100.0    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #define TINY 1.0e-20  
     Revision 1.83  2003/06/10 13:39:11  lievre
 static double maxarg1,maxarg2;    *** empty log message ***
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.82  2003/06/05 15:57:20  brouard
      Add log in  imach.c and  fullversion number is now printed.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)  */
   /*
 static double sqrarg;     Interpolated Markov Chain
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Short summary of the programme:
     
 int imx;    This program computes Healthy Life Expectancies from
 int stepm;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 /* Stepm, step in month: minimum step interpolation*/    first survey ("cross") where individuals from different ages are
     interviewed on their health status or degree of disability (in the
 int m,nb;    case of a health survey which is our main interest) -2- at least a
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    second wave of interviews ("longitudinal") which measure each change
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    (if any) in individual health status.  Health expectancies are
 double **pmmij, ***probs, ***mobaverage;    computed from the time spent in each health state according to a
 double dateintmean=0;    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
 double *weight;    simplest model is the multinomial logistic model where pij is the
 int **s; /* Status */    probability to be observed in state j at the second wave
 double *agedc, **covar, idx;    conditional to be observed in state i at the first wave. Therefore
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     'age' is age and 'sex' is a covariate. If you want to have a more
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    complex model than "constant and age", you should modify the program
 double ftolhess; /* Tolerance for computing hessian */    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
 /**************** split *************************/    convergence.
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    The advantage of this computer programme, compared to a simple
    char *s;                             /* pointer */    multinomial logistic model, is clear when the delay between waves is not
    int  l1, l2;                         /* length counters */    identical for each individual. Also, if a individual missed an
     intermediate interview, the information is lost, but taken into
    l1 = strlen( path );                 /* length of path */    account using an interpolation or extrapolation.  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows    hPijx is the probability to be observed in state i at age x+h
    s = strrchr( path, '\\' );           /* find last / */    conditional to the observed state i at age x. The delay 'h' can be
 #else    split into an exact number (nh*stepm) of unobserved intermediate
    s = strrchr( path, '/' );            /* find last / */    states. This elementary transition (by month, quarter,
 #endif    semester or year) is modelled as a multinomial logistic.  The hPx
    if ( s == NULL ) {                   /* no directory, so use current */    matrix is simply the matrix product of nh*stepm elementary matrices
 #if     defined(__bsd__)                /* get current working directory */    and the contribution of each individual to the likelihood is simply
       extern char       *getwd( );    hPijx.
   
       if ( getwd( dirc ) == NULL ) {    Also this programme outputs the covariance matrix of the parameters but also
 #else    of the life expectancies. It also computes the stable prevalence. 
       extern char       *getcwd( );    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {             Institut national d'études démographiques, Paris.
 #endif    This software have been partly granted by Euro-REVES, a concerted action
          return( GLOCK_ERROR_GETCWD );    from the European Union.
       }    It is copyrighted identically to a GNU software product, ie programme and
       strcpy( name, path );             /* we've got it */    software can be distributed freely for non commercial use. Latest version
    } else {                             /* strip direcotry from path */    can be accessed at http://euroreves.ined.fr/imach .
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
       strcpy( name, s );                /* save file name */    
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    **********************************************************************/
       dirc[l1-l2] = 0;                  /* add zero */  /*
    }    main
    l1 = strlen( dirc );                 /* length of directory */    read parameterfile
 #ifdef windows    read datafile
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    concatwav
 #else    freqsummary
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    if (mle >= 1)
 #endif      mlikeli
    s = strrchr( name, '.' );            /* find last / */    print results files
    s++;    if mle==1 
    strcpy(ext,s);                       /* save extension */       computes hessian
    l1= strlen( name);    read end of parameter file: agemin, agemax, bage, fage, estepm
    l2= strlen( s)+1;        begin-prev-date,...
    strncpy( finame, name, l1-l2);    open gnuplot file
    finame[l1-l2]= 0;    open html file
    return( 0 );                         /* we're done */    stable prevalence
 }     for age prevalim()
     h Pij x
     variance of p varprob
 /******************************************/    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
 void replace(char *s, char*t)    Variance-covariance of DFLE
 {    prevalence()
   int i;     movingaverage()
   int lg=20;    varevsij() 
   i=0;    if popbased==1 varevsij(,popbased)
   lg=strlen(t);    total life expectancies
   for(i=0; i<= lg; i++) {    Variance of stable prevalence
     (s[i] = t[i]);   end
     if (t[i]== '\\') s[i]='/';  */
   }  
 }  
   
 int nbocc(char *s, char occ)   
 {  #include <math.h>
   int i,j=0;  #include <stdio.h>
   int lg=20;  #include <stdlib.h>
   i=0;  #include <unistd.h>
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {  /* #include <sys/time.h> */
   if  (s[i] == occ ) j++;  #include <time.h>
   }  #include "timeval.h"
   return j;  
 }  /* #include <libintl.h> */
   /* #define _(String) gettext (String) */
 void cutv(char *u,char *v, char*t, char occ)  
 {  #define MAXLINE 256
   int i,lg,j,p=0;  #define GNUPLOTPROGRAM "gnuplot"
   i=0;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   for(j=0; j<=strlen(t)-1; j++) {  #define FILENAMELENGTH 132
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  /*#define DEBUG*/
   }  /*#define windows*/
   #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   lg=strlen(t);  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   }  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
      u[p]='\0';  
   #define NINTERVMAX 8
    for(j=0; j<= lg; j++) {  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
     if (j>=(p+1))(v[j-p-1] = t[j]);  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   }  #define NCOVMAX 8 /* Maximum number of covariates */
 }  #define MAXN 20000
   #define YEARM 12. /* Number of months per year */
 /********************** nrerror ********************/  #define AGESUP 130
   #define AGEBASE 40
 void nrerror(char error_text[])  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
 {  #ifdef UNIX
   fprintf(stderr,"ERREUR ...\n");  #define DIRSEPARATOR '/'
   fprintf(stderr,"%s\n",error_text);  #define ODIRSEPARATOR '\\'
   exit(1);  #else
 }  #define DIRSEPARATOR '\\'
 /*********************** vector *******************/  #define ODIRSEPARATOR '/'
 double *vector(int nl, int nh)  #endif
 {  
   double *v;  /* $Id$ */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  /* $State$ */
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;  char version[]="Imach version 0.98, September 2005, INED-EUROREVES ";
 }  char fullversion[]="$Revision$ $Date$"; 
   int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 /************************ free vector ******************/  int nvar;
 void free_vector(double*v, int nl, int nh)  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 {  int npar=NPARMAX;
   free((FREE_ARG)(v+nl-NR_END));  int nlstate=2; /* Number of live states */
 }  int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 /************************ivector *******************************/  int popbased=0;
 int *ivector(long nl,long nh)  
 {  int *wav; /* Number of waves for this individuual 0 is possible */
   int *v;  int maxwav; /* Maxim number of waves */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  int jmin, jmax; /* min, max spacing between 2 waves */
   if (!v) nrerror("allocation failure in ivector");  int gipmx, gsw; /* Global variables on the number of contributions 
   return v-nl+NR_END;                     to the likelihood and the sum of weights (done by funcone)*/
 }  int mle, weightopt;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 /******************free ivector **************************/  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 void free_ivector(int *v, long nl, long nh)  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 {             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   free((FREE_ARG)(v+nl-NR_END));  double jmean; /* Mean space between 2 waves */
 }  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 /******************* imatrix *******************************/  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 int **imatrix(long nrl, long nrh, long ncl, long nch)  FILE *ficlog, *ficrespow;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  int globpr; /* Global variable for printing or not */
 {  double fretone; /* Only one call to likelihood */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  long ipmx; /* Number of contributions */
   int **m;  double sw; /* Sum of weights */
    char filerespow[FILENAMELENGTH];
   /* allocate pointers to rows */  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  FILE *ficresilk;
   if (!m) nrerror("allocation failure 1 in matrix()");  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   m += NR_END;  FILE *ficresprobmorprev;
   m -= nrl;  FILE *fichtm, *fichtmcov; /* Html File */
    FILE *ficreseij;
    char filerese[FILENAMELENGTH];
   /* allocate rows and set pointers to them */  FILE  *ficresvij;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  char fileresv[FILENAMELENGTH];
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  FILE  *ficresvpl;
   m[nrl] += NR_END;  char fileresvpl[FILENAMELENGTH];
   m[nrl] -= ncl;  char title[MAXLINE];
    char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
    char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   /* return pointer to array of pointers to rows */  char command[FILENAMELENGTH];
   return m;  int  outcmd=0;
 }  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)  char filelog[FILENAMELENGTH]; /* Log file */
       int **m;  char filerest[FILENAMELENGTH];
       long nch,ncl,nrh,nrl;  char fileregp[FILENAMELENGTH];
      /* free an int matrix allocated by imatrix() */  char popfile[FILENAMELENGTH];
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   free((FREE_ARG) (m+nrl-NR_END));  
 }  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   struct timezone tzp;
 /******************* matrix *******************************/  extern int gettimeofday();
 double **matrix(long nrl, long nrh, long ncl, long nch)  struct tm tmg, tm, tmf, *gmtime(), *localtime();
 {  long time_value;
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  extern long time();
   double **m;  char strcurr[80], strfor[80];
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define NR_END 1
   if (!m) nrerror("allocation failure 1 in matrix()");  #define FREE_ARG char*
   m += NR_END;  #define FTOL 1.0e-10
   m -= nrl;  
   #define NRANSI 
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define ITMAX 200 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  #define TOL 2.0e-4 
   m[nrl] -= ncl;  
   #define CGOLD 0.3819660 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define ZEPS 1.0e-10 
   return m;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 }  
   #define GOLD 1.618034 
 /*************************free matrix ************************/  #define GLIMIT 100.0 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  #define TINY 1.0e-20 
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  static double maxarg1,maxarg2;
   free((FREE_ARG)(m+nrl-NR_END));  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 }  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     
 /******************* ma3x *******************************/  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  #define rint(a) floor(a+0.5)
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  static double sqrarg;
   double ***m;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int agegomp= AGEGOMP;
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  int imx; 
   m -= nrl;  int stepm=1;
   /* Stepm, step in month: minimum step interpolation*/
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int estepm;
   m[nrl] += NR_END;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   m[nrl] -= ncl;  
   int m,nb;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  long *num;
   int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  double **pmmij, ***probs;
   m[nrl][ncl] += NR_END;  double *ageexmed,*agecens;
   m[nrl][ncl] -= nll;  double dateintmean=0;
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;  double *weight;
    int **s; /* Status */
   for (i=nrl+1; i<=nrh; i++) {  double *agedc, **covar, idx;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   }  double ftolhess; /* Tolerance for computing hessian */
   return m;  
 }  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 /*************************free ma3x ************************/  {
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
 {       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    */ 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    char  *ss;                            /* pointer */
   free((FREE_ARG)(m+nrl-NR_END));    int   l1, l2;                         /* length counters */
 }  
     l1 = strlen(path );                   /* length of path */
 /***************** f1dim *************************/    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 extern int ncom;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 extern double *pcom,*xicom;    if ( ss == NULL ) {                   /* no directory, so use current */
 extern double (*nrfunc)(double []);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
          printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 double f1dim(double x)      /* get current working directory */
 {      /*    extern  char* getcwd ( char *buf , int len);*/
   int j;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   double f;        return( GLOCK_ERROR_GETCWD );
   double *xt;      }
        strcpy( name, path );               /* we've got it */
   xt=vector(1,ncom);    } else {                              /* strip direcotry from path */
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];      ss++;                               /* after this, the filename */
   f=(*nrfunc)(xt);      l2 = strlen( ss );                  /* length of filename */
   free_vector(xt,1,ncom);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   return f;      strcpy( name, ss );         /* save file name */
 }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
 /*****************brent *************************/    }
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    l1 = strlen( dirc );                  /* length of directory */
 {    /*#ifdef windows
   int iter;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   double a,b,d,etemp;  #else
   double fu,fv,fw,fx;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   double ftemp;  #endif
   double p,q,r,tol1,tol2,u,v,w,x,xm;    */
   double e=0.0;    ss = strrchr( name, '.' );            /* find last / */
      if (ss >0){
   a=(ax < cx ? ax : cx);      ss++;
   b=(ax > cx ? ax : cx);      strcpy(ext,ss);                     /* save extension */
   x=w=v=bx;      l1= strlen( name);
   fw=fv=fx=(*f)(x);      l2= strlen(ss)+1;
   for (iter=1;iter<=ITMAX;iter++) {      strncpy( finame, name, l1-l2);
     xm=0.5*(a+b);      finame[l1-l2]= 0;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    }
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    return( 0 );                          /* we're done */
     printf(".");fflush(stdout);  }
 #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);  
     /*          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))){  void replace_back_to_slash(char *s, char*t)
       *xmin=x;  {
       return fx;    int i;
     }    int lg=0;
     ftemp=fu;    i=0;
     if (fabs(e) > tol1) {    lg=strlen(t);
       r=(x-w)*(fx-fv);    for(i=0; i<= lg; i++) {
       q=(x-v)*(fx-fw);      (s[i] = t[i]);
       p=(x-v)*q-(x-w)*r;      if (t[i]== '\\') s[i]='/';
       q=2.0*(q-r);    }
       if (q > 0.0) p = -p;  }
       q=fabs(q);  
       etemp=e;  int nbocc(char *s, char occ)
       e=d;  {
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    int i,j=0;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    int lg=20;
       else {    i=0;
         d=p/q;    lg=strlen(s);
         u=x+d;    for(i=0; i<= lg; i++) {
         if (u-a < tol2 || b-u < tol2)    if  (s[i] == occ ) j++;
           d=SIGN(tol1,xm-x);    }
       }    return j;
     } else {  }
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  void cutv(char *u,char *v, char*t, char occ)
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  {
     fu=(*f)(u);    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
     if (fu <= fx) {       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       if (u >= x) a=x; else b=x;       gives u="abcedf" and v="ghi2j" */
       SHFT(v,w,x,u)    int i,lg,j,p=0;
         SHFT(fv,fw,fx,fu)    i=0;
         } else {    for(j=0; j<=strlen(t)-1; j++) {
           if (u < x) a=u; else b=u;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
           if (fu <= fw || w == x) {    }
             v=w;  
             w=u;    lg=strlen(t);
             fv=fw;    for(j=0; j<p; j++) {
             fw=fu;      (u[j] = t[j]);
           } else if (fu <= fv || v == x || v == w) {    }
             v=u;       u[p]='\0';
             fv=fu;  
           }     for(j=0; j<= lg; j++) {
         }      if (j>=(p+1))(v[j-p-1] = t[j]);
   }    }
   nrerror("Too many iterations in brent");  }
   *xmin=x;  
   return fx;  /********************** nrerror ********************/
 }  
   void nrerror(char error_text[])
 /****************** mnbrak ***********************/  {
     fprintf(stderr,"ERREUR ...\n");
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    fprintf(stderr,"%s\n",error_text);
             double (*func)(double))    exit(EXIT_FAILURE);
 {  }
   double ulim,u,r,q, dum;  /*********************** vector *******************/
   double fu;  double *vector(int nl, int nh)
    {
   *fa=(*func)(*ax);    double *v;
   *fb=(*func)(*bx);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   if (*fb > *fa) {    if (!v) nrerror("allocation failure in vector");
     SHFT(dum,*ax,*bx,dum)    return v-nl+NR_END;
       SHFT(dum,*fb,*fa,dum)  }
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);  /************************ free vector ******************/
   *fc=(*func)(*cx);  void free_vector(double*v, int nl, int nh)
   while (*fb > *fc) {  {
     r=(*bx-*ax)*(*fb-*fc);    free((FREE_ARG)(v+nl-NR_END));
     q=(*bx-*cx)*(*fb-*fa);  }
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  /************************ivector *******************************/
     ulim=(*bx)+GLIMIT*(*cx-*bx);  int *ivector(long nl,long nh)
     if ((*bx-u)*(u-*cx) > 0.0) {  {
       fu=(*func)(u);    int *v;
     } else if ((*cx-u)*(u-ulim) > 0.0) {    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       fu=(*func)(u);    if (!v) nrerror("allocation failure in ivector");
       if (fu < *fc) {    return v-nl+NR_END;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  }
           SHFT(*fb,*fc,fu,(*func)(u))  
           }  /******************free ivector **************************/
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  void free_ivector(int *v, long nl, long nh)
       u=ulim;  {
       fu=(*func)(u);    free((FREE_ARG)(v+nl-NR_END));
     } else {  }
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);  /************************lvector *******************************/
     }  long *lvector(long nl,long nh)
     SHFT(*ax,*bx,*cx,u)  {
       SHFT(*fa,*fb,*fc,fu)    long *v;
       }    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 }    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
 /*************** linmin ************************/  }
   
 int ncom;  /******************free lvector **************************/
 double *pcom,*xicom;  void free_lvector(long *v, long nl, long nh)
 double (*nrfunc)(double []);  {
      free((FREE_ARG)(v+nl-NR_END));
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  }
 {  
   double brent(double ax, double bx, double cx,  /******************* imatrix *******************************/
                double (*f)(double), double tol, double *xmin);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   double f1dim(double x);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  { 
               double *fc, double (*func)(double));    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   int j;    int **m; 
   double xx,xmin,bx,ax;    
   double fx,fb,fa;    /* allocate pointers to rows */ 
      m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   ncom=n;    if (!m) nrerror("allocation failure 1 in matrix()"); 
   pcom=vector(1,n);    m += NR_END; 
   xicom=vector(1,n);    m -= nrl; 
   nrfunc=func;    
   for (j=1;j<=n;j++) {    
     pcom[j]=p[j];    /* allocate rows and set pointers to them */ 
     xicom[j]=xi[j];    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   ax=0.0;    m[nrl] += NR_END; 
   xx=1.0;    m[nrl] -= ncl; 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 #ifdef DEBUG    
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    /* return pointer to array of pointers to rows */ 
 #endif    return m; 
   for (j=1;j<=n;j++) {  } 
     xi[j] *= xmin;  
     p[j] += xi[j];  /****************** free_imatrix *************************/
   }  void free_imatrix(m,nrl,nrh,ncl,nch)
   free_vector(xicom,1,n);        int **m;
   free_vector(pcom,1,n);        long nch,ncl,nrh,nrl; 
 }       /* free an int matrix allocated by imatrix() */ 
   { 
 /*************** powell ************************/    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    free((FREE_ARG) (m+nrl-NR_END)); 
             double (*func)(double []))  } 
 {  
   void linmin(double p[], double xi[], int n, double *fret,  /******************* matrix *******************************/
               double (*func)(double []));  double **matrix(long nrl, long nrh, long ncl, long nch)
   int i,ibig,j;  {
   double del,t,*pt,*ptt,*xit;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   double fp,fptt;    double **m;
   double *xits;  
   pt=vector(1,n);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   ptt=vector(1,n);    if (!m) nrerror("allocation failure 1 in matrix()");
   xit=vector(1,n);    m += NR_END;
   xits=vector(1,n);    m -= nrl;
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   for (*iter=1;;++(*iter)) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     fp=(*fret);    m[nrl] += NR_END;
     ibig=0;    m[nrl] -= ncl;
     del=0.0;  
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     for (i=1;i<=n;i++)    return m;
       printf(" %d %.12f",i, p[i]);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     printf("\n");     */
     for (i=1;i<=n;i++) {  }
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  /*************************free matrix ************************/
 #ifdef DEBUG  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       printf("fret=%lf \n",*fret);  {
 #endif    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       printf("%d",i);fflush(stdout);    free((FREE_ARG)(m+nrl-NR_END));
       linmin(p,xit,n,fret,func);  }
       if (fabs(fptt-(*fret)) > del) {  
         del=fabs(fptt-(*fret));  /******************* ma3x *******************************/
         ibig=i;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       }  {
 #ifdef DEBUG    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       printf("%d %.12e",i,(*fret));    double ***m;
       for (j=1;j<=n;j++) {  
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         printf(" x(%d)=%.12e",j,xit[j]);    if (!m) nrerror("allocation failure 1 in matrix()");
       }    m += NR_END;
       for(j=1;j<=n;j++)    m -= nrl;
         printf(" p=%.12e",p[j]);  
       printf("\n");    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 #endif    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     }    m[nrl] += NR_END;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    m[nrl] -= ncl;
 #ifdef DEBUG  
       int k[2],l;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       k[0]=1;  
       k[1]=-1;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       printf("Max: %.12e",(*func)(p));    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       for (j=1;j<=n;j++)    m[nrl][ncl] += NR_END;
         printf(" %.12e",p[j]);    m[nrl][ncl] -= nll;
       printf("\n");    for (j=ncl+1; j<=nch; j++) 
       for(l=0;l<=1;l++) {      m[nrl][j]=m[nrl][j-1]+nlay;
         for (j=1;j<=n;j++) {    
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    for (i=nrl+1; i<=nrh; i++) {
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         }      for (j=ncl+1; j<=nch; j++) 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        m[i][j]=m[i][j-1]+nlay;
       }    }
 #endif    return m; 
     /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
              &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       free_vector(xit,1,n);    */
       free_vector(xits,1,n);  }
       free_vector(ptt,1,n);  
       free_vector(pt,1,n);  /*************************free ma3x ************************/
       return;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     }  {
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     for (j=1;j<=n;j++) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       ptt[j]=2.0*p[j]-pt[j];    free((FREE_ARG)(m+nrl-NR_END));
       xit[j]=p[j]-pt[j];  }
       pt[j]=p[j];  
     }  /*************** function subdirf ***********/
     fptt=(*func)(ptt);  char *subdirf(char fileres[])
     if (fptt < fp) {  {
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    /* Caution optionfilefiname is hidden */
       if (t < 0.0) {    strcpy(tmpout,optionfilefiname);
         linmin(p,xit,n,fret,func);    strcat(tmpout,"/"); /* Add to the right */
         for (j=1;j<=n;j++) {    strcat(tmpout,fileres);
           xi[j][ibig]=xi[j][n];    return tmpout;
           xi[j][n]=xit[j];  }
         }  
 #ifdef DEBUG  /*************** function subdirf2 ***********/
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  char *subdirf2(char fileres[], char *preop)
         for(j=1;j<=n;j++)  {
           printf(" %.12e",xit[j]);    
         printf("\n");    /* Caution optionfilefiname is hidden */
 #endif    strcpy(tmpout,optionfilefiname);
       }    strcat(tmpout,"/");
     }    strcat(tmpout,preop);
   }    strcat(tmpout,fileres);
 }    return tmpout;
   }
 /**** Prevalence limit ****************/  
   /*************** function subdirf3 ***********/
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  char *subdirf3(char fileres[], char *preop, char *preop2)
 {  {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    
      matrix by transitions matrix until convergence is reached */    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
   int i, ii,j,k;    strcat(tmpout,"/");
   double min, max, maxmin, maxmax,sumnew=0.;    strcat(tmpout,preop);
   double **matprod2();    strcat(tmpout,preop2);
   double **out, cov[NCOVMAX], **pmij();    strcat(tmpout,fileres);
   double **newm;    return tmpout;
   double agefin, delaymax=50 ; /* Max number of years to converge */  }
   
   for (ii=1;ii<=nlstate+ndeath;ii++)  /***************** f1dim *************************/
     for (j=1;j<=nlstate+ndeath;j++){  extern int ncom; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  extern double *pcom,*xicom;
     }  extern double (*nrfunc)(double []); 
    
    cov[1]=1.;  double f1dim(double x) 
    { 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    int j; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    double f;
     newm=savm;    double *xt; 
     /* Covariates have to be included here again */   
      cov[2]=agefin;    xt=vector(1,ncom); 
      for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       for (k=1; k<=cptcovn;k++) {    f=(*nrfunc)(xt); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    free_vector(xt,1,ncom); 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    return f; 
       }  } 
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /*****************brent *************************/
       for (k=1; k<=cptcovprod;k++)  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  { 
     int iter; 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    double a,b,d,etemp;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    double fu,fv,fw,fx;
     double ftemp;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     double e=0.0; 
     savm=oldm;   
     oldm=newm;    a=(ax < cx ? ax : cx); 
     maxmax=0.;    b=(ax > cx ? ax : cx); 
     for(j=1;j<=nlstate;j++){    x=w=v=bx; 
       min=1.;    fw=fv=fx=(*f)(x); 
       max=0.;    for (iter=1;iter<=ITMAX;iter++) { 
       for(i=1; i<=nlstate; i++) {      xm=0.5*(a+b); 
         sumnew=0;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         prlim[i][j]= newm[i][j]/(1-sumnew);      printf(".");fflush(stdout);
         max=FMAX(max,prlim[i][j]);      fprintf(ficlog,".");fflush(ficlog);
         min=FMIN(min,prlim[i][j]);  #ifdef DEBUG
       }      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       maxmin=max-min;      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);
       maxmax=FMAX(maxmax,maxmin);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     }  #endif
     if(maxmax < ftolpl){      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       return prlim;        *xmin=x; 
     }        return fx; 
   }      } 
 }      ftemp=fu;
       if (fabs(e) > tol1) { 
 /*************** transition probabilities ***************/        r=(x-w)*(fx-fv); 
         q=(x-v)*(fx-fw); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        p=(x-v)*q-(x-w)*r; 
 {        q=2.0*(q-r); 
   double s1, s2;        if (q > 0.0) p = -p; 
   /*double t34;*/        q=fabs(q); 
   int i,j,j1, nc, ii, jj;        etemp=e; 
         e=d; 
     for(i=1; i<= nlstate; i++){        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     for(j=1; j<i;j++){          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        else { 
         /*s2 += param[i][j][nc]*cov[nc];*/          d=p/q; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          u=x+d; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/          if (u-a < tol2 || b-u < tol2) 
       }            d=SIGN(tol1,xm-x); 
       ps[i][j]=s2;        } 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      } else { 
     }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     for(j=i+1; j<=nlstate+ndeath;j++){      } 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      fu=(*f)(u); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      if (fu <= fx) { 
       }        if (u >= x) a=x; else b=x; 
       ps[i][j]=s2;        SHFT(v,w,x,u) 
     }          SHFT(fv,fw,fx,fu) 
   }          } else { 
     /*ps[3][2]=1;*/            if (u < x) a=u; else b=u; 
             if (fu <= fw || w == x) { 
   for(i=1; i<= nlstate; i++){              v=w; 
      s1=0;              w=u; 
     for(j=1; j<i; j++)              fv=fw; 
       s1+=exp(ps[i][j]);              fw=fu; 
     for(j=i+1; j<=nlstate+ndeath; j++)            } else if (fu <= fv || v == x || v == w) { 
       s1+=exp(ps[i][j]);              v=u; 
     ps[i][i]=1./(s1+1.);              fv=fu; 
     for(j=1; j<i; j++)            } 
       ps[i][j]= exp(ps[i][j])*ps[i][i];          } 
     for(j=i+1; j<=nlstate+ndeath; j++)    } 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    nrerror("Too many iterations in brent"); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    *xmin=x; 
   } /* end i */    return fx; 
   } 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  /****************** mnbrak ***********************/
       ps[ii][jj]=0;  
       ps[ii][ii]=1;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     }              double (*func)(double)) 
   }  { 
     double ulim,u,r,q, dum;
     double fu; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){   
     for(jj=1; jj<= nlstate+ndeath; jj++){    *fa=(*func)(*ax); 
      printf("%lf ",ps[ii][jj]);    *fb=(*func)(*bx); 
    }    if (*fb > *fa) { 
     printf("\n ");      SHFT(dum,*ax,*bx,dum) 
     }        SHFT(dum,*fb,*fa,dum) 
     printf("\n ");printf("%lf ",cov[2]);*/        } 
 /*    *cx=(*bx)+GOLD*(*bx-*ax); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    *fc=(*func)(*cx); 
   goto end;*/    while (*fb > *fc) { 
     return ps;      r=(*bx-*ax)*(*fb-*fc); 
 }      q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 /**************** Product of 2 matrices ******************/        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      if ((*bx-u)*(u-*cx) > 0.0) { 
 {        fu=(*func)(u); 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      } else if ((*cx-u)*(u-ulim) > 0.0) { 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        fu=(*func)(u); 
   /* in, b, out are matrice of pointers which should have been initialized        if (fu < *fc) { 
      before: only the contents of out is modified. The function returns          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
      a pointer to pointers identical to out */            SHFT(*fb,*fc,fu,(*func)(u)) 
   long i, j, k;            } 
   for(i=nrl; i<= nrh; i++)      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     for(k=ncolol; k<=ncoloh; k++)        u=ulim; 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        fu=(*func)(u); 
         out[i][k] +=in[i][j]*b[j][k];      } else { 
         u=(*cx)+GOLD*(*cx-*bx); 
   return out;        fu=(*func)(u); 
 }      } 
       SHFT(*ax,*bx,*cx,u) 
         SHFT(*fa,*fb,*fc,fu) 
 /************* Higher Matrix Product ***************/        } 
   } 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  
 {  /*************** linmin ************************/
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  
      duration (i.e. until  int ncom; 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  double *pcom,*xicom;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  double (*nrfunc)(double []); 
      (typically every 2 years instead of every month which is too big).   
      Model is determined by parameters x and covariates have to be  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
      included manually here.  { 
     double brent(double ax, double bx, double cx, 
      */                 double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
   int i, j, d, h, k;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   double **out, cov[NCOVMAX];                double *fc, double (*func)(double)); 
   double **newm;    int j; 
     double xx,xmin,bx,ax; 
   /* Hstepm could be zero and should return the unit matrix */    double fx,fb,fa;
   for (i=1;i<=nlstate+ndeath;i++)   
     for (j=1;j<=nlstate+ndeath;j++){    ncom=n; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);    pcom=vector(1,n); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);    xicom=vector(1,n); 
     }    nrfunc=func; 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    for (j=1;j<=n;j++) { 
   for(h=1; h <=nhstepm; h++){      pcom[j]=p[j]; 
     for(d=1; d <=hstepm; d++){      xicom[j]=xi[j]; 
       newm=savm;    } 
       /* Covariates have to be included here again */    ax=0.0; 
       cov[1]=1.;    xx=1.0; 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       for (k=1; k<=cptcovage;k++)  #ifdef DEBUG
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       for (k=1; k<=cptcovprod;k++)    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  #endif
     for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      p[j] += xi[j]; 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    } 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    free_vector(xicom,1,n); 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    free_vector(pcom,1,n); 
       savm=oldm;  } 
       oldm=newm;  
     }  char *asc_diff_time(long time_sec, char ascdiff[])
     for(i=1; i<=nlstate+ndeath; i++)  {
       for(j=1;j<=nlstate+ndeath;j++) {    long sec_left, days, hours, minutes;
         po[i][j][h]=newm[i][j];    days = (time_sec) / (60*60*24);
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    sec_left = (time_sec) % (60*60*24);
          */    hours = (sec_left) / (60*60) ;
       }    sec_left = (sec_left) %(60*60);
   } /* end h */    minutes = (sec_left) /60;
   return po;    sec_left = (sec_left) % (60);
 }    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     return ascdiff;
   }
 /*************** log-likelihood *************/  
 double func( double *x)  /*************** powell ************************/
 {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   int i, ii, j, k, mi, d, kk;              double (*func)(double [])) 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  { 
   double **out;    void linmin(double p[], double xi[], int n, double *fret, 
   double sw; /* Sum of weights */                double (*func)(double [])); 
   double lli; /* Individual log likelihood */    int i,ibig,j; 
   long ipmx;    double del,t,*pt,*ptt,*xit;
   /*extern weight */    double fp,fptt;
   /* We are differentiating ll according to initial status */    double *xits;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    int niterf, itmp;
   /*for(i=1;i<imx;i++)  
     printf(" %d\n",s[4][i]);    pt=vector(1,n); 
   */    ptt=vector(1,n); 
   cov[1]=1.;    xit=vector(1,n); 
     xits=vector(1,n); 
   for(k=1; k<=nlstate; k++) ll[k]=0.;    *fret=(*func)(p); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    for (*iter=1;;++(*iter)) { 
     for(mi=1; mi<= wav[i]-1; mi++){      fp=(*fret); 
       for (ii=1;ii<=nlstate+ndeath;ii++)      ibig=0; 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      del=0.0; 
       for(d=0; d<dh[mi][i]; d++){      last_time=curr_time;
         newm=savm;      (void) gettimeofday(&curr_time,&tzp);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      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 (kk=1; kk<=cptcovage;kk++) {      /*    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);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
         }      */
             for (i=1;i<=n;i++) {
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        printf(" %d %.12f",i, p[i]);
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        fprintf(ficlog," %d %.12lf",i, p[i]);
         savm=oldm;        fprintf(ficrespow," %.12lf", p[i]);
         oldm=newm;      }
              printf("\n");
              fprintf(ficlog,"\n");
       } /* end mult */      fprintf(ficrespow,"\n");fflush(ficrespow);
            if(*iter <=3){
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        tm = *localtime(&curr_time.tv_sec);
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        strcpy(strcurr,asctime(&tm));
       ipmx +=1;  /*       asctime_r(&tm,strcurr); */
       sw += weight[i];        forecast_time=curr_time; 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        itmp = strlen(strcurr);
     } /* end of wave */        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   } /* end of individual */          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(k=1,l=0.; k<=nlstate; k++) l += ll[k];        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        for(niterf=10;niterf<=30;niterf+=10){
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   return -l;          tmf = *localtime(&forecast_time.tv_sec);
 }  /*      asctime_r(&tmf,strfor); */
           strcpy(strfor,asctime(&tmf));
           itmp = strlen(strfor);
 /*********** Maximum Likelihood Estimation ***************/          if(strfor[itmp-1]=='\n')
           strfor[itmp-1]='\0';
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))          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);
   int i,j, iter;        }
   double **xi,*delti;      }
   double fret;      for (i=1;i<=n;i++) { 
   xi=matrix(1,npar,1,npar);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   for (i=1;i<=npar;i++)        fptt=(*fret); 
     for (j=1;j<=npar;j++)  #ifdef DEBUG
       xi[i][j]=(i==j ? 1.0 : 0.0);        printf("fret=%lf \n",*fret);
   printf("Powell\n");        fprintf(ficlog,"fret=%lf \n",*fret);
   powell(p,xi,npar,ftol,&iter,&fret,func);  #endif
         printf("%d",i);fflush(stdout);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        fprintf(ficlog,"%d",i);fflush(ficlog);
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
 }          del=fabs(fptt-(*fret)); 
           ibig=i; 
 /**** Computes Hessian and covariance matrix ***/        } 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  #ifdef DEBUG
 {        printf("%d %.12e",i,(*fret));
   double  **a,**y,*x,pd;        fprintf(ficlog,"%d %.12e",i,(*fret));
   double **hess;        for (j=1;j<=n;j++) {
   int i, j,jk;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   int *indx;          printf(" x(%d)=%.12e",j,xit[j]);
           fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   double hessii(double p[], double delta, int theta, double delti[]);        }
   double hessij(double p[], double delti[], int i, int j);        for(j=1;j<=n;j++) {
   void lubksb(double **a, int npar, int *indx, double b[]) ;          printf(" p=%.12e",p[j]);
   void ludcmp(double **a, int npar, int *indx, double *d) ;          fprintf(ficlog," p=%.12e",p[j]);
         }
   hess=matrix(1,npar,1,npar);        printf("\n");
         fprintf(ficlog,"\n");
   printf("\nCalculation of the hessian matrix. Wait...\n");  #endif
   for (i=1;i<=npar;i++){      } 
     printf("%d",i);fflush(stdout);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     hess[i][i]=hessii(p,ftolhess,i,delti);  #ifdef DEBUG
     /*printf(" %f ",p[i]);*/        int k[2],l;
     /*printf(" %lf ",hess[i][i]);*/        k[0]=1;
   }        k[1]=-1;
          printf("Max: %.12e",(*func)(p));
   for (i=1;i<=npar;i++) {        fprintf(ficlog,"Max: %.12e",(*func)(p));
     for (j=1;j<=npar;j++)  {        for (j=1;j<=n;j++) {
       if (j>i) {          printf(" %.12e",p[j]);
         printf(".%d%d",i,j);fflush(stdout);          fprintf(ficlog," %.12e",p[j]);
         hess[i][j]=hessij(p,delti,i,j);        }
         hess[j][i]=hess[i][j];            printf("\n");
         /*printf(" %lf ",hess[i][j]);*/        fprintf(ficlog,"\n");
       }        for(l=0;l<=1;l++) {
     }          for (j=1;j<=n;j++) {
   }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   printf("\n");            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]);
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          }
            printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   a=matrix(1,npar,1,npar);          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   y=matrix(1,npar,1,npar);        }
   x=vector(1,npar);  #endif
   indx=ivector(1,npar);  
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        free_vector(xit,1,n); 
   ludcmp(a,npar,indx,&pd);        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
   for (j=1;j<=npar;j++) {        free_vector(pt,1,n); 
     for (i=1;i<=npar;i++) x[i]=0;        return; 
     x[j]=1;      } 
     lubksb(a,npar,indx,x);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     for (i=1;i<=npar;i++){      for (j=1;j<=n;j++) { 
       matcov[i][j]=x[i];        ptt[j]=2.0*p[j]-pt[j]; 
     }        xit[j]=p[j]-pt[j]; 
   }        pt[j]=p[j]; 
       } 
   printf("\n#Hessian matrix#\n");      fptt=(*func)(ptt); 
   for (i=1;i<=npar;i++) {      if (fptt < fp) { 
     for (j=1;j<=npar;j++) {        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       printf("%.3e ",hess[i][j]);        if (t < 0.0) { 
     }          linmin(p,xit,n,fret,func); 
     printf("\n");          for (j=1;j<=n;j++) { 
   }            xi[j][ibig]=xi[j][n]; 
             xi[j][n]=xit[j]; 
   /* Recompute Inverse */          }
   for (i=1;i<=npar;i++)  #ifdef DEBUG
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   ludcmp(a,npar,indx,&pd);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           for(j=1;j<=n;j++){
   /*  printf("\n#Hessian matrix recomputed#\n");            printf(" %.12e",xit[j]);
             fprintf(ficlog," %.12e",xit[j]);
   for (j=1;j<=npar;j++) {          }
     for (i=1;i<=npar;i++) x[i]=0;          printf("\n");
     x[j]=1;          fprintf(ficlog,"\n");
     lubksb(a,npar,indx,x);  #endif
     for (i=1;i<=npar;i++){        }
       y[i][j]=x[i];      } 
       printf("%.3e ",y[i][j]);    } 
     }  } 
     printf("\n");  
   }  /**** Prevalence limit (stable prevalence)  ****************/
   */  
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   free_matrix(a,1,npar,1,npar);  {
   free_matrix(y,1,npar,1,npar);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   free_vector(x,1,npar);       matrix by transitions matrix until convergence is reached */
   free_ivector(indx,1,npar);  
   free_matrix(hess,1,npar,1,npar);    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
     double **matprod2();
 }    double **out, cov[NCOVMAX], **pmij();
     double **newm;
 /*************** hessian matrix ****************/    double agefin, delaymax=50 ; /* Max number of years to converge */
 double hessii( double x[], double delta, int theta, double delti[])  
 {    for (ii=1;ii<=nlstate+ndeath;ii++)
   int i;      for (j=1;j<=nlstate+ndeath;j++){
   int l=1, lmax=20;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double k1,k2;      }
   double p2[NPARMAX+1];  
   double res;     cov[1]=1.;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;   
   double fx;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   int k=0,kmax=10;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   double l1;      newm=savm;
       /* Covariates have to be included here again */
   fx=func(x);       cov[2]=agefin;
   for (i=1;i<=npar;i++) p2[i]=x[i];    
   for(l=0 ; l <=lmax; l++){        for (k=1; k<=cptcovn;k++) {
     l1=pow(10,l);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     delts=delt;          /*      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(k=1 ; k <kmax; k=k+1){        }
       delt = delta*(l1*k);        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       p2[theta]=x[theta] +delt;        for (k=1; k<=cptcovprod;k++)
       k1=func(p2)-fx;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       p2[theta]=x[theta]-delt;  
       k2=func(p2)-fx;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       /*res= (k1-2.0*fx+k2)/delt/delt; */        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        /*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);
 #ifdef DEBUG  
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);      savm=oldm;
 #endif      oldm=newm;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      maxmax=0.;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      for(j=1;j<=nlstate;j++){
         k=kmax;        min=1.;
       }        max=0.;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        for(i=1; i<=nlstate; i++) {
         k=kmax; l=lmax*10.;          sumnew=0;
       }          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          prlim[i][j]= newm[i][j]/(1-sumnew);
         delts=delt;          max=FMAX(max,prlim[i][j]);
       }          min=FMIN(min,prlim[i][j]);
     }        }
   }        maxmin=max-min;
   delti[theta]=delts;        maxmax=FMAX(maxmax,maxmin);
   return res;      }
        if(maxmax < ftolpl){
 }        return prlim;
       }
 double hessij( double x[], double delti[], int thetai,int thetaj)    }
 {  }
   int i;  
   int l=1, l1, lmax=20;  /*************** transition probabilities ***************/ 
   double k1,k2,k3,k4,res,fx;  
   double p2[NPARMAX+1];  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   int k;  {
     double s1, s2;
   fx=func(x);    /*double t34;*/
   for (k=1; k<=2; k++) {    int i,j,j1, nc, ii, jj;
     for (i=1;i<=npar;i++) p2[i]=x[i];  
     p2[thetai]=x[thetai]+delti[thetai]/k;      for(i=1; i<= nlstate; i++){
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        for(j=1; j<i;j++){
     k1=func(p2)-fx;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
              /*s2 += param[i][j][nc]*cov[nc];*/
     p2[thetai]=x[thetai]+delti[thetai]/k;            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
     k2=func(p2)-fx;          }
            ps[i][j]=s2;
     p2[thetai]=x[thetai]-delti[thetai]/k;  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        }
     k3=func(p2)-fx;        for(j=i+1; j<=nlstate+ndeath;j++){
            for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     p2[thetai]=x[thetai]-delti[thetai]/k;            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     k4=func(p2)-fx;          }
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          ps[i][j]=s2;
 #ifdef DEBUG        }
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);      }
 #endif      /*ps[3][2]=1;*/
   }      
   return res;      for(i=1; i<= nlstate; i++){
 }        s1=0;
         for(j=1; j<i; j++)
 /************** Inverse of matrix **************/          s1+=exp(ps[i][j]);
 void ludcmp(double **a, int n, int *indx, double *d)        for(j=i+1; j<=nlstate+ndeath; j++)
 {          s1+=exp(ps[i][j]);
   int i,imax,j,k;        ps[i][i]=1./(s1+1.);
   double big,dum,sum,temp;        for(j=1; j<i; j++)
   double *vv;          ps[i][j]= exp(ps[i][j])*ps[i][i];
          for(j=i+1; j<=nlstate+ndeath; j++)
   vv=vector(1,n);          ps[i][j]= exp(ps[i][j])*ps[i][i];
   *d=1.0;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   for (i=1;i<=n;i++) {      } /* end i */
     big=0.0;      
     for (j=1;j<=n;j++)      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       if ((temp=fabs(a[i][j])) > big) big=temp;        for(jj=1; jj<= nlstate+ndeath; jj++){
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          ps[ii][jj]=0;
     vv[i]=1.0/big;          ps[ii][ii]=1;
   }        }
   for (j=1;j<=n;j++) {      }
     for (i=1;i<j;i++) {      
       sum=a[i][j];  
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
       a[i][j]=sum;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
     }  /*         printf("ddd %lf ",ps[ii][jj]); */
     big=0.0;  /*       } */
     for (i=j;i<=n;i++) {  /*       printf("\n "); */
       sum=a[i][j];  /*        } */
       for (k=1;k<j;k++)  /*        printf("\n ");printf("%lf ",cov[2]); */
         sum -= a[i][k]*a[k][j];         /*
       a[i][j]=sum;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       if ( (dum=vv[i]*fabs(sum)) >= big) {        goto end;*/
         big=dum;      return ps;
         imax=i;  }
       }  
     }  /**************** Product of 2 matrices ******************/
     if (j != imax) {  
       for (k=1;k<=n;k++) {  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
         dum=a[imax][k];  {
         a[imax][k]=a[j][k];    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         a[j][k]=dum;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       }    /* in, b, out are matrice of pointers which should have been initialized 
       *d = -(*d);       before: only the contents of out is modified. The function returns
       vv[imax]=vv[j];       a pointer to pointers identical to out */
     }    long i, j, k;
     indx[j]=imax;    for(i=nrl; i<= nrh; i++)
     if (a[j][j] == 0.0) a[j][j]=TINY;      for(k=ncolol; k<=ncoloh; k++)
     if (j != n) {        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       dum=1.0/(a[j][j]);          out[i][k] +=in[i][j]*b[j][k];
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }    return out;
   }  }
   free_vector(vv,1,n);  /* Doesn't work */  
 ;  
 }  /************* Higher Matrix Product ***************/
   
 void lubksb(double **a, int n, int *indx, double b[])  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
 {  {
   int i,ii=0,ip,j;    /* Computes the transition matrix starting at age 'age' over 
   double sum;       'nhstepm*hstepm*stepm' months (i.e. until
         age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   for (i=1;i<=n;i++) {       nhstepm*hstepm matrices. 
     ip=indx[i];       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     sum=b[ip];       (typically every 2 years instead of every month which is too big 
     b[ip]=b[i];       for the memory).
     if (ii)       Model is determined by parameters x and covariates have to be 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];       included manually here. 
     else if (sum) ii=i;  
     b[i]=sum;       */
   }  
   for (i=n;i>=1;i--) {    int i, j, d, h, k;
     sum=b[i];    double **out, cov[NCOVMAX];
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    double **newm;
     b[i]=sum/a[i][i];  
   }    /* Hstepm could be zero and should return the unit matrix */
 }    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
 /************ Frequencies ********************/        oldm[i][j]=(i==j ? 1.0 : 0.0);
 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)        po[i][j][0]=(i==j ? 1.0 : 0.0);
 {  /* Some frequencies */      }
      /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    for(h=1; h <=nhstepm; h++){
   double ***freq; /* Frequencies */      for(d=1; d <=hstepm; d++){
   double *pp;        newm=savm;
   double pos, k2, dateintsum=0,k2cpt=0;        /* Covariates have to be included here again */
   FILE *ficresp;        cov[1]=1.;
   char fileresp[FILENAMELENGTH];        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
          for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   pp=vector(1,nlstate);        for (k=1; k<=cptcovage;k++)
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   strcpy(fileresp,"p");        for (k=1; k<=cptcovprod;k++)
   strcat(fileresp,fileres);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   if((ficresp=fopen(fileresp,"w"))==NULL) {  
     printf("Problem with prevalence resultfile: %s\n", fileresp);  
     exit(0);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   j1=0;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         savm=oldm;
   j=cptcoveff;        oldm=newm;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      }
       for(i=1; i<=nlstate+ndeath; i++)
   for(k1=1; k1<=j;k1++){        for(j=1;j<=nlstate+ndeath;j++) {
    for(i1=1; i1<=ncodemax[k1];i1++){          po[i][j][h]=newm[i][j];
        j1++;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);           */
          scanf("%d", i);*/        }
         for (i=-1; i<=nlstate+ndeath; i++)      } /* end h */
          for (jk=-1; jk<=nlstate+ndeath; jk++)      return po;
            for(m=agemin; m <= agemax+3; m++)  }
              freq[i][jk][m]=0;  
   
         dateintsum=0;  /*************** log-likelihood *************/
         k2cpt=0;  double func( double *x)
        for (i=1; i<=imx; i++) {  {
          bool=1;    int i, ii, j, k, mi, d, kk;
          if  (cptcovn>0) {    double l, ll[NLSTATEMAX], cov[NCOVMAX];
            for (z1=1; z1<=cptcoveff; z1++)    double **out;
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    double sw; /* Sum of weights */
                bool=0;    double lli; /* Individual log likelihood */
          }    int s1, s2;
          if (bool==1) {    double bbh, survp;
            for(m=firstpass; m<=lastpass; m++){    long ipmx;
              k2=anint[m][i]+(mint[m][i]/12.);    /*extern weight */
              if ((k2>=dateprev1) && (k2<=dateprev2)) {    /* We are differentiating ll according to initial status */
                if(agev[m][i]==0) agev[m][i]=agemax+1;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
                if(agev[m][i]==1) agev[m][i]=agemax+2;    /*for(i=1;i<imx;i++) 
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      printf(" %d\n",s[4][i]);
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    */
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    cov[1]=1.;
                  dateintsum=dateintsum+k2;  
                  k2cpt++;    for(k=1; k<=nlstate; k++) ll[k]=0.;
                }  
     if(mle==1){
              }      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++)
                    for (j=1;j<=nlstate+ndeath;j++){
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
         if  (cptcovn>0) {            }
          fprintf(ficresp, "\n#********** Variable ");          for(d=0; d<dh[mi][i]; d++){
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            newm=savm;
        fprintf(ficresp, "**********\n#");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         }            for (kk=1; kk<=cptcovage;kk++) {
        for(i=1; i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);            }
        fprintf(ficresp, "\n");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                                 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for(i=(int)agemin; i <= (int)agemax+3; i++){            savm=oldm;
     if(i==(int)agemax+3)            oldm=newm;
       printf("Total");          } /* end mult */
     else        
       printf("Age %d", i);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     for(jk=1; jk <=nlstate ; jk++){          /* But now since version 0.9 we anticipate for bias at large stepm.
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         pp[jk] += freq[jk][m][i];           * (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
     for(jk=1; jk <=nlstate ; jk++){           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       for(m=-1, pos=0; m <=0 ; m++)           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         pos += freq[jk][m][i];           * probability in order to take into account the bias as a fraction of the way
       if(pp[jk]>=1.e-10)           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);           * -stepm/2 to stepm/2 .
       else           * For stepm=1 the results are the same as for previous versions of Imach.
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);           * For stepm > 1 the results are less biased than in previous versions. 
     }           */
           s1=s[mw[mi][i]][i];
      for(jk=1; jk <=nlstate ; jk++){          s2=s[mw[mi+1][i]][i];
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          bbh=(double)bh[mi][i]/(double)stepm; 
         pp[jk] += freq[jk][m][i];          /* bias bh is positive if real duration
      }           * is higher than the multiple of stepm and negative otherwise.
            */
     for(jk=1,pos=0; jk <=nlstate ; jk++)          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       pos += pp[jk];          if( s2 > nlstate){ 
     for(jk=1; jk <=nlstate ; jk++){            /* i.e. if s2 is a death state and if the date of death is known 
       if(pos>=1.e-5)               then the contribution to the likelihood is the probability to 
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);               die between last step unit time and current  step unit time, 
       else               which is also equal to probability to die before dh 
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);               minus probability to die before dh-stepm . 
       if( i <= (int) agemax){               In version up to 0.92 likelihood was computed
         if(pos>=1.e-5){          as if date of death was unknown. Death was treated as any other
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          health state: the date of the interview describes the actual state
           probs[i][jk][j1]= pp[jk]/pos;          and not the date of a change in health state. The former idea was
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          to consider that at each interview the state was recorded
         }          (healthy, disable or death) and IMaCh was corrected; but when we
       else          introduced the exact date of death then we should have modified
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          the contribution of an exact death to the likelihood. This new
       }          contribution is smaller and very dependent of the step unit
     }          stepm. It is no more the probability to die between last interview
     for(jk=-1; jk <=nlstate+ndeath; jk++)          and month of death but the probability to survive from last
       for(m=-1; m <=nlstate+ndeath; m++)          interview up to one month before death multiplied by the
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          probability to die within a month. Thanks to Chris
     if(i <= (int) agemax)          Jackson for correcting this bug.  Former versions increased
       fprintf(ficresp,"\n");          mortality artificially. The bad side is that we add another loop
     printf("\n");          which slows down the processing. The difference can be up to 10%
     }          lower mortality.
     }            */
  }            lli=log(out[s1][s2] - savm[s1][s2]);
   dateintmean=dateintsum/k2cpt;  
    
   fclose(ficresp);          } else if  (s2==-2) {
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            for (j=1,survp=0. ; j<=nlstate; j++) 
   free_vector(pp,1,nlstate);              survp += out[s1][j];
             lli= survp;
   /* End of Freq */          }
 }  
   
 /************ Prevalence ********************/          else{
 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)            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 {  /* Some frequencies */            /*  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 */
            } 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double ***freq; /* Frequencies */          /*if(lli ==000.0)*/
   double *pp;          /*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); */
   double pos, k2;          ipmx +=1;
           sw += weight[i];
   pp=vector(1,nlstate);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        } /* end of wave */
        } /* end of individual */
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    }  else if(mle==2){
   j1=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   j=cptcoveff;        for(mi=1; mi<= wav[i]-1; mi++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
  for(k1=1; k1<=j;k1++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i1=1; i1<=ncodemax[k1];i1++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       j1++;            }
            for(d=0; d<=dh[mi][i]; d++){
       for (i=-1; i<=nlstate+ndeath; i++)              newm=savm;
         for (jk=-1; jk<=nlstate+ndeath; jk++)              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for(m=agemin; m <= agemax+3; m++)            for (kk=1; kk<=cptcovage;kk++) {
             freq[i][jk][m]=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                  }
       for (i=1; i<=imx; i++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         bool=1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if  (cptcovn>0) {            savm=oldm;
           for (z1=1; z1<=cptcoveff; z1++)            oldm=newm;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          } /* end mult */
               bool=0;        
         }          s1=s[mw[mi][i]][i];
         if (bool==1) {          s2=s[mw[mi+1][i]][i];
           for(m=firstpass; m<=lastpass; m++){          bbh=(double)bh[mi][i]/(double)stepm; 
             k2=anint[m][i]+(mint[m][i]/12.);          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 ((k2>=dateprev1) && (k2<=dateprev2)) {          ipmx +=1;
               if(agev[m][i]==0) agev[m][i]=agemax+1;          sw += weight[i];
               if(agev[m][i]==1) agev[m][i]=agemax+2;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        } /* end of wave */
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */      } /* end of individual */
             }    }  else if(mle==3){  /* exponential inter-extrapolation */
           }      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(i=(int)agemin; i <= (int)agemax+3; i++){          for (ii=1;ii<=nlstate+ndeath;ii++)
           for(jk=1; jk <=nlstate ; jk++){            for (j=1;j<=nlstate+ndeath;j++){
             for(m=-1, 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(jk=1; jk <=nlstate ; jk++){          for(d=0; d<dh[mi][i]; d++){
             for(m=-1, pos=0; m <=0 ; m++)            newm=savm;
             pos += freq[jk][m][i];            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++){            }
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
              pp[jk] += freq[jk][m][i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
          }            savm=oldm;
                      oldm=newm;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          } /* end mult */
         
          for(jk=1; jk <=nlstate ; jk++){                    s1=s[mw[mi][i]][i];
            if( i <= (int) agemax){          s2=s[mw[mi+1][i]][i];
              if(pos>=1.e-5){          bbh=(double)bh[mi][i]/(double)stepm; 
                probs[i][jk][j1]= pp[jk]/pos;          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
              }          ipmx +=1;
            }          sw += weight[i];
          }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                  } /* end of wave */
         }      } /* end of individual */
     }    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   }      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++){
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          for (ii=1;ii<=nlstate+ndeath;ii++)
   free_vector(pp,1,nlstate);            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 }  /* End of Freq */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
 /************* Waves Concatenation ***************/          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 {            for (kk=1; kk<=cptcovage;kk++) {
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      Death is a valid wave (if date is known).            }
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      and mw[mi+1][i]. dh depends on stepm.                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      */            savm=oldm;
             oldm=newm;
   int i, mi, m;          } /* end mult */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        
      double sum=0., jmean=0.;*/          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   int j, k=0,jk, ju, jl;          if( s2 > nlstate){ 
   double sum=0.;            lli=log(out[s1][s2] - savm[s1][s2]);
   jmin=1e+5;          }else{
   jmax=-1;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   jmean=0.;          }
   for(i=1; i<=imx; i++){          ipmx +=1;
     mi=0;          sw += weight[i];
     m=firstpass;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     while(s[m][i] <= 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]); */
       if(s[m][i]>=1)        } /* end of wave */
         mw[++mi][i]=m;      } /* end of individual */
       if(m >=lastpass)    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
         break;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       else        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         m++;        for(mi=1; mi<= wav[i]-1; mi++){
     }/* end while */          for (ii=1;ii<=nlstate+ndeath;ii++)
     if (s[m][i] > nlstate){            for (j=1;j<=nlstate+ndeath;j++){
       mi++;     /* Death is another wave */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       /* if(mi==0)  never been interviewed correctly before death */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
          /* Only death is a correct wave */            }
       mw[mi][i]=m;          for(d=0; d<dh[mi][i]; d++){
     }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     wav[i]=mi;            for (kk=1; kk<=cptcovage;kk++) {
     if(mi==0)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            }
   }          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for(i=1; i<=imx; i++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(mi=1; mi<wav[i];mi++){            savm=oldm;
       if (stepm <=0)            oldm=newm;
         dh[mi][i]=1;          } /* end mult */
       else{        
         if (s[mw[mi+1][i]][i] > nlstate) {          s1=s[mw[mi][i]][i];
           if (agedc[i] < 2*AGESUP) {          s2=s[mw[mi+1][i]][i];
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           if(j==0) j=1;  /* Survives at least one month after exam */          ipmx +=1;
           k=k+1;          sw += weight[i];
           if (j >= jmax) jmax=j;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           if (j <= jmin) jmin=j;          /*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]);*/
           sum=sum+j;        } /* end of wave */
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      } /* end of individual */
           }    } /* End of if */
         }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         else{    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           k=k+1;    return -l;
           if (j >= jmax) jmax=j;  }
           else if (j <= jmin)jmin=j;  
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  /*************** log-likelihood *************/
           sum=sum+j;  double funcone( double *x)
         }  {
         jk= j/stepm;    /* Same as likeli but slower because of a lot of printf and if */
         jl= j -jk*stepm;    int i, ii, j, k, mi, d, kk;
         ju= j -(jk+1)*stepm;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         if(jl <= -ju)    double **out;
           dh[mi][i]=jk;    double lli; /* Individual log likelihood */
         else    double llt;
           dh[mi][i]=jk+1;    int s1, s2;
         if(dh[mi][i]==0)    double bbh, survp;
           dh[mi][i]=1; /* At least one step */    /*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++) 
   jmean=sum/k;      printf(" %d\n",s[4][i]);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    */
  }    cov[1]=1.;
 /*********** Tricode ****************************/  
 void tricode(int *Tvar, int **nbcode, int imx)    for(k=1; k<=nlstate; k++) ll[k]=0.;
 {  
   int Ndum[20],ij=1, k, j, i;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int cptcode=0;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   cptcoveff=0;      for(mi=1; mi<= wav[i]-1; mi++){
          for (ii=1;ii<=nlstate+ndeath;ii++)
   for (k=0; k<19; k++) Ndum[k]=0;          for (j=1;j<=nlstate+ndeath;j++){
   for (k=1; k<=7; k++) ncodemax[k]=0;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          }
     for (i=1; i<=imx; i++) {        for(d=0; d<dh[mi][i]; d++){
       ij=(int)(covar[Tvar[j]][i]);          newm=savm;
       Ndum[ij]++;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          for (kk=1; kk<=cptcovage;kk++) {
       if (ij > cptcode) cptcode=ij;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     }          }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for (i=0; i<=cptcode; i++) {                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       if(Ndum[i]!=0) ncodemax[j]++;          savm=oldm;
     }          oldm=newm;
     ij=1;        } /* end mult */
         
         s1=s[mw[mi][i]][i];
     for (i=1; i<=ncodemax[j]; i++) {        s2=s[mw[mi+1][i]][i];
       for (k=0; k<=19; k++) {        bbh=(double)bh[mi][i]/(double)stepm; 
         if (Ndum[k] != 0) {        /* bias is positive if real duration
           nbcode[Tvar[j]][ij]=k;         * is higher than the multiple of stepm and negative otherwise.
           ij++;         */
         }        if( s2 > nlstate && (mle <5) ){  /* Jackson */
         if (ij > ncodemax[j]) break;          lli=log(out[s1][s2] - savm[s1][s2]);
       }          } else if (mle==1){
     }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   }          } 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 */
  for (k=0; k<19; k++) Ndum[k]=0;        } else if(mle==3){  /* exponential inter-extrapolation */
           lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
  for (i=1; i<=ncovmodel-2; i++) {        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       ij=Tvar[i];          lli=log(out[s1][s2]); /* Original formula */
       Ndum[ij]++;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
     }          lli=log(out[s1][s2]); /* Original formula */
         } /* End of if */
  ij=1;        ipmx +=1;
  for (i=1; i<=10; i++) {        sw += weight[i];
    if((Ndum[i]!=0) && (i<=ncov)){        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      Tvaraff[ij]=i;  /*       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]); */
      ij++;        if(globpr){
    }          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
  }   %10.6f %10.6f %10.6f ", \
                    num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     cptcoveff=ij-1;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
 }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             llt +=ll[k]*gipmx/gsw;
 /*********** Health Expectancies ****************/            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          fprintf(ficresilk," %10.6f\n", -llt);
 {        }
   /* Health expectancies */      } /* end of wave */
   int i, j, nhstepm, hstepm, h, nstepm, k;    } /* end of individual */
   double age, agelim,hf;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   double ***p3mat;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
      l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   fprintf(ficreseij,"# Health expectancies\n");    if(globpr==0){ /* First time we count the contributions and weights */
   fprintf(ficreseij,"# Age");      gipmx=ipmx;
   for(i=1; i<=nlstate;i++)      gsw=sw;
     for(j=1; j<=nlstate;j++)    }
       fprintf(ficreseij," %1d-%1d",i,j);    return -l;
   fprintf(ficreseij,"\n");  }
   
   k=1;             /* For example stepm=6 months */  
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */  /*************** function likelione ***********/
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.  {
      nhstepm is the number of hstepm from age to agelim    /* This routine should help understanding what is done with 
      nstepm is the number of stepm from age to agelin.       the selection of individuals/waves and
      Look at hpijx to understand the reason of that which relies in memory size       to check the exact contribution to the likelihood.
      and note for a fixed period like k years */       Plotting could be done.
   /* 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    int k;
      means that if the survival funtion is printed only each two years of age and if  
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    if(*globpri !=0){ /* Just counts and sums, no printings */
      results. So we changed our mind and took the option of the best precision.      strcpy(fileresilk,"ilk"); 
   */      strcat(fileresilk,fileres);
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", fileresilk);
   agelim=AGESUP;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      }
     /* nhstepm age range expressed in number of stepm */      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");
     nstepm=(int) rint((agelim-age)*YEARM/stepm);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     if (stepm >= YEARM) hstepm=1;      for(k=1; k<=nlstate; k++) 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      *fretone=(*funcone)(p);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    if(*globpri !=0){
     for(i=1; i<=nlstate;i++)      fclose(ficresilk);
       for(j=1; j<=nlstate;j++)      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){      fflush(fichtm); 
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    } 
           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/    return;
         }  }
     fprintf(ficreseij,"%3.0f",age );  
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){  /*********** Maximum Likelihood Estimation ***************/
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);  
       }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     fprintf(ficreseij,"\n");  {
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int i,j, iter;
   }    double **xi;
 }    double fret;
     double fretone; /* Only one call to likelihood */
 /************ Variance ******************/    /*  char filerespow[FILENAMELENGTH];*/
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    xi=matrix(1,npar,1,npar);
 {    for (i=1;i<=npar;i++)
   /* Variance of health expectancies */      for (j=1;j<=npar;j++)
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        xi[i][j]=(i==j ? 1.0 : 0.0);
   double **newm;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   double **dnewm,**doldm;    strcpy(filerespow,"pow"); 
   int i, j, nhstepm, hstepm, h;    strcat(filerespow,fileres);
   int k, cptcode;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   double *xp;      printf("Problem with resultfile: %s\n", filerespow);
   double **gp, **gm;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   double ***gradg, ***trgradg;    }
   double ***p3mat;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   double age,agelim;    for (i=1;i<=nlstate;i++)
   int theta;      for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
    fprintf(ficresvij,"# Covariances of life expectancies\n");    fprintf(ficrespow,"\n");
   fprintf(ficresvij,"# Age");  
   for(i=1; i<=nlstate;i++)    powell(p,xi,npar,ftol,&iter,&fret,func);
     for(j=1; j<=nlstate;j++)  
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    fclose(ficrespow);
   fprintf(ficresvij,"\n");    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   xp=vector(1,npar);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);  }
    
   hstepm=1*YEARM; /* Every year of age */  /**** Computes Hessian and covariance matrix ***/
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   agelim = AGESUP;  {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double  **a,**y,*x,pd;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double **hess;
     if (stepm >= YEARM) hstepm=1;    int i, j,jk;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    int *indx;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     gp=matrix(0,nhstepm,1,nlstate);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     gm=matrix(0,nhstepm,1,nlstate);    void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
     for(theta=1; theta <=npar; theta++){    double gompertz(double p[]);
       for(i=1; i<=npar; i++){ /* Computes gradient */    hess=matrix(1,npar,1,npar);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }    printf("\nCalculation of the hessian matrix. Wait...\n");
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for (i=1;i<=npar;i++){
       printf("%d",i);fflush(stdout);
       if (popbased==1) {      fprintf(ficlog,"%d",i);fflush(ficlog);
         for(i=1; i<=nlstate;i++)     
           prlim[i][i]=probs[(int)age][i][ij];       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       }      
        /*  printf(" %f ",p[i]);
       for(j=1; j<= nlstate; j++){          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
         for(h=0; h<=nhstepm; h++){    }
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    for (i=1;i<=npar;i++) {
         }      for (j=1;j<=npar;j++)  {
       }        if (j>i) { 
              printf(".%d%d",i,j);fflush(stdout);
       for(i=1; i<=npar; i++) /* Computes gradient */          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          hess[i][j]=hessij(p,delti,i,j,func,npar);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          hess[j][i]=hess[i][j];    
            /*printf(" %lf ",hess[i][j]);*/
       if (popbased==1) {        }
         for(i=1; i<=nlstate;i++)      }
           prlim[i][i]=probs[(int)age][i][ij];    }
       }    printf("\n");
     fprintf(ficlog,"\n");
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    
         }    a=matrix(1,npar,1,npar);
       }    y=matrix(1,npar,1,npar);
     x=vector(1,npar);
       for(j=1; j<= nlstate; j++)    indx=ivector(1,npar);
         for(h=0; h<=nhstepm; h++){    for (i=1;i<=npar;i++)
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         }    ludcmp(a,npar,indx,&pd);
     } /* End theta */  
     for (j=1;j<=npar;j++) {
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
     for(h=0; h<=nhstepm; h++)      lubksb(a,npar,indx,x);
       for(j=1; j<=nlstate;j++)      for (i=1;i<=npar;i++){ 
         for(theta=1; theta <=npar; theta++)        matcov[i][j]=x[i];
           trgradg[h][j][theta]=gradg[h][theta][j];      }
     }
     for(i=1;i<=nlstate;i++)  
       for(j=1;j<=nlstate;j++)    printf("\n#Hessian matrix#\n");
         vareij[i][j][(int)age] =0.;    fprintf(ficlog,"\n#Hessian matrix#\n");
     for(h=0;h<=nhstepm;h++){    for (i=1;i<=npar;i++) { 
       for(k=0;k<=nhstepm;k++){      for (j=1;j<=npar;j++) { 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        printf("%.3e ",hess[i][j]);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        fprintf(ficlog,"%.3e ",hess[i][j]);
         for(i=1;i<=nlstate;i++)      }
           for(j=1;j<=nlstate;j++)      printf("\n");
             vareij[i][j][(int)age] += doldm[i][j];      fprintf(ficlog,"\n");
       }    }
     }  
     h=1;    /* Recompute Inverse */
     if (stepm >= YEARM) h=stepm/YEARM;    for (i=1;i<=npar;i++)
     fprintf(ficresvij,"%.0f ",age );      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     for(i=1; i<=nlstate;i++)    ludcmp(a,npar,indx,&pd);
       for(j=1; j<=nlstate;j++){  
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    /*  printf("\n#Hessian matrix recomputed#\n");
       }  
     fprintf(ficresvij,"\n");    for (j=1;j<=npar;j++) {
     free_matrix(gp,0,nhstepm,1,nlstate);      for (i=1;i<=npar;i++) x[i]=0;
     free_matrix(gm,0,nhstepm,1,nlstate);      x[j]=1;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      lubksb(a,npar,indx,x);
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      for (i=1;i<=npar;i++){ 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        y[i][j]=x[i];
   } /* End age */        printf("%.3e ",y[i][j]);
          fprintf(ficlog,"%.3e ",y[i][j]);
   free_vector(xp,1,npar);      }
   free_matrix(doldm,1,nlstate,1,npar);      printf("\n");
   free_matrix(dnewm,1,nlstate,1,nlstate);      fprintf(ficlog,"\n");
     }
 }    */
   
 /************ Variance of prevlim ******************/    free_matrix(a,1,npar,1,npar);
 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)    free_matrix(y,1,npar,1,npar);
 {    free_vector(x,1,npar);
   /* Variance of prevalence limit */    free_ivector(indx,1,npar);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    free_matrix(hess,1,npar,1,npar);
   double **newm;  
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm;  }
   int k, cptcode;  
   double *xp;  /*************** hessian matrix ****************/
   double *gp, *gm;  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   double **gradg, **trgradg;  {
   double age,agelim;    int i;
   int theta;    int l=1, lmax=20;
        double k1,k2;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    double p2[NPARMAX+1];
   fprintf(ficresvpl,"# Age");    double res;
   for(i=1; i<=nlstate;i++)    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       fprintf(ficresvpl," %1d-%1d",i,i);    double fx;
   fprintf(ficresvpl,"\n");    int k=0,kmax=10;
     double l1;
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);    fx=func(x);
   doldm=matrix(1,nlstate,1,nlstate);    for (i=1;i<=npar;i++) p2[i]=x[i];
      for(l=0 ; l <=lmax; l++){
   hstepm=1*YEARM; /* Every year of age */      l1=pow(10,l);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      delts=delt;
   agelim = AGESUP;      for(k=1 ; k <kmax; k=k+1){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        delt = delta*(l1*k);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        p2[theta]=x[theta] +delt;
     if (stepm >= YEARM) hstepm=1;        k1=func(p2)-fx;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        p2[theta]=x[theta]-delt;
     gradg=matrix(1,npar,1,nlstate);        k2=func(p2)-fx;
     gp=vector(1,nlstate);        /*res= (k1-2.0*fx+k2)/delt/delt; */
     gm=vector(1,nlstate);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
     for(theta=1; theta <=npar; theta++){  #ifdef DEBUG
       for(i=1; i<=npar; i++){ /* Computes gradient */        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);
       }  #endif
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       for(i=1;i<=nlstate;i++)        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         gp[i] = prlim[i][i];          k=kmax;
            }
       for(i=1; i<=npar; i++) /* Computes gradient */        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          k=kmax; l=lmax*10.;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        }
       for(i=1;i<=nlstate;i++)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         gm[i] = prlim[i][i];          delts=delt;
         }
       for(i=1;i<=nlstate;i++)      }
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    }
     } /* End theta */    delti[theta]=delts;
     return res; 
     trgradg =matrix(1,nlstate,1,npar);    
   }
     for(j=1; j<=nlstate;j++)  
       for(theta=1; theta <=npar; theta++)  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
         trgradg[j][theta]=gradg[theta][j];  {
     int i;
     for(i=1;i<=nlstate;i++)    int l=1, l1, lmax=20;
       varpl[i][(int)age] =0.;    double k1,k2,k3,k4,res,fx;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    double p2[NPARMAX+1];
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    int k;
     for(i=1;i<=nlstate;i++)  
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    fx=func(x);
     for (k=1; k<=2; k++) {
     fprintf(ficresvpl,"%.0f ",age );      for (i=1;i<=npar;i++) p2[i]=x[i];
     for(i=1; i<=nlstate;i++)      p2[thetai]=x[thetai]+delti[thetai]/k;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     fprintf(ficresvpl,"\n");      k1=func(p2)-fx;
     free_vector(gp,1,nlstate);    
     free_vector(gm,1,nlstate);      p2[thetai]=x[thetai]+delti[thetai]/k;
     free_matrix(gradg,1,npar,1,nlstate);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     free_matrix(trgradg,1,nlstate,1,npar);      k2=func(p2)-fx;
   } /* End age */    
       p2[thetai]=x[thetai]-delti[thetai]/k;
   free_vector(xp,1,npar);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   free_matrix(doldm,1,nlstate,1,npar);      k3=func(p2)-fx;
   free_matrix(dnewm,1,nlstate,1,nlstate);    
       p2[thetai]=x[thetai]-delti[thetai]/k;
 }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k4=func(p2)-fx;
 /************ Variance of one-step probabilities  ******************/      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)  #ifdef DEBUG
 {      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   int i, j;      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   int k=0, cptcode;  #endif
   double **dnewm,**doldm;    }
   double *xp;    return res;
   double *gp, *gm;  }
   double **gradg, **trgradg;  
   double age,agelim, cov[NCOVMAX];  /************** Inverse of matrix **************/
   int theta;  void ludcmp(double **a, int n, int *indx, double *d) 
   char fileresprob[FILENAMELENGTH];  { 
     int i,imax,j,k; 
   strcpy(fileresprob,"prob");    double big,dum,sum,temp; 
   strcat(fileresprob,fileres);    double *vv; 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {   
     printf("Problem with resultfile: %s\n", fileresprob);    vv=vector(1,n); 
   }    *d=1.0; 
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    for (i=1;i<=n;i++) { 
        big=0.0; 
       for (j=1;j<=n;j++) 
   xp=vector(1,npar);        if ((temp=fabs(a[i][j])) > big) big=temp; 
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      vv[i]=1.0/big; 
      } 
   cov[1]=1;    for (j=1;j<=n;j++) { 
   for (age=bage; age<=fage; age ++){      for (i=1;i<j;i++) { 
     cov[2]=age;        sum=a[i][j]; 
     gradg=matrix(1,npar,1,9);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     trgradg=matrix(1,9,1,npar);        a[i][j]=sum; 
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      } 
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      big=0.0; 
          for (i=j;i<=n;i++) { 
     for(theta=1; theta <=npar; theta++){        sum=a[i][j]; 
       for(i=1; i<=npar; i++)        for (k=1;k<j;k++) 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          sum -= a[i][k]*a[k][j]; 
              a[i][j]=sum; 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
              big=dum; 
       k=0;          imax=i; 
       for(i=1; i<= (nlstate+ndeath); i++){        } 
         for(j=1; j<=(nlstate+ndeath);j++){      } 
            k=k+1;      if (j != imax) { 
           gp[k]=pmmij[i][j];        for (k=1;k<=n;k++) { 
         }          dum=a[imax][k]; 
       }          a[imax][k]=a[j][k]; 
           a[j][k]=dum; 
       for(i=1; i<=npar; i++)        } 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        *d = -(*d); 
            vv[imax]=vv[j]; 
       } 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      indx[j]=imax; 
       k=0;      if (a[j][j] == 0.0) a[j][j]=TINY; 
       for(i=1; i<=(nlstate+ndeath); i++){      if (j != n) { 
         for(j=1; j<=(nlstate+ndeath);j++){        dum=1.0/(a[j][j]); 
           k=k+1;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
           gm[k]=pmmij[i][j];      } 
         }    } 
       }    free_vector(vv,1,n);  /* Doesn't work */
        ;
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  } 
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    
     }  void lubksb(double **a, int n, int *indx, double b[]) 
   { 
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    int i,ii=0,ip,j; 
       for(theta=1; theta <=npar; theta++)    double sum; 
       trgradg[j][theta]=gradg[theta][j];   
      for (i=1;i<=n;i++) { 
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      ip=indx[i]; 
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);      sum=b[ip]; 
       b[ip]=b[i]; 
      pmij(pmmij,cov,ncovmodel,x,nlstate);      if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
      k=0;      else if (sum) ii=i; 
      for(i=1; i<=(nlstate+ndeath); i++){      b[i]=sum; 
        for(j=1; j<=(nlstate+ndeath);j++){    } 
          k=k+1;    for (i=n;i>=1;i--) { 
          gm[k]=pmmij[i][j];      sum=b[i]; 
         }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
      }      b[i]=sum/a[i][i]; 
          } 
      /*printf("\n%d ",(int)age);  } 
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  
          /************ Frequencies ********************/
   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)
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  {  /* Some frequencies */
      }*/    
     int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   fprintf(ficresprob,"\n%d ",(int)age);    int first;
     double ***freq; /* Frequencies */
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    double *pp, **prop;
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    FILE *ficresp;
   }    char fileresp[FILENAMELENGTH];
     
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    pp=vector(1,nlstate);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    prop=matrix(1,nlstate,iagemin,iagemax+3);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    strcpy(fileresp,"p");
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    strcat(fileresp,fileres);
 }    if((ficresp=fopen(fileresp,"w"))==NULL) {
  free_vector(xp,1,npar);      printf("Problem with prevalence resultfile: %s\n", fileresp);
 fclose(ficresprob);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       exit(0);
 }    }
     freq= ma3x(-2,nlstate+ndeath,-2,nlstate+ndeath,iagemin,iagemax+3);
 /******************* Printing html file ***********/    j1=0;
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){    
   int jj1, k1, i1, cpt;    j=cptcoveff;
   FILE *fichtm;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   /*char optionfilehtm[FILENAMELENGTH];*/  
     first=1;
   strcpy(optionfilehtm,optionfile);  
   strcat(optionfilehtm,".htm");    for(k1=1; k1<=j;k1++){
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      for(i1=1; i1<=ncodemax[k1];i1++){
     printf("Problem with %s \n",optionfilehtm), exit(0);        j1++;
   }        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           scanf("%d", i);*/
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71c </font> <hr size=\"2\" color=\"#EC5E5E\">        for (i=-2; i<=nlstate+ndeath; i++)  
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>          for (jk=-2; jk<=nlstate+ndeath; jk++)  
             for(m=iagemin; m <= iagemax+3; m++)
 Total number of observations=%d <br>              freq[i][jk][m]=0;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>  
 <hr  size=\"2\" color=\"#EC5E5E\">      for (i=1; i<=nlstate; i++)  
 <li>Outputs files<br><br>\n        for(m=iagemin; m <= iagemax+3; m++)
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          prop[i][m]=0;
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>        
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>        dateintsum=0;
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>        k2cpt=0;
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>        for (i=1; i<=imx; i++) {
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>          bool=1;
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>          if  (cptcovn>0) {
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>            for (z1=1; z1<=cptcoveff; z1++) 
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>                bool=0;
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>          }
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);          if (bool==1){
              for(m=firstpass; m<=lastpass; m++){
 fprintf(fichtm," <li>Graphs</li><p>");              k2=anint[m][i]+(mint[m][i]/12.);
               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
  m=cptcoveff;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
  jj1=0;                if (m<lastpass) {
  for(k1=1; k1<=m;k1++){                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
    for(i1=1; i1<=ncodemax[k1];i1++){                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
        jj1++;                }
        if (cptcovn > 0) {                
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
          for (cpt=1; cpt<=cptcoveff;cpt++)                  dateintsum=dateintsum+k2;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);                  k2cpt++;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");                }
        }                /*}*/
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>            }
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              }
        for(cpt=1; cpt<nlstate;cpt++){        }
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>         
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
        }  
     for(cpt=1; cpt<=nlstate;cpt++) {        if  (cptcovn>0) {
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          fprintf(ficresp, "\n#********** Variable "); 
 interval) in state (%d): v%s%d%d.gif <br>          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            fprintf(ficresp, "**********\n#");
      }        }
      for(cpt=1; cpt<=nlstate;cpt++) {        for(i=1; i<=nlstate;i++) 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        fprintf(ficresp, "\n");
      }        
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        for(i=iagemin; i <= iagemax+3; i++){
 health expectancies in states (1) and (2): e%s%d.gif<br>          if(i==iagemax+3){
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            fprintf(ficlog,"Total");
 fprintf(fichtm,"\n</body>");          }else{
    }            if(first==1){
    }              first=0;
 fclose(fichtm);              printf("See log file for details...\n");
 }            }
             fprintf(ficlog,"Age %d", i);
 /******************* Gnuplot file **************/          }
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;              pp[jk] += freq[jk][m][i]; 
           }
   strcpy(optionfilegnuplot,optionfilefiname);          for(jk=1; jk <=nlstate ; jk++){
   strcat(optionfilegnuplot,".plt");            for(m=-1, pos=0; m <=0 ; m++)
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {              pos += freq[jk][m][i];
     printf("Problem with file %s",optionfilegnuplot);            if(pp[jk]>=1.e-10){
   }              if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 #ifdef windows              }
     fprintf(ficgp,"cd \"%s\" \n",pathc);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 #endif            }else{
 m=pow(2,cptcoveff);              if(first==1)
                  printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
  /* 1eme*/              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   for (cpt=1; cpt<= nlstate ; cpt ++) {            }
    for (k1=1; k1<= m ; k1 ++) {          }
   
 #ifdef windows          for(jk=1; jk <=nlstate ; jk++){
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 #endif              pp[jk] += freq[jk][m][i];
 #ifdef unix          }       
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
 #endif            pos += pp[jk];
             posprop += prop[jk][i];
 for (i=1; i<= nlstate ; i ++) {          }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for(jk=1; jk <=nlstate ; jk++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");            if(pos>=1.e-5){
 }              if(first==1)
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for (i=1; i<= nlstate ; i ++) {              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            }else{
   else fprintf(ficgp," \%%*lf (\%%*lf)");              if(first==1)
 }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
      for (i=1; i<= nlstate ; i ++) {            }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            if( i <= iagemax){
   else fprintf(ficgp," \%%*lf (\%%*lf)");              if(pos>=1.e-5){
 }                  fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));                /*probs[i][jk][j1]= pp[jk]/pos;*/
 #ifdef unix                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
 fprintf(ficgp,"\nset ter gif small size 400,300");              }
 #endif              else
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
    }            }
   }          }
   /*2 eme*/          
           for(jk=-1; jk <=nlstate+ndeath; jk++)
   for (k1=1; k1<= m ; k1 ++) {            for(m=-1; m <=nlstate+ndeath; m++)
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);              if(freq[jk][m][i] !=0 ) {
                  if(first==1)
     for (i=1; i<= nlstate+1 ; i ++) {                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
       k=2*i;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);              }
       for (j=1; j<= nlstate+1 ; j ++) {          if(i <= iagemax)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            fprintf(ficresp,"\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");          if(first==1)
 }              printf("Others in log...\n");
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          fprintf(ficlog,"\n");
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        }
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      }
       for (j=1; j<= nlstate+1 ; j ++) {    }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    dateintmean=dateintsum/k2cpt; 
         else fprintf(ficgp," \%%*lf (\%%*lf)");   
 }      fclose(ficresp);
       fprintf(ficgp,"\" t\"\" w l 0,");    free_ma3x(freq,-2,nlstate+ndeath,-2,nlstate+ndeath, iagemin, iagemax+3);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    free_vector(pp,1,nlstate);
       for (j=1; j<= nlstate+1 ; j ++) {    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /* End of Freq */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  }
 }    
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  /************ Prevalence ********************/
       else fprintf(ficgp,"\" t\"\" w l 0,");  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)
     }  {  
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   }       in each health status at the date of interview (if between dateprev1 and dateprev2).
         We still use firstpass and lastpass as another selection.
   /*3eme*/    */
    
   for (k1=1; k1<= m ; k1 ++) {    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     for (cpt=1; cpt<= nlstate ; cpt ++) {    double ***freq; /* Frequencies */
       k=2+nlstate*(cpt-1);    double *pp, **prop;
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);    double pos,posprop; 
       for (i=1; i< nlstate ; i ++) {    double  y2; /* in fractional years */
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);    int iagemin, iagemax;
       }  
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    iagemin= (int) agemin;
     }    iagemax= (int) agemax;
     }    /*pp=vector(1,nlstate);*/
      prop=matrix(1,nlstate,iagemin,iagemax+3); 
   /* CV preval stat */    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     for (k1=1; k1<= m ; k1 ++) {    j1=0;
     for (cpt=1; cpt<nlstate ; cpt ++) {    
       k=3;    j=cptcoveff;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
       for (i=1; i< nlstate ; i ++)    for(k1=1; k1<=j;k1++){
         fprintf(ficgp,"+$%d",k+i+1);      for(i1=1; i1<=ncodemax[k1];i1++){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        j1++;
              
       l=3+(nlstate+ndeath)*cpt;        for (i=1; i<=nlstate; i++)  
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          for(m=iagemin; m <= iagemax+3; m++)
       for (i=1; i< nlstate ; i ++) {            prop[i][m]=0.0;
         l=3+(nlstate+ndeath)*cpt;       
         fprintf(ficgp,"+$%d",l+i+1);        for (i=1; i<=imx; i++) { /* Each individual */
       }          bool=1;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            if  (cptcovn>0) {
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            for (z1=1; z1<=cptcoveff; z1++) 
     }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   }                  bool=0;
            } 
   /* proba elementaires */          if (bool==1) { 
    for(i=1,jk=1; i <=nlstate; i++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     for(k=1; k <=(nlstate+ndeath); k++){              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       if (k != i) {              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         for(j=1; j <=ncovmodel; j++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                        if(agev[m][i]==1) agev[m][i]=iagemax+2;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);                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); 
           jk++;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
           fprintf(ficgp,"\n");                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
         }                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       }                  prop[s[m][i]][iagemax+3] += weight[i]; 
     }                } 
     }              }
             } /* end selection of waves */
     for(jk=1; jk <=m; jk++) {          }
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);        }
    i=1;        for(i=iagemin; i <= iagemax+3; i++){  
    for(k2=1; k2<=nlstate; k2++) {          
      k3=i;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
      for(k=1; k<=(nlstate+ndeath); k++) {            posprop += prop[jk][i]; 
        if (k != k2){          } 
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  
 ij=1;          for(jk=1; jk <=nlstate ; jk++){     
         for(j=3; j <=ncovmodel; j++) {            if( i <=  iagemax){ 
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              if(posprop>=1.e-5){ 
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                probs[i][jk][j1]= prop[jk][i]/posprop;
             ij++;              } 
           }            } 
           else          }/* end jk */ 
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        }/* end i */ 
         }      } /* end i1 */
           fprintf(ficgp,")/(1");    } /* end k1 */
            
         for(k1=1; k1 <=nlstate; k1++){      /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    /*free_vector(pp,1,nlstate);*/
 ij=1;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
           for(j=3; j <=ncovmodel; j++){  }  /* End of prevalence */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  /************* Waves Concatenation ***************/
             ij++;  
           }  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)
           else  {
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
           }       Death is a valid wave (if date is known).
           fprintf(ficgp,")");       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]
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);       and mw[mi+1][i]. dh depends on stepm.
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");       */
         i=i+ncovmodel;  
        }    int i, mi, m;
      }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
    }       double sum=0., jmean=0.;*/
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    int first;
    }    int j, k=0,jk, ju, jl;
        double sum=0.;
   fclose(ficgp);    first=0;
 }  /* end gnuplot */    jmin=1e+5;
     jmax=-1;
     jmean=0.;
 /*************** Moving average **************/    for(i=1; i<=imx; i++){
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){      mi=0;
       m=firstpass;
   int i, cpt, cptcod;      while(s[m][i] <= nlstate){
     for (agedeb=agemin; agedeb<=fage; agedeb++)        if(s[m][i]>=1 || s[m][i]==-2)
       for (i=1; i<=nlstate;i++)          mw[++mi][i]=m;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        if(m >=lastpass)
           mobaverage[(int)agedeb][i][cptcod]=0.;          break;
            else
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){          m++;
       for (i=1; i<=nlstate;i++){      }/* end while */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      if (s[m][i] > nlstate){
           for (cpt=0;cpt<=4;cpt++){        mi++;     /* Death is another wave */
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        /* if(mi==0)  never been interviewed correctly before death */
           }           /* Only death is a correct wave */
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        mw[mi][i]=m;
         }      }
       }  
     }      wav[i]=mi;
          if(mi==0){
 }        nbwarn++;
         if(first==0){
           printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
 /************** Forecasting ******************/          first=1;
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){        }
          if(first==1){
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
   int *popage;        }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      } /* end mi==0 */
   double *popeffectif,*popcount;    } /* End individuals */
   double ***p3mat;  
   char fileresf[FILENAMELENGTH];    for(i=1; i<=imx; i++){
       for(mi=1; mi<wav[i];mi++){
  agelim=AGESUP;        if (stepm <=0)
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          dh[mi][i]=1;
         else{
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
              if (agedc[i] < 2*AGESUP) {
                j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   strcpy(fileresf,"f");              if(j==0) j=1;  /* Survives at least one month after exam */
   strcat(fileresf,fileres);              else if(j<0){
   if((ficresf=fopen(fileresf,"w"))==NULL) {                nberr++;
     printf("Problem with forecast resultfile: %s\n", fileresf);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   }                j=1; /* Temporary Dangerous patch */
   printf("Computing forecasting: result on file '%s' \n", fileresf);                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);
                 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]);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;                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);
               }
   if (mobilav==1) {              k=k+1;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              if (j >= jmax) jmax=j;
     movingaverage(agedeb, fage, agemin, mobaverage);              if (j <= jmin) jmin=j;
   }              sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   stepsize=(int) (stepm+YEARM-1)/YEARM;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   if (stepm<=12) stepsize=1;            }
            }
   agelim=AGESUP;          else{
              j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   hstepm=1;  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
   hstepm=hstepm/stepm;  
   yp1=modf(dateintmean,&yp);            k=k+1;
   anprojmean=yp;            if (j >= jmax) jmax=j;
   yp2=modf((yp1*12),&yp);            else if (j <= jmin)jmin=j;
   mprojmean=yp;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   yp1=modf((yp2*30.5),&yp);            /*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]);*/
   jprojmean=yp;            if(j<0){
   if(jprojmean==0) jprojmean=1;              nberr++;
   if(mprojmean==0) jprojmean=1;              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]);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);            }
              sum=sum+j;
   for(cptcov=1;cptcov<=i2;cptcov++){          }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          jk= j/stepm;
       k=k+1;          jl= j -jk*stepm;
       fprintf(ficresf,"\n#******");          ju= j -(jk+1)*stepm;
       for(j=1;j<=cptcoveff;j++) {          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            if(jl==0){
       }              dh[mi][i]=jk;
       fprintf(ficresf,"******\n");              bh[mi][i]=0;
       fprintf(ficresf,"# StartingAge FinalAge");            }else{ /* We want a negative bias in order to only have interpolation ie
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);                    * at the price of an extra matrix product in likelihood */
                    dh[mi][i]=jk+1;
                    bh[mi][i]=ju;
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {            }
         fprintf(ficresf,"\n");          }else{
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);              if(jl <= -ju){
               dh[mi][i]=jk;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){              bh[mi][i]=jl;       /* bias is positive if real duration
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                                   * is higher than the multiple of stepm and negative otherwise.
           nhstepm = nhstepm/hstepm;                                   */
                      }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            else{
           oldm=oldms;savm=savms;              dh[mi][i]=jk+1;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                bh[mi][i]=ju;
                    }
           for (h=0; h<=nhstepm; h++){            if(dh[mi][i]==0){
             if (h==(int) (calagedate+YEARM*cpt)) {              dh[mi][i]=1; /* At least one step */
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);              bh[mi][i]=ju; /* At least one step */
             }              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
             for(j=1; j<=nlstate+ndeath;j++) {            }
               kk1=0.;kk2=0;          } /* end if mle */
               for(i=1; i<=nlstate;i++) {                      }
                 if (mobilav==1)      } /* end wave */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    }
                 else {    jmean=sum/k;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
                 }    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
                   }
               }  
               if (h==(int)(calagedate+12*cpt)){  /*********** Tricode ****************************/
                 fprintf(ficresf," %.3f", kk1);  void tricode(int *Tvar, int **nbcode, int imx)
                          {
               }    
             }    int Ndum[20],ij=1, k, j, i, maxncov=19;
           }    int cptcode=0;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    cptcoveff=0; 
         }   
       }    for (k=0; k<maxncov; k++) Ndum[k]=0;
     }    for (k=1; k<=7; k++) ncodemax[k]=0;
   }  
            for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
   fclose(ficresf);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
 }        Ndum[ij]++; /*store the modality */
 /************** Forecasting ******************/        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                                           Tvar[j]. If V=sex and male is 0 and 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                                         female is 1, then  cptcode=1.*/
   int *popage;      }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  
   double *popeffectif,*popcount;      for (i=0; i<=cptcode; i++) {
   double ***p3mat,***tabpop,***tabpopprev;        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 */
   char filerespop[FILENAMELENGTH];      }
   
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      ij=1; 
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (i=1; i<=ncodemax[j]; i++) {
   agelim=AGESUP;        for (k=0; k<= maxncov; k++) {
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          if (Ndum[k] != 0) {
              nbcode[Tvar[j]][ij]=k; 
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            /* 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; */
              
              ij++;
   strcpy(filerespop,"pop");          }
   strcat(filerespop,fileres);          if (ij > ncodemax[j]) break; 
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        }  
     printf("Problem with forecast resultfile: %s\n", filerespop);      } 
   }    }  
   printf("Computing forecasting: result on file '%s' \n", filerespop);  
    for (k=0; k< maxncov; k++) Ndum[k]=0;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
    for (i=1; i<=ncovmodel-2; i++) { 
   if (mobilav==1) {     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     ij=Tvar[i];
     movingaverage(agedeb, fage, agemin, mobaverage);     Ndum[ij]++;
   }   }
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;   ij=1;
   if (stepm<=12) stepsize=1;   for (i=1; i<= maxncov; i++) {
       if((Ndum[i]!=0) && (i<=ncovcol)){
   agelim=AGESUP;       Tvaraff[ij]=i; /*For printing */
         ij++;
   hstepm=1;     }
   hstepm=hstepm/stepm;   }
     
   if (popforecast==1) {   cptcoveff=ij-1; /*Number of simple covariates*/
     if((ficpop=fopen(popfile,"r"))==NULL) {  }
       printf("Problem with population file : %s\n",popfile);exit(0);  
     }  /*********** Health Expectancies ****************/
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);  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 )
     popcount=vector(0,AGESUP);  
      {
     i=1;      /* Health expectancies */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
        double age, agelim, hf;
     imx=i;    double ***p3mat,***varhe;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    double **dnewm,**doldm;
   }    double *xp;
     double **gp, **gm;
   for(cptcov=1;cptcov<=i2;cptcov++){    double ***gradg, ***trgradg;
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    int theta;
       k=k+1;  
       fprintf(ficrespop,"\n#******");    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       for(j=1;j<=cptcoveff;j++) {    xp=vector(1,npar);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    dnewm=matrix(1,nlstate*nlstate,1,npar);
       }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       fprintf(ficrespop,"******\n");    
       fprintf(ficrespop,"# Age");    fprintf(ficreseij,"# Health expectancies\n");
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    fprintf(ficreseij,"# Age");
       if (popforecast==1)  fprintf(ficrespop," [Population]");    for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate;j++)
       for (cpt=0; cpt<=0;cpt++) {        fprintf(ficreseij," %1d-%1d (SE)",i,j);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      fprintf(ficreseij,"\n");
          
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){    if(estepm < stepm){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      printf ("Problem %d lower than %d\n",estepm, stepm);
           nhstepm = nhstepm/hstepm;    }
              else  hstepm=estepm;   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* We compute the life expectancy from trapezoids spaced every estepm months
           oldm=oldms;savm=savms;     * This is mainly to measure the difference between two models: for example
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       * 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 (h=0; h<=nhstepm; h++){     * progression in between and thus overestimating or underestimating according
             if (h==(int) (calagedate+YEARM*cpt)) {     * to the curvature of the survival function. If, for the same date, we 
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
             }     * to compare the new estimate of Life expectancy with the same linear 
             for(j=1; j<=nlstate+ndeath;j++) {     * hypothesis. A more precise result, taking into account a more precise
               kk1=0.;kk2=0;     * curvature will be obtained if estepm is as small as stepm. */
               for(i=1; i<=nlstate;i++) {                
                 if (mobilav==1)    /* For example we decided to compute the life expectancy with the smallest unit */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                 else {       nhstepm is the number of hstepm from age to agelim 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];       nstepm is the number of stepm from age to agelin. 
                 }       Look at hpijx to understand the reason of that which relies in memory size
               }       and note for a fixed period like estepm months */
               if (h==(int)(calagedate+12*cpt)){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;       survival function given by stepm (the optimization length). Unfortunately it
                   /*fprintf(ficrespop," %.3f", kk1);       means that if the survival funtion is printed only each two years of age and if
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/       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.
             }    */
             for(i=1; i<=nlstate;i++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
               kk1=0.;  
                 for(j=1; j<=nlstate;j++){    agelim=AGESUP;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                 }      /* nhstepm age range expressed in number of stepm */
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
             }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
         }      gm=matrix(0,nhstepm,1,nlstate*nlstate);
       }  
        /* Computed by stepm unit matrices, product of hstepm matrices, stored
   /******/         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
       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>=(agemin-((int)calagedate %12)/12.); agedeb--){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;      /* Computing  Variances of health expectancies */
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       for(theta=1; theta <=npar; theta++){
           oldm=oldms;savm=savms;        for(i=1; i<=npar; i++){ 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            xp[i] = x[i] + (i==theta ?delti[theta]:0);
           for (h=0; h<=nhstepm; h++){        }
             if (h==(int) (calagedate+YEARM*cpt)) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    
             }        cptj=0;
             for(j=1; j<=nlstate+ndeath;j++) {        for(j=1; j<= nlstate; j++){
               kk1=0.;kk2=0;          for(i=1; i<=nlstate; i++){
               for(i=1; i<=nlstate;i++) {                          cptj=cptj+1;
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
               }              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);            }
             }          }
           }        }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       
         }       
       }        for(i=1; i<=npar; i++) 
    }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        cptj=0;
         for(j=1; j<= nlstate; j++){
   if (popforecast==1) {          for(i=1;i<=nlstate;i++){
     free_ivector(popage,0,AGESUP);            cptj=cptj+1;
     free_vector(popeffectif,0,AGESUP);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     free_vector(popcount,0,AGESUP);  
   }              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            }
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
   fclose(ficrespop);        }
 }        for(j=1; j<= nlstate*nlstate; j++)
           for(h=0; h<=nhstepm-1; h++){
 /***********************************************/            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 /**************** Main Program *****************/          }
 /***********************************************/       } 
      
 int main(int argc, char *argv[])  /* End theta */
 {  
        trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;  
   double agedeb, agefin,hf;       for(h=0; h<=nhstepm-1; h++)
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;        for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
   double fret;            trgradg[h][j][theta]=gradg[h][theta][j];
   double **xi,tmp,delta;       
   
   double dum; /* Dummy variable */       for(i=1;i<=nlstate*nlstate;i++)
   double ***p3mat;        for(j=1;j<=nlstate*nlstate;j++)
   int *indx;          varhe[i][j][(int)age] =0.;
   char line[MAXLINE], linepar[MAXLINE];  
   char title[MAXLINE];       printf("%d|",(int)age);fflush(stdout);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];       for(h=0;h<=nhstepm-1;h++){
          for(k=0;k<=nhstepm-1;k++){
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   char filerest[FILENAMELENGTH];          for(i=1;i<=nlstate*nlstate;i++)
   char fileregp[FILENAMELENGTH];            for(j=1;j<=nlstate*nlstate;j++)
   char popfile[FILENAMELENGTH];              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        }
   int firstobs=1, lastobs=10;      }
   int sdeb, sfin; /* Status at beginning and end */      /* Computing expectancies */
   int c,  h , cpt,l;      for(i=1; i<=nlstate;i++)
   int ju,jl, mi;        for(j=1; j<=nlstate;j++)
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   int mobilav=0,popforecast=0;            
   int hstepm, nhstepm;  /* 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]);*/
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;  
           }
   double bage, fage, age, agelim, agebase;  
   double ftolpl=FTOL;      fprintf(ficreseij,"%3.0f",age );
   double **prlim;      cptj=0;
   double *severity;      for(i=1; i<=nlstate;i++)
   double ***param; /* Matrix of parameters */        for(j=1; j<=nlstate;j++){
   double  *p;          cptj++;
   double **matcov; /* Matrix of covariance */          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   double ***delti3; /* Scale */        }
   double *delti; /* Scale */      fprintf(ficreseij,"\n");
   double ***eij, ***vareij;     
   double **varpl; /* Variances of prevalence limits by age */      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   double *epj, vepp;      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   double kk1, kk2;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }
   char version[80]="Imach version 0.71c, March 2002, INED-EUROREVES ";    printf("\n");
   char *alph[]={"a","a","b","c","d","e"}, str[4];    fprintf(ficlog,"\n");
   
     free_vector(xp,1,npar);
   char z[1]="c", occ;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
 #include <sys/time.h>    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
 #include <time.h>    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  }
    
   /* long total_usecs;  /************ Variance ******************/
   struct timeval start_time, end_time;  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)
    {
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
   printf("\n%s",version);    double **dnewm,**doldm;
   if(argc <=1){    double **dnewmp,**doldmp;
     printf("\nEnter the parameter file name: ");    int i, j, nhstepm, hstepm, h, nstepm ;
     scanf("%s",pathtot);    int k, cptcode;
   }    double *xp;
   else{    double **gp, **gm;  /* for var eij */
     strcpy(pathtot,argv[1]);    double ***gradg, ***trgradg; /*for var eij */
   }    double **gradgp, **trgradgp; /* for var p point j */
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    double *gpp, *gmp; /* for var p point j */
   /*cygwin_split_path(pathtot,path,optionfile);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    double ***p3mat;
   /* cutv(path,optionfile,pathtot,'\\');*/    double age,agelim, hf;
     double ***mobaverage;
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    int theta;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    char digit[4];
   chdir(path);    char digitp[25];
   replace(pathc,path);  
     char fileresprobmorprev[FILENAMELENGTH];
 /*-------- arguments in the command line --------*/  
     if(popbased==1){
   strcpy(fileres,"r");      if(mobilav!=0)
   strcat(fileres, optionfilefiname);        strcpy(digitp,"-populbased-mobilav-");
   strcat(fileres,".txt");    /* Other files have txt extension */      else strcpy(digitp,"-populbased-nomobil-");
     }
   /*---------arguments file --------*/    else 
       strcpy(digitp,"-stablbased-");
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  
     printf("Problem with optionfile %s\n",optionfile);    if (mobilav!=0) {
     goto end;      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);
   strcpy(filereso,"o");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   strcat(filereso,fileres);      }
   if((ficparo=fopen(filereso,"w"))==NULL) {    }
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  
   }    strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
   /* Reads comments: lines beginning with '#' */    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   while((c=getc(ficpar))=='#' && c!= EOF){    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     ungetc(c,ficpar);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     fgets(line, MAXLINE, ficpar);    strcat(fileresprobmorprev,fileres);
     puts(line);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     fputs(line,ficparo);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   ungetc(c,ficpar);    }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
 while((c=getc(ficpar))=='#' && c!= EOF){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     ungetc(c,ficpar);      fprintf(ficresprobmorprev," p.%-d SE",j);
     fgets(line, MAXLINE, ficpar);      for(i=1; i<=nlstate;i++)
     puts(line);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     fputs(line,ficparo);    }  
   }    fprintf(ficresprobmorprev,"\n");
   ungetc(c,ficpar);    fprintf(ficgp,"\n# Routine varevsij");
      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
        fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   covar=matrix(0,NCOVMAX,1,n);  /*   } */
   cptcovn=0;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  
     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");
   ncovmodel=2+cptcovn;    fprintf(ficresvij,"# Age");
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
   /* Read guess parameters */        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   /* Reads comments: lines beginning with '#' */    fprintf(ficresvij,"\n");
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    xp=vector(1,npar);
     fgets(line, MAXLINE, ficpar);    dnewm=matrix(1,nlstate,1,npar);
     puts(line);    doldm=matrix(1,nlstate,1,nlstate);
     fputs(line,ficparo);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   ungetc(c,ficpar);  
      gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    gpp=vector(nlstate+1,nlstate+ndeath);
     for(i=1; i <=nlstate; i++)    gmp=vector(nlstate+1,nlstate+ndeath);
     for(j=1; j <=nlstate+ndeath-1; j++){    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       fscanf(ficpar,"%1d%1d",&i1,&j1);    
       fprintf(ficparo,"%1d%1d",i1,j1);    if(estepm < stepm){
       printf("%1d%1d",i,j);      printf ("Problem %d lower than %d\n",estepm, stepm);
       for(k=1; k<=ncovmodel;k++){    }
         fscanf(ficpar," %lf",&param[i][j][k]);    else  hstepm=estepm;   
         printf(" %lf",param[i][j][k]);    /* For example we decided to compute the life expectancy with the smallest unit */
         fprintf(ficparo," %lf",param[i][j][k]);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       }       nhstepm is the number of hstepm from age to agelim 
       fscanf(ficpar,"\n");       nstepm is the number of stepm from age to agelin. 
       printf("\n");       Look at hpijx to understand the reason of that which relies in memory size
       fprintf(ficparo,"\n");       and note for a fixed period like k years */
     }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         survival function given by stepm (the optimization length). Unfortunately it
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;       means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   p=param[1][1];       results. So we changed our mind and took the option of the best precision.
      */
   /* Reads comments: lines beginning with '#' */    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   while((c=getc(ficpar))=='#' && c!= EOF){    agelim = AGESUP;
     ungetc(c,ficpar);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     fgets(line, MAXLINE, ficpar);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     puts(line);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     fputs(line,ficparo);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   ungetc(c,ficpar);      gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  
   for(i=1; i <=nlstate; i++){      for(theta=1; theta <=npar; theta++){
     for(j=1; j <=nlstate+ndeath-1; j++){        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       fscanf(ficpar,"%1d%1d",&i1,&j1);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       printf("%1d%1d",i,j);        }
       fprintf(ficparo,"%1d%1d",i1,j1);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       for(k=1; k<=ncovmodel;k++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         fscanf(ficpar,"%le",&delti3[i][j][k]);  
         printf(" %le",delti3[i][j][k]);        if (popbased==1) {
         fprintf(ficparo," %le",delti3[i][j][k]);          if(mobilav ==0){
       }            for(i=1; i<=nlstate;i++)
       fscanf(ficpar,"\n");              prlim[i][i]=probs[(int)age][i][ij];
       printf("\n");          }else{ /* mobilav */ 
       fprintf(ficparo,"\n");            for(i=1; i<=nlstate;i++)
     }              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
   delti=delti3[1][1];        }
      
   /* Reads comments: lines beginning with '#' */        for(j=1; j<= nlstate; j++){
   while((c=getc(ficpar))=='#' && c!= EOF){          for(h=0; h<=nhstepm; h++){
     ungetc(c,ficpar);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     puts(line);          }
     fputs(line,ficparo);        }
   }        /* This for computing probability of death (h=1 means
   ungetc(c,ficpar);           computed over hstepm matrices product = hstepm*stepm months) 
             as a weighted average of prlim.
   matcov=matrix(1,npar,1,npar);        */
   for(i=1; i <=npar; i++){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     fscanf(ficpar,"%s",&str);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     printf("%s",str);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     fprintf(ficparo,"%s",str);        }    
     for(j=1; j <=i; j++){        /* end probability of death */
       fscanf(ficpar," %le",&matcov[i][j]);  
       printf(" %.5le",matcov[i][j]);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
       fprintf(ficparo," %.5le",matcov[i][j]);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     fscanf(ficpar,"\n");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     printf("\n");   
     fprintf(ficparo,"\n");        if (popbased==1) {
   }          if(mobilav ==0){
   for(i=1; i <=npar; i++)            for(i=1; i<=nlstate;i++)
     for(j=i+1;j<=npar;j++)              prlim[i][i]=probs[(int)age][i][ij];
       matcov[i][j]=matcov[j][i];          }else{ /* mobilav */ 
                for(i=1; i<=nlstate;i++)
   printf("\n");              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     /*-------- Rewriting paramater file ----------*/  
      strcpy(rfileres,"r");    /* "Rparameterfile */        for(j=1; j<= nlstate; j++){
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/          for(h=0; h<=nhstepm; h++){
      strcat(rfileres,".");    /* */            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
      strcat(rfileres,optionfilext);    /* Other files have txt extension */              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     if((ficres =fopen(rfileres,"w"))==NULL) {          }
       printf("Problem writing new parameter file: %s\n", fileres);goto end;        }
     }        /* This for computing probability of death (h=1 means
     fprintf(ficres,"#%s\n",version);           computed over hstepm matrices product = hstepm*stepm months) 
               as a weighted average of prlim.
     /*-------- data file ----------*/        */
     if((fic=fopen(datafile,"r"))==NULL)    {        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       printf("Problem with datafile: %s\n", datafile);goto end;          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
     n= lastobs;        /* end probability of death */
     severity = vector(1,maxwav);  
     outcome=imatrix(1,maxwav+1,1,n);        for(j=1; j<= nlstate; j++) /* vareij */
     num=ivector(1,n);          for(h=0; h<=nhstepm; h++){
     moisnais=vector(1,n);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     annais=vector(1,n);          }
     moisdc=vector(1,n);  
     andc=vector(1,n);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     agedc=vector(1,n);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     cod=ivector(1,n);        }
     weight=vector(1,n);  
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      } /* End theta */
     mint=matrix(1,maxwav,1,n);  
     anint=matrix(1,maxwav,1,n);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     s=imatrix(1,maxwav+1,1,n);  
     adl=imatrix(1,maxwav+1,1,n);          for(h=0; h<=nhstepm; h++) /* veij */
     tab=ivector(1,NCOVMAX);        for(j=1; j<=nlstate;j++)
     ncodemax=ivector(1,8);          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
     i=1;  
     while (fgets(line, MAXLINE, fic) != NULL)    {      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       if ((i >= firstobs) && (i <=lastobs)) {        for(theta=1; theta <=npar; theta++)
                  trgradgp[j][theta]=gradgp[theta][j];
         for (j=maxwav;j>=1;j--){    
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  
           strcpy(line,stra);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      for(i=1;i<=nlstate;i++)
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        for(j=1;j<=nlstate;j++)
         }          vareij[i][j][(int)age] =0.;
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      for(h=0;h<=nhstepm;h++){
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         for (j=ncov;j>=1;j--){        }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      }
         }    
         num[i]=atol(stra);      /* pptj */
              matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
           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(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
         i=i+1;          varppt[j][i]=doldmp[j][i];
       }      /* end ppptj */
     }      /*  x centered again */
     /* printf("ii=%d", ij);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
        scanf("%d",i);*/      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   imx=i-1; /* Number of individuals */   
       if (popbased==1) {
   /* for (i=1; i<=imx; i++){        if(mobilav ==0){
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          for(i=1; i<=nlstate;i++)
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;            prlim[i][i]=probs[(int)age][i][ij];
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;        }else{ /* mobilav */ 
     }          for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
     for (i=1; i<=imx; i++)        }
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/      }
                
   /* Calculation of the number of parameter from char model*/      /* This for computing probability of death (h=1 means
   Tvar=ivector(1,15);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   Tprod=ivector(1,15);         as a weighted average of prlim.
   Tvaraff=ivector(1,15);      */
   Tvard=imatrix(1,15,1,2);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
   Tage=ivector(1,15);              for(i=1,gmp[j]=0.;i<= nlstate; i++) 
              gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   if (strlen(model) >1){      }    
     j=0, j1=0, k1=1, k2=1;      /* end probability of death */
     j=nbocc(model,'+');  
     j1=nbocc(model,'*');      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     cptcovn=j+1;      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     cptcovprod=j1;        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
            for(i=1; i<=nlstate;i++){
              fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     strcpy(modelsav,model);        }
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      } 
       printf("Error. Non available option model=%s ",model);      fprintf(ficresprobmorprev,"\n");
       goto end;  
     }      fprintf(ficresvij,"%.0f ",age );
          for(i=1; i<=nlstate;i++)
     for(i=(j+1); i>=1;i--){        for(j=1; j<=nlstate;j++){
       cutv(stra,strb,modelsav,'+');          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        }
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      fprintf(ficresvij,"\n");
       /*scanf("%d",i);*/      free_matrix(gp,0,nhstepm,1,nlstate);
       if (strchr(strb,'*')) {      free_matrix(gm,0,nhstepm,1,nlstate);
         cutv(strd,strc,strb,'*');      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
         if (strcmp(strc,"age")==0) {      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
           cptcovprod--;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           cutv(strb,stre,strd,'V');    } /* End age */
           Tvar[i]=atoi(stre);    free_vector(gpp,nlstate+1,nlstate+ndeath);
           cptcovage++;    free_vector(gmp,nlstate+1,nlstate+ndeath);
             Tage[cptcovage]=i;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
             /*printf("stre=%s ", stre);*/    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         }    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
         else if (strcmp(strd,"age")==0) {    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
           cptcovprod--;    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
           cutv(strb,stre,strc,'V');  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
           Tvar[i]=atoi(stre);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
           cptcovage++;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
           Tage[cptcovage]=i;    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
         }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
         else {    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
           cutv(strb,stre,strc,'V');    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
           Tvar[i]=ncov+k1;    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
           cutv(strb,strc,strd,'V');    /*  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);
           Tprod[k1]=i;  */
           Tvard[k1][1]=atoi(strc);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
           Tvard[k1][2]=atoi(stre);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
           Tvar[cptcovn+k2]=Tvard[k1][1];  
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    free_vector(xp,1,npar);
           for (k=1; k<=lastobs;k++)    free_matrix(doldm,1,nlstate,1,nlstate);
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    free_matrix(dnewm,1,nlstate,1,npar);
           k1++;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           k2=k2+2;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
         }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       else {    fclose(ficresprobmorprev);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    fflush(ficgp);
        /*  scanf("%d",i);*/    fflush(fichtm); 
       cutv(strd,strc,strb,'V');  }  /* end varevsij */
       Tvar[i]=atoi(strc);  
       }  /************ Variance of prevlim ******************/
       strcpy(modelsav,stra);    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)
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  {
         scanf("%d",i);*/    /* Variance of prevalence limit */
     }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
 }    double **newm;
      double **dnewm,**doldm;
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    int i, j, nhstepm, hstepm;
   printf("cptcovprod=%d ", cptcovprod);    int k, cptcode;
   scanf("%d ",i);*/    double *xp;
     fclose(fic);    double *gp, *gm;
     double **gradg, **trgradg;
     /*  if(mle==1){*/    double age,agelim;
     if (weightopt != 1) { /* Maximisation without weights*/    int theta;
       for(i=1;i<=n;i++) weight[i]=1.0;     
     }    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     /*-calculation of age at interview from date of interview and age at death -*/    fprintf(ficresvpl,"# Age");
     agev=matrix(1,maxwav,1,imx);    for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
    for (i=1; i<=imx; i++)    fprintf(ficresvpl,"\n");
      for(m=2; (m<= maxwav); m++)  
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    xp=vector(1,npar);
          anint[m][i]=9999;    dnewm=matrix(1,nlstate,1,npar);
          s[m][i]=-1;    doldm=matrix(1,nlstate,1,nlstate);
        }    
        hstepm=1*YEARM; /* Every year of age */
     for (i=1; i<=imx; i++)  {    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    agelim = AGESUP;
       for(m=1; (m<= maxwav); m++){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         if(s[m][i] >0){      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           if (s[m][i] == nlstate+1) {      if (stepm >= YEARM) hstepm=1;
             if(agedc[i]>0)      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
               if(moisdc[i]!=99 && andc[i]!=9999)      gradg=matrix(1,npar,1,nlstate);
               agev[m][i]=agedc[i];      gp=vector(1,nlstate);
             else {      gm=vector(1,nlstate);
               if (andc[i]!=9999){  
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      for(theta=1; theta <=npar; theta++){
               agev[m][i]=-1;        for(i=1; i<=npar; i++){ /* Computes gradient */
               }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             }        }
           }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           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]);          gp[i] = prlim[i][i];
             if(mint[m][i]==99 || anint[m][i]==9999)      
               agev[m][i]=1;        for(i=1; i<=npar; i++) /* Computes gradient */
             else if(agev[m][i] <agemin){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
               agemin=agev[m][i];        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/        for(i=1;i<=nlstate;i++)
             }          gm[i] = prlim[i][i];
             else if(agev[m][i] >agemax){  
               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);*/          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
             }      } /* End theta */
             /*agev[m][i]=anint[m][i]-annais[i];*/  
             /*   agev[m][i] = age[i]+2*m;*/      trgradg =matrix(1,nlstate,1,npar);
           }  
           else { /* =9 */      for(j=1; j<=nlstate;j++)
             agev[m][i]=1;        for(theta=1; theta <=npar; theta++)
             s[m][i]=-1;          trgradg[j][theta]=gradg[theta][j];
           }  
         }      for(i=1;i<=nlstate;i++)
         else /*= 0 Unknown */        varpl[i][(int)age] =0.;
           agev[m][i]=1;      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       }      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
          for(i=1;i<=nlstate;i++)
     }        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     for (i=1; i<=imx; i++)  {  
       for(m=1; (m<= maxwav); m++){      fprintf(ficresvpl,"%.0f ",age );
         if (s[m][i] > (nlstate+ndeath)) {      for(i=1; i<=nlstate;i++)
           printf("Error: Wrong value in nlstate or ndeath\n");          fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
           goto end;      fprintf(ficresvpl,"\n");
         }      free_vector(gp,1,nlstate);
       }      free_vector(gm,1,nlstate);
     }      free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    } /* End age */
   
     free_vector(severity,1,maxwav);    free_vector(xp,1,npar);
     free_imatrix(outcome,1,maxwav+1,1,n);    free_matrix(doldm,1,nlstate,1,npar);
     free_vector(moisnais,1,n);    free_matrix(dnewm,1,nlstate,1,nlstate);
     free_vector(annais,1,n);  
     /* free_matrix(mint,1,maxwav,1,n);  }
        free_matrix(anint,1,maxwav,1,n);*/  
     free_vector(moisdc,1,n);  /************ Variance of one-step probabilities  ******************/
     free_vector(andc,1,n);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   {
        int i, j=0,  i1, k1, l1, t, tj;
     wav=ivector(1,imx);    int k2, l2, j1,  z1;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    int k=0,l, cptcode;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    int first=1, first1;
        double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     /* Concatenates waves */    double **dnewm,**doldm;
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
       Tcode=ivector(1,100);    double **mu;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    double age,agelim, cov[NCOVMAX];
       ncodemax[1]=1;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    int theta;
          char fileresprob[FILENAMELENGTH];
    codtab=imatrix(1,100,1,10);    char fileresprobcov[FILENAMELENGTH];
    h=0;    char fileresprobcor[FILENAMELENGTH];
    m=pow(2,cptcoveff);  
      double ***varpij;
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){    strcpy(fileresprob,"prob"); 
        for(j=1; j <= ncodemax[k]; j++){    strcat(fileresprob,fileres);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
            h++;      printf("Problem with resultfile: %s\n", fileresprob);
            if (h>m) h=1;codtab[h][k]=j;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
          }    }
        }    strcpy(fileresprobcov,"probcov"); 
      }    strcat(fileresprobcov,fileres);
    }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
    /*for(i=1; i <=m ;i++){    }
      for(k=1; k <=cptcovn; k++){    strcpy(fileresprobcor,"probcor"); 
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);    strcat(fileresprobcor,fileres);
      }    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
      printf("\n");      printf("Problem with resultfile: %s\n", fileresprobcor);
    }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
    scanf("%d",i);*/    }
        printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
    /* Calculates basic frequencies. Computes observed prevalence at single age    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
        and prints on file fileres'p'. */    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
        printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
        fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprob,"# Age");
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fprintf(ficresprobcov,"# Age");
          fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     /* For Powell, parameters are in a vector p[] starting at p[1]    fprintf(ficresprobcov,"# Age");
        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) */  
     for(i=1; i<=nlstate;i++)
     if(mle==1){      for(j=1; j<=(nlstate+ndeath);j++){
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
     }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
            fprintf(ficresprobcor," p%1d-%1d ",i,j);
     /*--------- results files --------------*/      }  
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);   /* fprintf(ficresprob,"\n");
      fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    jk=1;   */
    fprintf(ficres,"# Parameters\n");   xp=vector(1,npar);
    printf("# Parameters\n");    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
    for(i=1,jk=1; i <=nlstate; i++){    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      for(k=1; k <=(nlstate+ndeath); k++){    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
        if (k != i)    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
          {    first=1;
            printf("%d%d ",i,k);    fprintf(ficgp,"\n# Routine varprob");
            fprintf(ficres,"%1d%1d ",i,k);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
            for(j=1; j <=ncovmodel; j++){    fprintf(fichtm,"\n");
              printf("%f ",p[jk]);  
              fprintf(ficres,"%f ",p[jk]);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
              jk++;    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
            }    file %s<br>\n",optionfilehtmcov);
            printf("\n");    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
            fprintf(ficres,"\n");  and drawn. It helps understanding how is the covariance between two incidences.\
          }   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
      }    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
    }  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
  if(mle==1){  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
     /* Computing hessian and covariance matrix */  standard deviations wide on each axis. <br>\
     ftolhess=ftol; /* Usually correct */   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
     hesscov(matcov, p, npar, delti, ftolhess, func);   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
  }  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
     fprintf(ficres,"# Scales\n");  
     printf("# Scales\n");    cov[1]=1;
      for(i=1,jk=1; i <=nlstate; i++){    tj=cptcoveff;
       for(j=1; j <=nlstate+ndeath; j++){    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
         if (j!=i) {    j1=0;
           fprintf(ficres,"%1d%1d",i,j);    for(t=1; t<=tj;t++){
           printf("%1d%1d",i,j);      for(i1=1; i1<=ncodemax[t];i1++){ 
           for(k=1; k<=ncovmodel;k++){        j1++;
             printf(" %.5e",delti[jk]);        if  (cptcovn>0) {
             fprintf(ficres," %.5e",delti[jk]);          fprintf(ficresprob, "\n#********** Variable "); 
             jk++;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           }          fprintf(ficresprob, "**********\n#\n");
           printf("\n");          fprintf(ficresprobcov, "\n#********** Variable "); 
           fprintf(ficres,"\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         }          fprintf(ficresprobcov, "**********\n#\n");
       }          
      }          fprintf(ficgp, "\n#********** Variable "); 
              for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     k=1;          fprintf(ficgp, "**********\n#\n");
     fprintf(ficres,"# Covariance\n");          
     printf("# Covariance\n");          
     for(i=1;i<=npar;i++){          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       /*  if (k>nlstate) k=1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       i1=(i-1)/(ncovmodel*nlstate)+1;          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          
       printf("%s%d%d",alph[k],i1,tab[i]);*/          fprintf(ficresprobcor, "\n#********** Variable ");    
       fprintf(ficres,"%3d",i);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       printf("%3d",i);          fprintf(ficresprobcor, "**********\n#");    
       for(j=1; j<=i;j++){        }
         fprintf(ficres," %.5e",matcov[i][j]);        
         printf(" %.5e",matcov[i][j]);        for (age=bage; age<=fage; age ++){ 
       }          cov[2]=age;
       fprintf(ficres,"\n");          for (k=1; k<=cptcovn;k++) {
       printf("\n");            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
       k++;          }
     }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
              for (k=1; k<=cptcovprod;k++)
     while((c=getc(ficpar))=='#' && c!= EOF){            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       ungetc(c,ficpar);          
       fgets(line, MAXLINE, ficpar);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
       puts(line);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       fputs(line,ficparo);          gp=vector(1,(nlstate)*(nlstate+ndeath));
     }          gm=vector(1,(nlstate)*(nlstate+ndeath));
     ungetc(c,ficpar);      
            for(theta=1; theta <=npar; theta++){
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);            for(i=1; i<=npar; i++)
                  xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
     if (fage <= 2) {            
       bage = agemin;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       fage = agemaxpar;            
     }            k=0;
                for(i=1; i<= (nlstate); i++){
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");              for(j=1; j<=(nlstate+ndeath);j++){
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);                k=k+1;
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);                gp[k]=pmmij[i][j];
                }
     while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);            
     fgets(line, MAXLINE, ficpar);            for(i=1; i<=npar; i++)
     puts(line);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     fputs(line,ficparo);      
   }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   ungetc(c,ficpar);            k=0;
              for(i=1; i<=(nlstate); i++){
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);              for(j=1; j<=(nlstate+ndeath);j++){
   fprintf(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);                gm[k]=pmmij[i][j];
                    }
   while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);       
     fgets(line, MAXLINE, ficpar);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     puts(line);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     fputs(line,ficparo);          }
   }  
   ungetc(c,ficpar);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
              for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   fscanf(ficpar,"pop_based=%d\n",&popbased);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   fprintf(ficparo,"pop_based=%d\n",popbased);            free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   fprintf(ficres,"pop_based=%d\n",popbased);            free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
            free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);          pmij(pmmij,cov,ncovmodel,x,nlstate);
     fgets(line, MAXLINE, ficpar);          
     puts(line);          k=0;
     fputs(line,ficparo);          for(i=1; i<=(nlstate); i++){
   }            for(j=1; j<=(nlstate+ndeath);j++){
   ungetc(c,ficpar);              k=k+1;
               mu[k][(int) age]=pmmij[i][j];
   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);            }
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          }
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);          /*printf("\n%d ",(int)age);
     fgets(line, MAXLINE, ficpar);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     puts(line);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     fputs(line,ficparo);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   }            }*/
   ungetc(c,ficpar);  
           fprintf(ficresprob,"\n%d ",(int)age);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);          fprintf(ficresprobcov,"\n%d ",(int)age);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          fprintf(ficresprobcor,"\n%d ",(int)age);
   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 (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
 /*------------ gnuplot -------------*/            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
            }
 /*------------ free_vector  -------------*/          i=0;
  chdir(path);          for (k=1; k<=(nlstate);k++){
              for (l=1; l<=(nlstate+ndeath);l++){ 
  free_ivector(wav,1,imx);              i=i++;
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
  free_ivector(num,1,n);              for (j=1; j<=i;j++){
  free_vector(agedc,1,n);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
  fclose(ficparo);              }
  fclose(ficres);            }
           }/* end of loop for state */
 /*--------- index.htm --------*/        } /* end of loop for age */
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);        /* Confidence intervalle of pij  */
         /*
            fprintf(ficgp,"\nset noparametric;unset label");
   /*--------------- Prevalence limit --------------*/          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
            fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   strcpy(filerespl,"pl");          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);
   strcat(filerespl,fileres);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   }        */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  
   fprintf(ficrespl,"#Prevalence limit\n");        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   fprintf(ficrespl,"#Age ");        first1=1;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        for (k2=1; k2<=(nlstate);k2++){
   fprintf(ficrespl,"\n");          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
              if(l2==k2) continue;
   prlim=matrix(1,nlstate,1,nlstate);            j=(k2-1)*(nlstate+ndeath)+l2;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for (k1=1; k1<=(nlstate);k1++){
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                if(l1==k1) continue;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                i=(k1-1)*(nlstate+ndeath)+l1;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                if(i<=j) continue;
   k=0;                for (age=bage; age<=fage; age ++){ 
   agebase=agemin;                  if ((int)age %5==0){
   agelim=agemaxpar;                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   ftolpl=1.e-10;                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   i1=cptcoveff;                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   if (cptcovn < 1){i1=1;}                    mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
   for(cptcov=1;cptcov<=i1;cptcov++){                    c12=cv12/sqrt(v1*v2);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    /* Computing eigen value of matrix of covariance */
         k=k+1;                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
         fprintf(ficrespl,"\n#******");                    /* Eigen vectors */
         for(j=1;j<=cptcoveff;j++)                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    /*v21=sqrt(1.-v11*v11); *//* error */
         fprintf(ficrespl,"******\n");                    v21=(lc1-v1)/cv12*v11;
                            v12=-v21;
         for (age=agebase; age<=agelim; age++){                    v22=v11;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                    tnalp=v21/v11;
           fprintf(ficrespl,"%.0f",age );                    if(first1==1){
           for(i=1; i<=nlstate;i++)                      first1=0;
           fprintf(ficrespl," %.5f", prlim[i][i]);                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
           fprintf(ficrespl,"\n");                    }
         }                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
       }                    /*printf(fignu*/
     }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   fclose(ficrespl);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
   /*------------- h Pij x at various ages ------------*/                      first=0;
                        fprintf(ficgp,"\nset parametric;unset label");
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);                      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);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                      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\">\
   printf("Computing pij: result on file '%s' \n", filerespij);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                                subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
   stepsize=(int) (stepm+YEARM-1)/YEARM;                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   /*if (stepm<=24) stepsize=2;*/                      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);
   agelim=AGESUP;                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   hstepm=stepsize*YEARM; /* Every year of age */                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                        fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   k=0;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   for(cptcov=1;cptcov<=i1;cptcov++){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    }else{
       k=k+1;                      first=0;
         fprintf(ficrespij,"\n#****** ");                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
         for(j=1;j<=cptcoveff;j++)                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
         fprintf(ficrespij,"******\n");                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                                      mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                    }/* if first */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                  } /* age mod 5 */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                } /* end loop age */
           oldm=oldms;savm=savms;                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                  first=1;
           fprintf(ficrespij,"# Age");              } /*l12 */
           for(i=1; i<=nlstate;i++)            } /* k12 */
             for(j=1; j<=nlstate+ndeath;j++)          } /*l1 */
               fprintf(ficrespij," %1d-%1d",i,j);        }/* k1 */
           fprintf(ficrespij,"\n");      } /* loop covariates */
           for (h=0; h<=nhstepm; h++){    }
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
             for(i=1; i<=nlstate;i++)    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
               for(j=1; j<=nlstate+ndeath;j++)    free_vector(xp,1,npar);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    fclose(ficresprob);
             fprintf(ficrespij,"\n");    fclose(ficresprobcov);
           }    fclose(ficresprobcor);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fflush(ficgp);
           fprintf(ficrespij,"\n");    fflush(fichtmcov);
         }  }
     }  
   }  
   /******************* Printing html file ***********/
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
   fclose(ficrespij);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
   /*---------- Forecasting ------------------*/                    double jprev2, double mprev2,double anprev2){
   if((stepm == 1) && (strcmp(model,".")==0)){    int jj1, k1, i1, cpt;
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);  
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
     free_matrix(mint,1,maxwav,1,n);   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
     free_vector(weight,1,n);}     fprintf(fichtm,"\
   else{   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
     erreur=108;             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
     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(fichtm,"\
   }   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
               subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
   /*---------- Health expectancies and variances ------------*/   - Life expectancies by age and initial health status (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
   strcpy(filerest,"t");             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   strcat(filerest,fileres);  
   if((ficrest=fopen(filerest,"w"))==NULL) {  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  
   }   m=cptcoveff;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
   strcpy(filerese,"e");   for(k1=1; k1<=m;k1++){
   strcat(filerese,fileres);     for(i1=1; i1<=ncodemax[k1];i1++){
   if((ficreseij=fopen(filerese,"w"))==NULL) {       jj1++;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);       if (cptcovn > 0) {
   }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);         for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
  strcpy(fileresv,"v");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   strcat(fileresv,fileres);       }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {       /* Pij */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);       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> \
   }  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);       /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   k=0;   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   for(cptcov=1;cptcov<=i1;cptcov++){  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         /* Stable prevalence in each health state */
       k=k+1;         for(cpt=1; cpt<nlstate;cpt++){
       fprintf(ficrest,"\n#****** ");           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
       for(j=1;j<=cptcoveff;j++)  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         }
       fprintf(ficrest,"******\n");       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> \
       fprintf(ficreseij,"\n#****** ");  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
       for(j=1;j<=cptcoveff;j++)       }
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);     } /* end i1 */
       fprintf(ficreseij,"******\n");   }/* End k1 */
    fprintf(fichtm,"</ul>");
       fprintf(ficresvij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);   fprintf(fichtm,"\
       fprintf(ficresvij,"******\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);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);             subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);   fprintf(fichtm,"\
       oldm=oldms;savm=savms;   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
      
    fprintf(fichtm,"\
     - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);   fprintf(fichtm,"\
       fprintf(ficrest,"\n");   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
       hf=1;   fprintf(fichtm,"\
       if (stepm >= YEARM) hf=stepm/YEARM;   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
       epj=vector(1,nlstate+1);           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
       for(age=bage; age <=fage ;age++){   fprintf(fichtm,"\
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
         if (popbased==1) {           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
           for(i=1; i<=nlstate;i++)  
             prlim[i][i]=probs[(int)age][i][k];  /*  if(popforecast==1) fprintf(fichtm,"\n */
         }  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
          /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
         fprintf(ficrest," %.0f",age);  /*      <br>",fileres,fileres,fileres,fileres); */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  /*  else  */
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  /*    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); */
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];   fflush(fichtm);
           }   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
           epj[nlstate+1] +=epj[j];  
         }   m=cptcoveff;
         for(i=1, vepp=0.;i <=nlstate;i++)   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
           for(j=1;j <=nlstate;j++)  
             vepp += vareij[i][j][(int)age];   jj1=0;
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));   for(k1=1; k1<=m;k1++){
         for(j=1;j <=nlstate;j++){     for(i1=1; i1<=ncodemax[k1];i1++){
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));       jj1++;
         }       if (cptcovn > 0) {
         fprintf(ficrest,"\n");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       }         for (cpt=1; cpt<=cptcoveff;cpt++) 
     }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
   fclose(ficreseij);       for(cpt=1; cpt<=nlstate;cpt++) {
   fclose(ficresvij);         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   fclose(ficrest);  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   fclose(ficpar);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
   free_vector(epj,1,nlstate+1);       }
         fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   /*------- Variance limit prevalence------*/    health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
   strcpy(fileresvpl,"vpl");     } /* end i1 */
   strcat(fileresvpl,fileres);   }/* End k1 */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {   fprintf(fichtm,"</ul>");
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);   fflush(fichtm);
     exit(0);  }
   }  
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){    char dirfileres[132],optfileres[132];
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
       k=k+1;    int ng;
       fprintf(ficresvpl,"\n#****** ");  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
       for(j=1;j<=cptcoveff;j++)  /*     printf("Problem with file %s",optionfilegnuplot); */
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
       fprintf(ficresvpl,"******\n");  /*   } */
        
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    /*#ifdef windows */
       oldm=oldms;savm=savms;    fprintf(ficgp,"cd \"%s\" \n",pathc);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      /*#endif */
     }    m=pow(2,cptcoveff);
  }  
     strcpy(dirfileres,optionfilefiname);
   fclose(ficresvpl);    strcpy(optfileres,"vpl");
    /* 1eme*/
   /*---------- End : free ----------------*/    for (cpt=1; cpt<= nlstate ; cpt ++) {
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);     for (k1=1; k1<= m ; k1 ++) {
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);       fprintf(ficgp,"set xlabel \"Age\" \n\
    set ylabel \"Probability\" \n\
    set ter png small\n\
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  set size 0.65,0.65\n\
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);       for (i=1; i<= nlstate ; i ++) {
           if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   free_matrix(matcov,1,npar,1,npar);         else fprintf(ficgp," \%%*lf (\%%*lf)");
   free_vector(delti,1,npar);       }
   free_matrix(agev,1,maxwav,1,imx);       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);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   if(erreur >0)         else fprintf(ficgp," \%%*lf (\%%*lf)");
     printf("End of Imach with error %d\n",erreur);       } 
   else   printf("End of Imach\n");       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */       for (i=1; i<= nlstate ; i ++) {
           if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/         else fprintf(ficgp," \%%*lf (\%%*lf)");
   /*printf("Total time was %d uSec.\n", total_usecs);*/       }  
   /*------ End -----------*/       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
  end:    /*2 eme*/
 #ifdef windows    
   /* chdir(pathcd);*/    for (k1=1; k1<= m ; k1 ++) { 
 #endif      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
  /*system("wgnuplot graph.plt");*/      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
  /*system("../gp37mgw/wgnuplot graph.plt");*/      
  /*system("cd ../gp37mgw");*/      for (i=1; i<= nlstate+1 ; i ++) {
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        k=2*i;
  strcpy(plotcmd,GNUPLOTPROGRAM);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
  strcat(plotcmd," ");        for (j=1; j<= nlstate+1 ; j ++) {
  strcat(plotcmd,optionfilegnuplot);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
  system(plotcmd);          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
 #ifdef windows        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   while (z[0] != 'q') {        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
     chdir(path);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");        for (j=1; j<= nlstate+1 ; j ++) {
     scanf("%s",z);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     if (z[0] == 'c') system("./imach");          else fprintf(ficgp," \%%*lf (\%%*lf)");
     else if (z[0] == 'e') {        }   
       chdir(path);        fprintf(ficgp,"\" t\"\" w l 0,");
       system(optionfilehtm);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     }        for (j=1; j<= nlstate+1 ; j ++) {
     else if (z[0] == 'q') exit(0);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   }          else fprintf(ficgp," \%%*lf (\%%*lf)");
 #endif        }   
 }        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       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);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i]==1 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i]==0 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         if (wav[i]>1 & agecens[i]>15) {
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov){
     int i;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       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 || s[m][i]==-2){
           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.1.32  
changed lines
  Added in v.1.104


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