Diff for /imach/src/imach.c between versions 1.36 and 1.101

version 1.36, 2002/03/29 15:27:27 version 1.101, 2004/09/15 10:38:38
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.101  2004/09/15 10:38:38  brouard
      Fix on curr_time
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.100  2004/07/12 18:29:06  brouard
   first survey ("cross") where individuals from different ages are    Add version for Mac OS X. Just define UNIX in Makefile
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.99  2004/06/05 08:57:40  brouard
   second wave of interviews ("longitudinal") which measure each change    *** empty log message ***
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.98  2004/05/16 15:05:56  brouard
   model. More health states you consider, more time is necessary to reach the    New version 0.97 . First attempt to estimate force of mortality
   Maximum Likelihood of the parameters involved in the model.  The    directly from the data i.e. without the need of knowing the health
   simplest model is the multinomial logistic model where pij is the    state at each age, but using a Gompertz model: log u =a + b*age .
   probabibility to be observed in state j at the second wave    This is the basic analysis of mortality and should be done before any
   conditional to be observed in state i at the first wave. Therefore    other analysis, in order to test if the mortality estimated from the
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    cross-longitudinal survey is different from the mortality estimated
   'age' is age and 'sex' is a covariate. If you want to have a more    from other sources like vital statistic data.
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    The same imach parameter file can be used but the option for mle should be -3.
   you to do it.  More covariates you add, slower the  
   convergence.    Agnès, who wrote this part of the code, tried to keep most of the
     former routines in order to include the new code within the former code.
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    The output is very simple: only an estimate of the intercept and of
   identical for each individual. Also, if a individual missed an    the slope with 95% confident intervals.
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Current limitations:
     A) Even if you enter covariates, i.e. with the
   hPijx is the probability to be observed in state i at age x+h    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   conditional to the observed state i at age x. The delay 'h' can be    B) There is no computation of Life Expectancy nor Life Table.
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    Revision 1.97  2004/02/20 13:25:42  lievre
   semester or year) is model as a multinomial logistic.  The hPx    Version 0.96d. Population forecasting command line is (temporarily)
   matrix is simply the matrix product of nh*stepm elementary matrices    suppressed.
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Revision 1.96  2003/07/15 15:38:55  brouard
     * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   Also this programme outputs the covariance matrix of the parameters but also    rewritten within the same printf. Workaround: many printfs.
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.95  2003/07/08 07:54:34  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    * imach.c (Repository):
            Institut national d'études démographiques, Paris.    (Repository): Using imachwizard code to output a more meaningful covariance
   This software have been partly granted by Euro-REVES, a concerted action    matrix (cov(a12,c31) instead of numbers.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.94  2003/06/27 13:00:02  brouard
   software can be distributed freely for non commercial use. Latest version    Just cleaning
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.93  2003/06/25 16:33:55  brouard
      (Module): On windows (cygwin) function asctime_r doesn't
 #include <math.h>    exist so I changed back to asctime which exists.
 #include <stdio.h>    (Module): Version 0.96b
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 #define MAXLINE 256    exist so I changed back to asctime which exists.
 #define GNUPLOTPROGRAM "wgnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.91  2003/06/25 15:30:29  brouard
 #define FILENAMELENGTH 80    * imach.c (Repository): Duplicated warning errors corrected.
 /*#define DEBUG*/    (Repository): Elapsed time after each iteration is now output. It
 #define windows    helps to forecast when convergence will be reached. Elapsed time
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    is stamped in powell.  We created a new html file for the graphs
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    concerning matrix of covariance. It has extension -cov.htm.
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.90  2003/06/24 12:34:15  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 #define NINTERVMAX 8    of the covariance matrix to be input.
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.89  2003/06/24 12:30:52  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    (Module): Some bugs corrected for windows. Also, when
 #define MAXN 20000    mle=-1 a template is output in file "or"mypar.txt with the design
 #define YEARM 12. /* Number of months per year */    of the covariance matrix to be input.
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.88  2003/06/23 17:54:56  brouard
     * 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.
   
 int erreur; /* Error number */    Revision 1.87  2003/06/18 12:26:01  brouard
 int nvar;    Version 0.96
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.86  2003/06/17 20:04:08  brouard
 int nlstate=2; /* Number of live states */    (Module): Change position of html and gnuplot routines and added
 int ndeath=1; /* Number of dead states */    routine fileappend.
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
 int *wav; /* Number of waves for this individuual 0 is possible */    current date of interview. It may happen when the death was just
 int maxwav; /* Maxim number of waves */    prior to the death. In this case, dh was negative and likelihood
 int jmin, jmax; /* min, max spacing between 2 waves */    was wrong (infinity). We still send an "Error" but patch by
 int mle, weightopt;    assuming that the date of death was just one stepm after the
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    interview.
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    (Repository): Because some people have very long ID (first column)
 double jmean; /* Mean space between 2 waves */    we changed int to long in num[] and we added a new lvector for
 double **oldm, **newm, **savm; /* Working pointers to matrices */    memory allocation. But we also truncated to 8 characters (left
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    truncation)
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    (Repository): No more line truncation errors.
 FILE *ficgp,*ficresprob,*ficpop;  
 FILE *ficreseij;    Revision 1.84  2003/06/13 21:44:43  brouard
   char filerese[FILENAMELENGTH];    * imach.c (Repository): Replace "freqsummary" at a correct
  FILE  *ficresvij;    place. It differs from routine "prevalence" which may be called
   char fileresv[FILENAMELENGTH];    many times. Probs is memory consuming and must be used with
  FILE  *ficresvpl;    parcimony.
   char fileresvpl[FILENAMELENGTH];    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 #define NR_END 1    Revision 1.83  2003/06/10 13:39:11  lievre
 #define FREE_ARG char*    *** empty log message ***
 #define FTOL 1.0e-10  
     Revision 1.82  2003/06/05 15:57:20  brouard
 #define NRANSI    Add log in  imach.c and  fullversion number is now printed.
 #define ITMAX 200  
   */
 #define TOL 2.0e-4  /*
      Interpolated Markov Chain
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Short summary of the programme:
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    
     This program computes Healthy Life Expectancies from
 #define GOLD 1.618034    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #define GLIMIT 100.0    first survey ("cross") where individuals from different ages are
 #define TINY 1.0e-20    interviewed on their health status or degree of disability (in the
     case of a health survey which is our main interest) -2- at least a
 static double maxarg1,maxarg2;    second wave of interviews ("longitudinal") which measure each change
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    (if any) in individual health status.  Health expectancies are
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    computed from the time spent in each health state according to a
      model. More health states you consider, more time is necessary to reach the
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Maximum Likelihood of the parameters involved in the model.  The
 #define rint(a) floor(a+0.5)    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
 static double sqrarg;    conditional to be observed in state i at the first wave. Therefore
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    'age' is age and 'sex' is a covariate. If you want to have a more
     complex model than "constant and age", you should modify the program
 int imx;    where the markup *Covariates have to be included here again* invites
 int stepm;    you to do it.  More covariates you add, slower the
 /* Stepm, step in month: minimum step interpolation*/    convergence.
   
 int estepm;    The advantage of this computer programme, compared to a simple
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    multinomial logistic model, is clear when the delay between waves is not
     identical for each individual. Also, if a individual missed an
 int m,nb;    intermediate interview, the information is lost, but taken into
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    account using an interpolation or extrapolation.  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    hPijx is the probability to be observed in state i at age x+h
 double dateintmean=0;    conditional to the observed state i at age x. The delay 'h' can be
     split into an exact number (nh*stepm) of unobserved intermediate
 double *weight;    states. This elementary transition (by month, quarter,
 int **s; /* Status */    semester or year) is modelled as a multinomial logistic.  The hPx
 double *agedc, **covar, idx;    matrix is simply the matrix product of nh*stepm elementary matrices
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    and the contribution of each individual to the likelihood is simply
     hPijx.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the stable prevalence. 
 /**************** split *************************/    
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 {             Institut national d'études démographiques, Paris.
    char *s;                             /* pointer */    This software have been partly granted by Euro-REVES, a concerted action
    int  l1, l2;                         /* length counters */    from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
    l1 = strlen( path );                 /* length of path */    software can be distributed freely for non commercial use. Latest version
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    can be accessed at http://euroreves.ined.fr/imach .
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #else    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
    s = strrchr( path, '/' );            /* find last / */    
 #endif    **********************************************************************/
    if ( s == NULL ) {                   /* no directory, so use current */  /*
 #if     defined(__bsd__)                /* get current working directory */    main
       extern char       *getwd( );    read parameterfile
     read datafile
       if ( getwd( dirc ) == NULL ) {    concatwav
 #else    freqsummary
       extern char       *getcwd( );    if (mle >= 1)
       mlikeli
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    print results files
 #endif    if mle==1 
          return( GLOCK_ERROR_GETCWD );       computes hessian
       }    read end of parameter file: agemin, agemax, bage, fage, estepm
       strcpy( name, path );             /* we've got it */        begin-prev-date,...
    } else {                             /* strip direcotry from path */    open gnuplot file
       s++;                              /* after this, the filename */    open html file
       l2 = strlen( s );                 /* length of filename */    stable prevalence
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );     for age prevalim()
       strcpy( name, s );                /* save file name */    h Pij x
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    variance of p varprob
       dirc[l1-l2] = 0;                  /* add zero */    forecasting if prevfcast==1 prevforecast call prevalence()
    }    health expectancies
    l1 = strlen( dirc );                 /* length of directory */    Variance-covariance of DFLE
 #ifdef windows    prevalence()
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }     movingaverage()
 #else    varevsij() 
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    if popbased==1 varevsij(,popbased)
 #endif    total life expectancies
    s = strrchr( name, '.' );            /* find last / */    Variance of stable prevalence
    s++;   end
    strcpy(ext,s);                       /* save extension */  */
    l1= strlen( name);  
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;   
    return( 0 );                         /* we're done */  #include <math.h>
 }  #include <stdio.h>
   #include <stdlib.h>
   #include <unistd.h>
 /******************************************/  
   /* #include <sys/time.h> */
 void replace(char *s, char*t)  #include <time.h>
 {  #include "timeval.h"
   int i;  
   int lg=20;  /* #include <libintl.h> */
   i=0;  /* #define _(String) gettext (String) */
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {  #define MAXLINE 256
     (s[i] = t[i]);  #define GNUPLOTPROGRAM "gnuplot"
     if (t[i]== '\\') s[i]='/';  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   }  #define FILENAMELENGTH 132
 }  /*#define DEBUG*/
   /*#define windows*/
 int nbocc(char *s, char occ)  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 {  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   int i,j=0;  
   int lg=20;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   i=0;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {  #define NINTERVMAX 8
   if  (s[i] == occ ) j++;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   }  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   return j;  #define NCOVMAX 8 /* Maximum number of covariates */
 }  #define MAXN 20000
   #define YEARM 12. /* Number of months per year */
 void cutv(char *u,char *v, char*t, char occ)  #define AGESUP 130
 {  #define AGEBASE 40
   int i,lg,j,p=0;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   i=0;  #ifdef UNIX
   for(j=0; j<=strlen(t)-1; j++) {  #define DIRSEPARATOR '/'
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  #define ODIRSEPARATOR '\\'
   }  #else
   #define DIRSEPARATOR '\\'
   lg=strlen(t);  #define ODIRSEPARATOR '/'
   for(j=0; j<p; j++) {  #endif
     (u[j] = t[j]);  
   }  /* $Id$ */
      u[p]='\0';  /* $State$ */
   
    for(j=0; j<= lg; j++) {  char version[]="Imach version 0.97b, May 2004, INED-EUROREVES ";
     if (j>=(p+1))(v[j-p-1] = t[j]);  char fullversion[]="$Revision$ $Date$"; 
   }  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 }  int nvar;
   int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 /********************** nrerror ********************/  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
 void nrerror(char error_text[])  int ndeath=1; /* Number of dead states */
 {  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   fprintf(stderr,"ERREUR ...\n");  int popbased=0;
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  int *wav; /* Number of waves for this individuual 0 is possible */
 }  int maxwav; /* Maxim number of waves */
 /*********************** vector *******************/  int jmin, jmax; /* min, max spacing between 2 waves */
 double *vector(int nl, int nh)  int gipmx, gsw; /* Global variables on the number of contributions 
 {                     to the likelihood and the sum of weights (done by funcone)*/
   double *v;  int mle, weightopt;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   if (!v) nrerror("allocation failure in vector");  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   return v-nl+NR_END;  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. */
   double jmean; /* Mean space between 2 waves */
 /************************ free vector ******************/  double **oldm, **newm, **savm; /* Working pointers to matrices */
 void free_vector(double*v, int nl, int nh)  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 {  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   free((FREE_ARG)(v+nl-NR_END));  FILE *ficlog, *ficrespow;
 }  int globpr; /* Global variable for printing or not */
   double fretone; /* Only one call to likelihood */
 /************************ivector *******************************/  long ipmx; /* Number of contributions */
 int *ivector(long nl,long nh)  double sw; /* Sum of weights */
 {  char filerespow[FILENAMELENGTH];
   int *v;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  FILE *ficresilk;
   if (!v) nrerror("allocation failure in ivector");  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   return v-nl+NR_END;  FILE *ficresprobmorprev;
 }  FILE *fichtm, *fichtmcov; /* Html File */
   FILE *ficreseij;
 /******************free ivector **************************/  char filerese[FILENAMELENGTH];
 void free_ivector(int *v, long nl, long nh)  FILE  *ficresvij;
 {  char fileresv[FILENAMELENGTH];
   free((FREE_ARG)(v+nl-NR_END));  FILE  *ficresvpl;
 }  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
 /******************* imatrix *******************************/  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 int **imatrix(long nrl, long nrh, long ncl, long nch)  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 {  char command[FILENAMELENGTH];
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  int  outcmd=0;
   int **m;  
    char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  char filelog[FILENAMELENGTH]; /* Log file */
   if (!m) nrerror("allocation failure 1 in matrix()");  char filerest[FILENAMELENGTH];
   m += NR_END;  char fileregp[FILENAMELENGTH];
   m -= nrl;  char popfile[FILENAMELENGTH];
    
    char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  struct timezone tzp;
   m[nrl] += NR_END;  extern int gettimeofday();
   m[nrl] -= ncl;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
    long time_value;
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  extern long time();
    char strcurr[80], strfor[80];
   /* return pointer to array of pointers to rows */  
   return m;  #define NR_END 1
 }  #define FREE_ARG char*
   #define FTOL 1.0e-10
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)  #define NRANSI 
       int **m;  #define ITMAX 200 
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */  #define TOL 2.0e-4 
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #define CGOLD 0.3819660 
   free((FREE_ARG) (m+nrl-NR_END));  #define ZEPS 1.0e-10 
 }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
 /******************* matrix *******************************/  #define GOLD 1.618034 
 double **matrix(long nrl, long nrh, long ncl, long nch)  #define GLIMIT 100.0 
 {  #define TINY 1.0e-20 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;  static double maxarg1,maxarg2;
   #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   if (!m) nrerror("allocation failure 1 in matrix()");    
   m += NR_END;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   m -= nrl;  #define rint(a) floor(a+0.5)
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  static double sqrarg;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   m[nrl] += NR_END;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   m[nrl] -= ncl;  int agegomp= AGEGOMP;
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int imx; 
   return m;  int stepm=1;
 }  /* Stepm, step in month: minimum step interpolation*/
   
 /*************************free matrix ************************/  int estepm;
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int m,nb;
   free((FREE_ARG)(m+nrl-NR_END));  long *num;
 }  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 /******************* ma3x *******************************/  double **pmmij, ***probs;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  double *ageexmed,*agecens;
 {  double dateintmean=0;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  double *weight;
   int **s; /* Status */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  double *agedc, **covar, idx;
   if (!m) nrerror("allocation failure 1 in matrix()");  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   m += NR_END;  
   m -= nrl;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   double ftolhess; /* Tolerance for computing hessian */
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /**************** split *************************/
   m[nrl] += NR_END;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   m[nrl] -= ncl;  {
     /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     */ 
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    char  *ss;                            /* pointer */
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    int   l1, l2;                         /* length counters */
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;    l1 = strlen(path );                   /* length of path */
   for (j=ncl+1; j<=nch; j++)    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     m[nrl][j]=m[nrl][j-1]+nlay;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
      if ( ss == NULL ) {                   /* no directory, so use current */
   for (i=nrl+1; i<=nrh; i++) {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     for (j=ncl+1; j<=nch; j++)      /* get current working directory */
       m[i][j]=m[i][j-1]+nlay;      /*    extern  char* getcwd ( char *buf , int len);*/
   }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   return m;        return( GLOCK_ERROR_GETCWD );
 }      }
       strcpy( name, path );               /* we've got it */
 /*************************free ma3x ************************/    } else {                              /* strip direcotry from path */
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)      ss++;                               /* after this, the filename */
 {      l2 = strlen( ss );                  /* length of filename */
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   free((FREE_ARG)(m[nrl]+ncl-NR_END));      strcpy( name, ss );         /* save file name */
   free((FREE_ARG)(m+nrl-NR_END));      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 }      dirc[l1-l2] = 0;                    /* add zero */
     }
 /***************** f1dim *************************/    l1 = strlen( dirc );                  /* length of directory */
 extern int ncom;    /*#ifdef windows
 extern double *pcom,*xicom;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 extern double (*nrfunc)(double []);  #else
      if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 double f1dim(double x)  #endif
 {    */
   int j;    ss = strrchr( name, '.' );            /* find last / */
   double f;    if (ss >0){
   double *xt;      ss++;
        strcpy(ext,ss);                     /* save extension */
   xt=vector(1,ncom);      l1= strlen( name);
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];      l2= strlen(ss)+1;
   f=(*nrfunc)(xt);      strncpy( finame, name, l1-l2);
   free_vector(xt,1,ncom);      finame[l1-l2]= 0;
   return f;    }
 }    return( 0 );                          /* we're done */
   }
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {  /******************************************/
   int iter;  
   double a,b,d,etemp;  void replace_back_to_slash(char *s, char*t)
   double fu,fv,fw,fx;  {
   double ftemp;    int i;
   double p,q,r,tol1,tol2,u,v,w,x,xm;    int lg=0;
   double e=0.0;    i=0;
      lg=strlen(t);
   a=(ax < cx ? ax : cx);    for(i=0; i<= lg; i++) {
   b=(ax > cx ? ax : cx);      (s[i] = t[i]);
   x=w=v=bx;      if (t[i]== '\\') s[i]='/';
   fw=fv=fx=(*f)(x);    }
   for (iter=1;iter<=ITMAX;iter++) {  }
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  int nbocc(char *s, char occ)
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  {
     printf(".");fflush(stdout);    int i,j=0;
 #ifdef DEBUG    int lg=20;
     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);    i=0;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    lg=strlen(s);
 #endif    for(i=0; i<= lg; i++) {
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    if  (s[i] == occ ) j++;
       *xmin=x;    }
       return fx;    return j;
     }  }
     ftemp=fu;  
     if (fabs(e) > tol1) {  void cutv(char *u,char *v, char*t, char occ)
       r=(x-w)*(fx-fv);  {
       q=(x-v)*(fx-fw);    /* cuts string t into u and v where u is ended by char occ excluding it
       p=(x-v)*q-(x-w)*r;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
       q=2.0*(q-r);       gives u="abcedf" and v="ghi2j" */
       if (q > 0.0) p = -p;    int i,lg,j,p=0;
       q=fabs(q);    i=0;
       etemp=e;    for(j=0; j<=strlen(t)-1; j++) {
       e=d;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    }
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  
       else {    lg=strlen(t);
         d=p/q;    for(j=0; j<p; j++) {
         u=x+d;      (u[j] = t[j]);
         if (u-a < tol2 || b-u < tol2)    }
           d=SIGN(tol1,xm-x);       u[p]='\0';
       }  
     } else {     for(j=0; j<= lg; j++) {
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      if (j>=(p+1))(v[j-p-1] = t[j]);
     }    }
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  }
     fu=(*f)(u);  
     if (fu <= fx) {  /********************** nrerror ********************/
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)  void nrerror(char error_text[])
         SHFT(fv,fw,fx,fu)  {
         } else {    fprintf(stderr,"ERREUR ...\n");
           if (u < x) a=u; else b=u;    fprintf(stderr,"%s\n",error_text);
           if (fu <= fw || w == x) {    exit(EXIT_FAILURE);
             v=w;  }
             w=u;  /*********************** vector *******************/
             fv=fw;  double *vector(int nl, int nh)
             fw=fu;  {
           } else if (fu <= fv || v == x || v == w) {    double *v;
             v=u;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
             fv=fu;    if (!v) nrerror("allocation failure in vector");
           }    return v-nl+NR_END;
         }  }
   }  
   nrerror("Too many iterations in brent");  /************************ free vector ******************/
   *xmin=x;  void free_vector(double*v, int nl, int nh)
   return fx;  {
 }    free((FREE_ARG)(v+nl-NR_END));
   }
 /****************** mnbrak ***********************/  
   /************************ivector *******************************/
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  int *ivector(long nl,long nh)
             double (*func)(double))  {
 {    int *v;
   double ulim,u,r,q, dum;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   double fu;    if (!v) nrerror("allocation failure in ivector");
      return v-nl+NR_END;
   *fa=(*func)(*ax);  }
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  /******************free ivector **************************/
     SHFT(dum,*ax,*bx,dum)  void free_ivector(int *v, long nl, long nh)
       SHFT(dum,*fb,*fa,dum)  {
       }    free((FREE_ARG)(v+nl-NR_END));
   *cx=(*bx)+GOLD*(*bx-*ax);  }
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  /************************lvector *******************************/
     r=(*bx-*ax)*(*fb-*fc);  long *lvector(long nl,long nh)
     q=(*bx-*cx)*(*fb-*fa);  {
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    long *v;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     ulim=(*bx)+GLIMIT*(*cx-*bx);    if (!v) nrerror("allocation failure in ivector");
     if ((*bx-u)*(u-*cx) > 0.0) {    return v-nl+NR_END;
       fu=(*func)(u);  }
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  /******************free lvector **************************/
       if (fu < *fc) {  void free_lvector(long *v, long nl, long nh)
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  {
           SHFT(*fb,*fc,fu,(*func)(u))    free((FREE_ARG)(v+nl-NR_END));
           }  }
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  /******************* imatrix *******************************/
       fu=(*func)(u);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     } else {       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       u=(*cx)+GOLD*(*cx-*bx);  { 
       fu=(*func)(u);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     }    int **m; 
     SHFT(*ax,*bx,*cx,u)    
       SHFT(*fa,*fb,*fc,fu)    /* allocate pointers to rows */ 
       }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 }    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
 /*************** linmin ************************/    m -= nrl; 
     
 int ncom;    
 double *pcom,*xicom;    /* allocate rows and set pointers to them */ 
 double (*nrfunc)(double []);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
      if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    m[nrl] += NR_END; 
 {    m[nrl] -= ncl; 
   double brent(double ax, double bx, double cx,    
                double (*f)(double), double tol, double *xmin);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   double f1dim(double x);    
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    /* return pointer to array of pointers to rows */ 
               double *fc, double (*func)(double));    return m; 
   int j;  } 
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  /****************** free_imatrix *************************/
    void free_imatrix(m,nrl,nrh,ncl,nch)
   ncom=n;        int **m;
   pcom=vector(1,n);        long nch,ncl,nrh,nrl; 
   xicom=vector(1,n);       /* free an int matrix allocated by imatrix() */ 
   nrfunc=func;  { 
   for (j=1;j<=n;j++) {    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     pcom[j]=p[j];    free((FREE_ARG) (m+nrl-NR_END)); 
     xicom[j]=xi[j];  } 
   }  
   ax=0.0;  /******************* matrix *******************************/
   xx=1.0;  double **matrix(long nrl, long nrh, long ncl, long nch)
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  {
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 #ifdef DEBUG    double **m;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   for (j=1;j<=n;j++) {    if (!m) nrerror("allocation failure 1 in matrix()");
     xi[j] *= xmin;    m += NR_END;
     p[j] += xi[j];    m -= nrl;
   }  
   free_vector(xicom,1,n);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   free_vector(pcom,1,n);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 }    m[nrl] += NR_END;
     m[nrl] -= ncl;
 /*************** powell ************************/  
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
             double (*func)(double []))    return m;
 {    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   void linmin(double p[], double xi[], int n, double *fret,     */
               double (*func)(double []));  }
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;  /*************************free matrix ************************/
   double fp,fptt;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double *xits;  {
   pt=vector(1,n);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   ptt=vector(1,n);    free((FREE_ARG)(m+nrl-NR_END));
   xit=vector(1,n);  }
   xits=vector(1,n);  
   *fret=(*func)(p);  /******************* ma3x *******************************/
   for (j=1;j<=n;j++) pt[j]=p[j];  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   for (*iter=1;;++(*iter)) {  {
     fp=(*fret);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     ibig=0;    double ***m;
     del=0.0;  
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     for (i=1;i<=n;i++)    if (!m) nrerror("allocation failure 1 in matrix()");
       printf(" %d %.12f",i, p[i]);    m += NR_END;
     printf("\n");    m -= nrl;
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       fptt=(*fret);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 #ifdef DEBUG    m[nrl] += NR_END;
       printf("fret=%lf \n",*fret);    m[nrl] -= ncl;
 #endif  
       printf("%d",i);fflush(stdout);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         del=fabs(fptt-(*fret));    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
         ibig=i;    m[nrl][ncl] += NR_END;
       }    m[nrl][ncl] -= nll;
 #ifdef DEBUG    for (j=ncl+1; j<=nch; j++) 
       printf("%d %.12e",i,(*fret));      m[nrl][j]=m[nrl][j-1]+nlay;
       for (j=1;j<=n;j++) {    
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    for (i=nrl+1; i<=nrh; i++) {
         printf(" x(%d)=%.12e",j,xit[j]);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       }      for (j=ncl+1; j<=nch; j++) 
       for(j=1;j<=n;j++)        m[i][j]=m[i][j-1]+nlay;
         printf(" p=%.12e",p[j]);    }
       printf("\n");    return m; 
 #endif    /*  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)
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    */
 #ifdef DEBUG  }
       int k[2],l;  
       k[0]=1;  /*************************free ma3x ************************/
       k[1]=-1;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       printf("Max: %.12e",(*func)(p));  {
       for (j=1;j<=n;j++)    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
         printf(" %.12e",p[j]);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       printf("\n");    free((FREE_ARG)(m+nrl-NR_END));
       for(l=0;l<=1;l++) {  }
         for (j=1;j<=n;j++) {  
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  /*************** function subdirf ***********/
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  char *subdirf(char fileres[])
         }  {
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    /* Caution optionfilefiname is hidden */
       }    strcpy(tmpout,optionfilefiname);
 #endif    strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
     return tmpout;
       free_vector(xit,1,n);  }
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);  /*************** function subdirf2 ***********/
       free_vector(pt,1,n);  char *subdirf2(char fileres[], char *preop)
       return;  {
     }    
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    /* Caution optionfilefiname is hidden */
     for (j=1;j<=n;j++) {    strcpy(tmpout,optionfilefiname);
       ptt[j]=2.0*p[j]-pt[j];    strcat(tmpout,"/");
       xit[j]=p[j]-pt[j];    strcat(tmpout,preop);
       pt[j]=p[j];    strcat(tmpout,fileres);
     }    return tmpout;
     fptt=(*func)(ptt);  }
     if (fptt < fp) {  
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  /*************** function subdirf3 ***********/
       if (t < 0.0) {  char *subdirf3(char fileres[], char *preop, char *preop2)
         linmin(p,xit,n,fret,func);  {
         for (j=1;j<=n;j++) {    
           xi[j][ibig]=xi[j][n];    /* Caution optionfilefiname is hidden */
           xi[j][n]=xit[j];    strcpy(tmpout,optionfilefiname);
         }    strcat(tmpout,"/");
 #ifdef DEBUG    strcat(tmpout,preop);
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    strcat(tmpout,preop2);
         for(j=1;j<=n;j++)    strcat(tmpout,fileres);
           printf(" %.12e",xit[j]);    return tmpout;
         printf("\n");  }
 #endif  
       }  /***************** f1dim *************************/
     }  extern int ncom; 
   }  extern double *pcom,*xicom;
 }  extern double (*nrfunc)(double []); 
    
 /**** Prevalence limit ****************/  double f1dim(double x) 
   { 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    int j; 
 {    double f;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    double *xt; 
      matrix by transitions matrix until convergence is reached */   
     xt=vector(1,ncom); 
   int i, ii,j,k;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   double min, max, maxmin, maxmax,sumnew=0.;    f=(*nrfunc)(xt); 
   double **matprod2();    free_vector(xt,1,ncom); 
   double **out, cov[NCOVMAX], **pmij();    return f; 
   double **newm;  } 
   double agefin, delaymax=50 ; /* Max number of years to converge */  
   /*****************brent *************************/
   for (ii=1;ii<=nlstate+ndeath;ii++)  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     for (j=1;j<=nlstate+ndeath;j++){  { 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    int iter; 
     }    double a,b,d,etemp;
     double fu,fv,fw,fx;
    cov[1]=1.;    double ftemp;
      double p,q,r,tol1,tol2,u,v,w,x,xm; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    double e=0.0; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){   
     newm=savm;    a=(ax < cx ? ax : cx); 
     /* Covariates have to be included here again */    b=(ax > cx ? ax : cx); 
      cov[2]=agefin;    x=w=v=bx; 
      fw=fv=fx=(*f)(x); 
       for (k=1; k<=cptcovn;k++) {    for (iter=1;iter<=ITMAX;iter++) { 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      xm=0.5*(a+b); 
         /*      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]]);*/      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      printf(".");fflush(stdout);
       for (k=1; k<=cptcovprod;k++)      fprintf(ficlog,".");fflush(ficlog);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  #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);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      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);
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  #endif
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         *xmin=x; 
     savm=oldm;        return fx; 
     oldm=newm;      } 
     maxmax=0.;      ftemp=fu;
     for(j=1;j<=nlstate;j++){      if (fabs(e) > tol1) { 
       min=1.;        r=(x-w)*(fx-fv); 
       max=0.;        q=(x-v)*(fx-fw); 
       for(i=1; i<=nlstate; i++) {        p=(x-v)*q-(x-w)*r; 
         sumnew=0;        q=2.0*(q-r); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        if (q > 0.0) p = -p; 
         prlim[i][j]= newm[i][j]/(1-sumnew);        q=fabs(q); 
         max=FMAX(max,prlim[i][j]);        etemp=e; 
         min=FMIN(min,prlim[i][j]);        e=d; 
       }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       maxmin=max-min;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       maxmax=FMAX(maxmax,maxmin);        else { 
     }          d=p/q; 
     if(maxmax < ftolpl){          u=x+d; 
       return prlim;          if (u-a < tol2 || b-u < tol2) 
     }            d=SIGN(tol1,xm-x); 
   }        } 
 }      } else { 
         d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 /*************** transition probabilities ***************/      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      fu=(*f)(u); 
 {      if (fu <= fx) { 
   double s1, s2;        if (u >= x) a=x; else b=x; 
   /*double t34;*/        SHFT(v,w,x,u) 
   int i,j,j1, nc, ii, jj;          SHFT(fv,fw,fx,fu) 
           } else { 
     for(i=1; i<= nlstate; i++){            if (u < x) a=u; else b=u; 
     for(j=1; j<i;j++){            if (fu <= fw || w == x) { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){              v=w; 
         /*s2 += param[i][j][nc]*cov[nc];*/              w=u; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];              fv=fw; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/              fw=fu; 
       }            } else if (fu <= fv || v == x || v == w) { 
       ps[i][j]=s2;              v=u; 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/              fv=fu; 
     }            } 
     for(j=i+1; j<=nlstate+ndeath;j++){          } 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    } 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    nrerror("Too many iterations in brent"); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    *xmin=x; 
       }    return fx; 
       ps[i][j]=s2;  } 
     }  
   }  /****************** mnbrak ***********************/
     /*ps[3][2]=1;*/  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   for(i=1; i<= nlstate; i++){              double (*func)(double)) 
      s1=0;  { 
     for(j=1; j<i; j++)    double ulim,u,r,q, dum;
       s1+=exp(ps[i][j]);    double fu; 
     for(j=i+1; j<=nlstate+ndeath; j++)   
       s1+=exp(ps[i][j]);    *fa=(*func)(*ax); 
     ps[i][i]=1./(s1+1.);    *fb=(*func)(*bx); 
     for(j=1; j<i; j++)    if (*fb > *fa) { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];      SHFT(dum,*ax,*bx,dum) 
     for(j=i+1; j<=nlstate+ndeath; j++)        SHFT(dum,*fb,*fa,dum) 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        } 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    *cx=(*bx)+GOLD*(*bx-*ax); 
   } /* end i */    *fc=(*func)(*cx); 
     while (*fb > *fc) { 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      r=(*bx-*ax)*(*fb-*fc); 
     for(jj=1; jj<= nlstate+ndeath; jj++){      q=(*bx-*cx)*(*fb-*fa); 
       ps[ii][jj]=0;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       ps[ii][ii]=1;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     }      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   }      if ((*bx-u)*(u-*cx) > 0.0) { 
         fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        fu=(*func)(u); 
     for(jj=1; jj<= nlstate+ndeath; jj++){        if (fu < *fc) { 
      printf("%lf ",ps[ii][jj]);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
    }            SHFT(*fb,*fc,fu,(*func)(u)) 
     printf("\n ");            } 
     }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     printf("\n ");printf("%lf ",cov[2]);*/        u=ulim; 
 /*        fu=(*func)(u); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      } else { 
   goto end;*/        u=(*cx)+GOLD*(*cx-*bx); 
     return ps;        fu=(*func)(u); 
 }      } 
       SHFT(*ax,*bx,*cx,u) 
 /**************** Product of 2 matrices ******************/        SHFT(*fa,*fb,*fc,fu) 
         } 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  } 
 {  
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  /*************** linmin ************************/
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized  int ncom; 
      before: only the contents of out is modified. The function returns  double *pcom,*xicom;
      a pointer to pointers identical to out */  double (*nrfunc)(double []); 
   long i, j, k;   
   for(i=nrl; i<= nrh; i++)  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     for(k=ncolol; k<=ncoloh; k++)  { 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    double brent(double ax, double bx, double cx, 
         out[i][k] +=in[i][j]*b[j][k];                 double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
   return out;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 }                double *fc, double (*func)(double)); 
     int j; 
     double xx,xmin,bx,ax; 
 /************* Higher Matrix Product ***************/    double fx,fb,fa;
    
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    ncom=n; 
 {    pcom=vector(1,n); 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    xicom=vector(1,n); 
      duration (i.e. until    nrfunc=func; 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    for (j=1;j<=n;j++) { 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      pcom[j]=p[j]; 
      (typically every 2 years instead of every month which is too big).      xicom[j]=xi[j]; 
      Model is determined by parameters x and covariates have to be    } 
      included manually here.    ax=0.0; 
     xx=1.0; 
      */    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   int i, j, d, h, k;  #ifdef DEBUG
   double **out, cov[NCOVMAX];    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   double **newm;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   #endif
   /* Hstepm could be zero and should return the unit matrix */    for (j=1;j<=n;j++) { 
   for (i=1;i<=nlstate+ndeath;i++)      xi[j] *= xmin; 
     for (j=1;j<=nlstate+ndeath;j++){      p[j] += xi[j]; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);    } 
       po[i][j][0]=(i==j ? 1.0 : 0.0);    free_vector(xicom,1,n); 
     }    free_vector(pcom,1,n); 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  } 
   for(h=1; h <=nhstepm; h++){  
     for(d=1; d <=hstepm; d++){  char *asc_diff_time(long time_sec, char ascdiff[])
       newm=savm;  {
       /* Covariates have to be included here again */    long sec_left, days, hours, minutes;
       cov[1]=1.;    days = (time_sec) / (60*60*24);
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    sec_left = (time_sec) % (60*60*24);
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    hours = (sec_left) / (60*60) ;
       for (k=1; k<=cptcovage;k++)    sec_left = (sec_left) %(60*60);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    minutes = (sec_left) /60;
       for (k=1; k<=cptcovprod;k++)    sec_left = (sec_left) % (60);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     return ascdiff;
   }
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  /*************** powell ************************/
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));              double (*func)(double [])) 
       savm=oldm;  { 
       oldm=newm;    void linmin(double p[], double xi[], int n, double *fret, 
     }                double (*func)(double [])); 
     for(i=1; i<=nlstate+ndeath; i++)    int i,ibig,j; 
       for(j=1;j<=nlstate+ndeath;j++) {    double del,t,*pt,*ptt,*xit;
         po[i][j][h]=newm[i][j];    double fp,fptt;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    double *xits;
          */    int niterf, itmp;
       }  
   } /* end h */    pt=vector(1,n); 
   return po;    ptt=vector(1,n); 
 }    xit=vector(1,n); 
     xits=vector(1,n); 
     *fret=(*func)(p); 
 /*************** log-likelihood *************/    for (j=1;j<=n;j++) pt[j]=p[j]; 
 double func( double *x)    for (*iter=1;;++(*iter)) { 
 {      fp=(*fret); 
   int i, ii, j, k, mi, d, kk;      ibig=0; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      del=0.0; 
   double **out;      last_time=curr_time;
   double sw; /* Sum of weights */      (void) gettimeofday(&curr_time,&tzp);
   double lli; /* Individual log likelihood */      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);
   long ipmx;      /*    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);
   /*extern weight */      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   /* We are differentiating ll according to initial status */      */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/     for (i=1;i<=n;i++) {
   /*for(i=1;i<imx;i++)        printf(" %d %.12f",i, p[i]);
     printf(" %d\n",s[4][i]);        fprintf(ficlog," %d %.12lf",i, p[i]);
   */        fprintf(ficrespow," %.12lf", p[i]);
   cov[1]=1.;      }
       printf("\n");
   for(k=1; k<=nlstate; k++) ll[k]=0.;      fprintf(ficlog,"\n");
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      fprintf(ficrespow,"\n");fflush(ficrespow);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      if(*iter <=3){
     for(mi=1; mi<= wav[i]-1; mi++){        tm = *localtime(&curr_time.tv_sec);
       for (ii=1;ii<=nlstate+ndeath;ii++)        strcpy(strcurr,asctime(&tm));
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /*       asctime_r(&tm,strcurr); */
       for(d=0; d<dh[mi][i]; d++){        forecast_time=curr_time; 
         newm=savm;        itmp = strlen(strcurr);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         for (kk=1; kk<=cptcovage;kk++) {          strcurr[itmp-1]='\0';
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         }        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
                for(niterf=10;niterf<=30;niterf+=10){
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));          tmf = *localtime(&forecast_time.tv_sec);
         savm=oldm;  /*      asctime_r(&tmf,strfor); */
         oldm=newm;          strcpy(strfor,asctime(&tmf));
                  itmp = strlen(strfor);
                  if(strfor[itmp-1]=='\n')
       } /* end mult */          strfor[itmp-1]='\0';
                printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);          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);
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        }
       ipmx +=1;      }
       sw += weight[i];      for (i=1;i<=n;i++) { 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     } /* end of wave */        fptt=(*fret); 
   } /* end of individual */  #ifdef DEBUG
         printf("fret=%lf \n",*fret);
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        fprintf(ficlog,"fret=%lf \n",*fret);
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  #endif
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        printf("%d",i);fflush(stdout);
   return -l;        fprintf(ficlog,"%d",i);fflush(ficlog);
 }        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
           del=fabs(fptt-(*fret)); 
 /*********** Maximum Likelihood Estimation ***************/          ibig=i; 
         } 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  #ifdef DEBUG
 {        printf("%d %.12e",i,(*fret));
   int i,j, iter;        fprintf(ficlog,"%d %.12e",i,(*fret));
   double **xi,*delti;        for (j=1;j<=n;j++) {
   double fret;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   xi=matrix(1,npar,1,npar);          printf(" x(%d)=%.12e",j,xit[j]);
   for (i=1;i<=npar;i++)          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     for (j=1;j<=npar;j++)        }
       xi[i][j]=(i==j ? 1.0 : 0.0);        for(j=1;j<=n;j++) {
   printf("Powell\n");          printf(" p=%.12e",p[j]);
   powell(p,xi,npar,ftol,&iter,&fret,func);          fprintf(ficlog," p=%.12e",p[j]);
         }
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        printf("\n");
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        fprintf(ficlog,"\n");
   #endif
 }      } 
       if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
 /**** Computes Hessian and covariance matrix ***/  #ifdef DEBUG
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        int k[2],l;
 {        k[0]=1;
   double  **a,**y,*x,pd;        k[1]=-1;
   double **hess;        printf("Max: %.12e",(*func)(p));
   int i, j,jk;        fprintf(ficlog,"Max: %.12e",(*func)(p));
   int *indx;        for (j=1;j<=n;j++) {
           printf(" %.12e",p[j]);
   double hessii(double p[], double delta, int theta, double delti[]);          fprintf(ficlog," %.12e",p[j]);
   double hessij(double p[], double delti[], int i, int j);        }
   void lubksb(double **a, int npar, int *indx, double b[]) ;        printf("\n");
   void ludcmp(double **a, int npar, int *indx, double *d) ;        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
   hess=matrix(1,npar,1,npar);          for (j=1;j<=n;j++) {
             ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   printf("\nCalculation of the hessian matrix. Wait...\n");            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   for (i=1;i<=npar;i++){            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     printf("%d",i);fflush(stdout);          }
     hess[i][i]=hessii(p,ftolhess,i,delti);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     /*printf(" %f ",p[i]);*/          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     /*printf(" %lf ",hess[i][i]);*/        }
   }  #endif
    
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++)  {        free_vector(xit,1,n); 
       if (j>i) {        free_vector(xits,1,n); 
         printf(".%d%d",i,j);fflush(stdout);        free_vector(ptt,1,n); 
         hess[i][j]=hessij(p,delti,i,j);        free_vector(pt,1,n); 
         hess[j][i]=hess[i][j];            return; 
         /*printf(" %lf ",hess[i][j]);*/      } 
       }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     }      for (j=1;j<=n;j++) { 
   }        ptt[j]=2.0*p[j]-pt[j]; 
   printf("\n");        xit[j]=p[j]-pt[j]; 
         pt[j]=p[j]; 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      } 
        fptt=(*func)(ptt); 
   a=matrix(1,npar,1,npar);      if (fptt < fp) { 
   y=matrix(1,npar,1,npar);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   x=vector(1,npar);        if (t < 0.0) { 
   indx=ivector(1,npar);          linmin(p,xit,n,fret,func); 
   for (i=1;i<=npar;i++)          for (j=1;j<=n;j++) { 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];            xi[j][ibig]=xi[j][n]; 
   ludcmp(a,npar,indx,&pd);            xi[j][n]=xit[j]; 
           }
   for (j=1;j<=npar;j++) {  #ifdef DEBUG
     for (i=1;i<=npar;i++) x[i]=0;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     x[j]=1;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     lubksb(a,npar,indx,x);          for(j=1;j<=n;j++){
     for (i=1;i<=npar;i++){            printf(" %.12e",xit[j]);
       matcov[i][j]=x[i];            fprintf(ficlog," %.12e",xit[j]);
     }          }
   }          printf("\n");
           fprintf(ficlog,"\n");
   printf("\n#Hessian matrix#\n");  #endif
   for (i=1;i<=npar;i++) {        }
     for (j=1;j<=npar;j++) {      } 
       printf("%.3e ",hess[i][j]);    } 
     }  } 
     printf("\n");  
   }  /**** Prevalence limit (stable prevalence)  ****************/
   
   /* Recompute Inverse */  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   for (i=1;i<=npar;i++)  {
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   ludcmp(a,npar,indx,&pd);       matrix by transitions matrix until convergence is reached */
   
   /*  printf("\n#Hessian matrix recomputed#\n");    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
   for (j=1;j<=npar;j++) {    double **matprod2();
     for (i=1;i<=npar;i++) x[i]=0;    double **out, cov[NCOVMAX], **pmij();
     x[j]=1;    double **newm;
     lubksb(a,npar,indx,x);    double agefin, delaymax=50 ; /* Max number of years to converge */
     for (i=1;i<=npar;i++){  
       y[i][j]=x[i];    for (ii=1;ii<=nlstate+ndeath;ii++)
       printf("%.3e ",y[i][j]);      for (j=1;j<=nlstate+ndeath;j++){
     }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     printf("\n");      }
   }  
   */     cov[1]=1.;
    
   free_matrix(a,1,npar,1,npar);   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   free_matrix(y,1,npar,1,npar);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   free_vector(x,1,npar);      newm=savm;
   free_ivector(indx,1,npar);      /* Covariates have to be included here again */
   free_matrix(hess,1,npar,1,npar);       cov[2]=agefin;
     
         for (k=1; k<=cptcovn;k++) {
 }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
 /*************** hessian matrix ****************/        }
 double hessii( double x[], double delta, int theta, double delti[])        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 {        for (k=1; k<=cptcovprod;k++)
   int i;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   int l=1, lmax=20;  
   double k1,k2;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   double p2[NPARMAX+1];        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   double res;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   double fx;  
   int k=0,kmax=10;      savm=oldm;
   double l1;      oldm=newm;
       maxmax=0.;
   fx=func(x);      for(j=1;j<=nlstate;j++){
   for (i=1;i<=npar;i++) p2[i]=x[i];        min=1.;
   for(l=0 ; l <=lmax; l++){        max=0.;
     l1=pow(10,l);        for(i=1; i<=nlstate; i++) {
     delts=delt;          sumnew=0;
     for(k=1 ; k <kmax; k=k+1){          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       delt = delta*(l1*k);          prlim[i][j]= newm[i][j]/(1-sumnew);
       p2[theta]=x[theta] +delt;          max=FMAX(max,prlim[i][j]);
       k1=func(p2)-fx;          min=FMIN(min,prlim[i][j]);
       p2[theta]=x[theta]-delt;        }
       k2=func(p2)-fx;        maxmin=max-min;
       /*res= (k1-2.0*fx+k2)/delt/delt; */        maxmax=FMAX(maxmax,maxmin);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      }
            if(maxmax < ftolpl){
 #ifdef DEBUG        return prlim;
       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);      }
 #endif    }
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  }
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  
         k=kmax;  /*************** transition probabilities ***************/ 
       }  
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         k=kmax; l=lmax*10.;  {
       }    double s1, s2;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    /*double t34;*/
         delts=delt;    int i,j,j1, nc, ii, jj;
       }  
     }      for(i=1; i<= nlstate; i++){
   }        for(j=1; j<i;j++){
   delti[theta]=delts;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   return res;            /*s2 += param[i][j][nc]*cov[nc];*/
              s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 }  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
           }
 double hessij( double x[], double delti[], int thetai,int thetaj)          ps[i][j]=s2;
 {  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
   int i;        }
   int l=1, l1, lmax=20;        for(j=i+1; j<=nlstate+ndeath;j++){
   double k1,k2,k3,k4,res,fx;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   double p2[NPARMAX+1];            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   int k;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
           }
   fx=func(x);          ps[i][j]=s2;
   for (k=1; k<=2; k++) {        }
     for (i=1;i<=npar;i++) p2[i]=x[i];      }
     p2[thetai]=x[thetai]+delti[thetai]/k;      /*ps[3][2]=1;*/
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      
     k1=func(p2)-fx;      for(i=1; i<= nlstate; i++){
          s1=0;
     p2[thetai]=x[thetai]+delti[thetai]/k;        for(j=1; j<i; j++)
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          s1+=exp(ps[i][j]);
     k2=func(p2)-fx;        for(j=i+1; j<=nlstate+ndeath; j++)
            s1+=exp(ps[i][j]);
     p2[thetai]=x[thetai]-delti[thetai]/k;        ps[i][i]=1./(s1+1.);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        for(j=1; j<i; j++)
     k3=func(p2)-fx;          ps[i][j]= exp(ps[i][j])*ps[i][i];
          for(j=i+1; j<=nlstate+ndeath; j++)
     p2[thetai]=x[thetai]-delti[thetai]/k;          ps[i][j]= exp(ps[i][j])*ps[i][i];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     k4=func(p2)-fx;      } /* end i */
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      
 #ifdef DEBUG      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     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);        for(jj=1; jj<= nlstate+ndeath; jj++){
 #endif          ps[ii][jj]=0;
   }          ps[ii][ii]=1;
   return res;        }
 }      }
       
 /************** Inverse of matrix **************/  
 void ludcmp(double **a, int n, int *indx, double *d)  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
 {  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   int i,imax,j,k;  /*         printf("ddd %lf ",ps[ii][jj]); */
   double big,dum,sum,temp;  /*       } */
   double *vv;  /*       printf("\n "); */
    /*        } */
   vv=vector(1,n);  /*        printf("\n ");printf("%lf ",cov[2]); */
   *d=1.0;         /*
   for (i=1;i<=n;i++) {        for(i=1; i<= npar; i++) printf("%f ",x[i]);
     big=0.0;        goto end;*/
     for (j=1;j<=n;j++)      return ps;
       if ((temp=fabs(a[i][j])) > big) big=temp;  }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  
     vv[i]=1.0/big;  /**************** Product of 2 matrices ******************/
   }  
   for (j=1;j<=n;j++) {  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     for (i=1;i<j;i++) {  {
       sum=a[i][j];    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       a[i][j]=sum;    /* in, b, out are matrice of pointers which should have been initialized 
     }       before: only the contents of out is modified. The function returns
     big=0.0;       a pointer to pointers identical to out */
     for (i=j;i<=n;i++) {    long i, j, k;
       sum=a[i][j];    for(i=nrl; i<= nrh; i++)
       for (k=1;k<j;k++)      for(k=ncolol; k<=ncoloh; k++)
         sum -= a[i][k]*a[k][j];        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       a[i][j]=sum;          out[i][k] +=in[i][j]*b[j][k];
       if ( (dum=vv[i]*fabs(sum)) >= big) {  
         big=dum;    return out;
         imax=i;  }
       }  
     }  
     if (j != imax) {  /************* Higher Matrix Product ***************/
       for (k=1;k<=n;k++) {  
         dum=a[imax][k];  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         a[imax][k]=a[j][k];  {
         a[j][k]=dum;    /* Computes the transition matrix starting at age 'age' over 
       }       'nhstepm*hstepm*stepm' months (i.e. until
       *d = -(*d);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       vv[imax]=vv[j];       nhstepm*hstepm matrices. 
     }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     indx[j]=imax;       (typically every 2 years instead of every month which is too big 
     if (a[j][j] == 0.0) a[j][j]=TINY;       for the memory).
     if (j != n) {       Model is determined by parameters x and covariates have to be 
       dum=1.0/(a[j][j]);       included manually here. 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }       */
   }  
   free_vector(vv,1,n);  /* Doesn't work */    int i, j, d, h, k;
 ;    double **out, cov[NCOVMAX];
 }    double **newm;
   
 void lubksb(double **a, int n, int *indx, double b[])    /* Hstepm could be zero and should return the unit matrix */
 {    for (i=1;i<=nlstate+ndeath;i++)
   int i,ii=0,ip,j;      for (j=1;j<=nlstate+ndeath;j++){
   double sum;        oldm[i][j]=(i==j ? 1.0 : 0.0);
          po[i][j][0]=(i==j ? 1.0 : 0.0);
   for (i=1;i<=n;i++) {      }
     ip=indx[i];    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     sum=b[ip];    for(h=1; h <=nhstepm; h++){
     b[ip]=b[i];      for(d=1; d <=hstepm; d++){
     if (ii)        newm=savm;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        /* Covariates have to be included here again */
     else if (sum) ii=i;        cov[1]=1.;
     b[i]=sum;        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]]];
   for (i=n;i>=1;i--) {        for (k=1; k<=cptcovage;k++)
     sum=b[i];          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        for (k=1; k<=cptcovprod;k++)
     b[i]=sum/a[i][i];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   }  
 }  
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
 /************ Frequencies ********************/        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
 {  /* Some frequencies */                     pmij(pmmij,cov,ncovmodel,x,nlstate));
          savm=oldm;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        oldm=newm;
   double ***freq; /* Frequencies */      }
   double *pp;      for(i=1; i<=nlstate+ndeath; i++)
   double pos, k2, dateintsum=0,k2cpt=0;        for(j=1;j<=nlstate+ndeath;j++) {
   FILE *ficresp;          po[i][j][h]=newm[i][j];
   char fileresp[FILENAMELENGTH];          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
             */
   pp=vector(1,nlstate);        }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    } /* end h */
   strcpy(fileresp,"p");    return po;
   strcat(fileresp,fileres);  }
   if((ficresp=fopen(fileresp,"w"))==NULL) {  
     printf("Problem with prevalence resultfile: %s\n", fileresp);  
     exit(0);  /*************** log-likelihood *************/
   }  double func( double *x)
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  {
   j1=0;    int i, ii, j, k, mi, d, kk;
      double l, ll[NLSTATEMAX], cov[NCOVMAX];
   j=cptcoveff;    double **out;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    double sw; /* Sum of weights */
      double lli; /* Individual log likelihood */
   for(k1=1; k1<=j;k1++){    int s1, s2;
     for(i1=1; i1<=ncodemax[k1];i1++){    double bbh, survp;
       j1++;    long ipmx;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    /*extern weight */
         scanf("%d", i);*/    /* We are differentiating ll according to initial status */
       for (i=-1; i<=nlstate+ndeath; i++)      /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         for (jk=-1; jk<=nlstate+ndeath; jk++)      /*for(i=1;i<imx;i++) 
           for(m=agemin; m <= agemax+3; m++)      printf(" %d\n",s[4][i]);
             freq[i][jk][m]=0;    */
          cov[1]=1.;
       dateintsum=0;  
       k2cpt=0;    for(k=1; k<=nlstate; k++) ll[k]=0.;
       for (i=1; i<=imx; i++) {  
         bool=1;    if(mle==1){
         if  (cptcovn>0) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           for (z1=1; z1<=cptcoveff; z1++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        for(mi=1; mi<= wav[i]-1; mi++){
               bool=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
         }            for (j=1;j<=nlstate+ndeath;j++){
         if (bool==1) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(m=firstpass; m<=lastpass; m++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             k2=anint[m][i]+(mint[m][i]/12.);            }
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          for(d=0; d<dh[mi][i]; d++){
               if(agev[m][i]==0) agev[m][i]=agemax+1;            newm=savm;
               if(agev[m][i]==1) agev[m][i]=agemax+2;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
               if (m<lastpass) {            for (kk=1; kk<=cptcovage;kk++) {
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];            }
               }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {            savm=oldm;
                 dateintsum=dateintsum+k2;            oldm=newm;
                 k2cpt++;          } /* end mult */
               }        
             }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           }          /* But now since version 0.9 we anticipate for bias at large stepm.
         }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       }           * (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
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
       if  (cptcovn>0) {           * probability in order to take into account the bias as a fraction of the way
         fprintf(ficresp, "\n#********** Variable ");           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);           * -stepm/2 to stepm/2 .
         fprintf(ficresp, "**********\n#");           * For stepm=1 the results are the same as for previous versions of Imach.
       }           * For stepm > 1 the results are less biased than in previous versions. 
       for(i=1; i<=nlstate;i++)           */
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          s1=s[mw[mi][i]][i];
       fprintf(ficresp, "\n");          s2=s[mw[mi+1][i]][i];
                bbh=(double)bh[mi][i]/(double)stepm; 
       for(i=(int)agemin; i <= (int)agemax+3; i++){          /* bias bh is positive if real duration
         if(i==(int)agemax+3)           * is higher than the multiple of stepm and negative otherwise.
           printf("Total");           */
         else          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           printf("Age %d", i);          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 then the contribution
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)               to the likelihood is the probability to die between last step unit time and current 
             pp[jk] += freq[jk][m][i];               step unit time, which is also equal to probability to die before dh 
         }               minus probability to die before dh-stepm . 
         for(jk=1; jk <=nlstate ; jk++){               In version up to 0.92 likelihood was computed
           for(m=-1, pos=0; m <=0 ; m++)          as if date of death was unknown. Death was treated as any other
             pos += freq[jk][m][i];          health state: the date of the interview describes the actual state
           if(pp[jk]>=1.e-10)          and not the date of a change in health state. The former idea was
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          to consider that at each interview the state was recorded
           else          (healthy, disable or death) and IMaCh was corrected; but when we
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          introduced the exact date of death then we should have modified
         }          the contribution of an exact death to the likelihood. This new
           contribution is smaller and very dependent of the step unit
         for(jk=1; jk <=nlstate ; jk++){          stepm. It is no more the probability to die between last interview
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          and month of death but the probability to survive from last
             pp[jk] += freq[jk][m][i];          interview up to one month before death multiplied by the
         }          probability to die within a month. Thanks to Chris
           Jackson for correcting this bug.  Former versions increased
         for(jk=1,pos=0; jk <=nlstate ; jk++)          mortality artificially. The bad side is that we add another loop
           pos += pp[jk];          which slows down the processing. The difference can be up to 10%
         for(jk=1; jk <=nlstate ; jk++){          lower mortality.
           if(pos>=1.e-5)            */
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            lli=log(out[s1][s2] - savm[s1][s2]);
           else          }else{
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           if( i <= (int) agemax){            /*  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(pos>=1.e-5){          } 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
               probs[i][jk][j1]= pp[jk]/pos;          /*if(lli ==000.0)*/
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
             }          ipmx +=1;
             else          sw += weight[i];
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           }        } /* end of wave */
         }      } /* end of individual */
            }  else if(mle==2){
         for(jk=-1; jk <=nlstate+ndeath; jk++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           for(m=-1; m <=nlstate+ndeath; m++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        for(mi=1; mi<= wav[i]-1; mi++){
         if(i <= (int) agemax)          for (ii=1;ii<=nlstate+ndeath;ii++)
           fprintf(ficresp,"\n");            for (j=1;j<=nlstate+ndeath;j++){
         printf("\n");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     }            }
   }          for(d=0; d<=dh[mi][i]; d++){
   dateintmean=dateintsum/k2cpt;            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fclose(ficresp);            for (kk=1; kk<=cptcovage;kk++) {
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   free_vector(pp,1,nlstate);            }
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* End of Freq */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }            savm=oldm;
             oldm=newm;
 /************ Prevalence ********************/          } /* end mult */
 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)        
 {  /* Some frequencies */          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          bbh=(double)bh[mi][i]/(double)stepm; 
   double ***freq; /* 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 */
   double *pp;          ipmx +=1;
   double pos, k2;          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   pp=vector(1,nlstate);        } /* end of wave */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      } /* end of individual */
      }  else if(mle==3){  /* exponential inter-extrapolation */
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   j1=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
   j=cptcoveff;          for (ii=1;ii<=nlstate+ndeath;ii++)
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  for(k1=1; k1<=j;k1++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i1=1; i1<=ncodemax[k1];i1++){            }
       j1++;          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
       for (i=-1; i<=nlstate+ndeath; i++)              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for (jk=-1; jk<=nlstate+ndeath; jk++)              for (kk=1; kk<=cptcovage;kk++) {
           for(m=agemin; m <= agemax+3; m++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             freq[i][jk][m]=0;            }
                  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));
         bool=1;            savm=oldm;
         if  (cptcovn>0) {            oldm=newm;
           for (z1=1; z1<=cptcoveff; z1++)          } /* end mult */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        
               bool=0;          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
         if (bool==1) {          bbh=(double)bh[mi][i]/(double)stepm; 
           for(m=firstpass; m<=lastpass; m++){          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 */
             k2=anint[m][i]+(mint[m][i]/12.);          ipmx +=1;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          sw += weight[i];
               if(agev[m][i]==0) agev[m][i]=agemax+1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
               if(agev[m][i]==1) agev[m][i]=agemax+2;        } /* end of wave */
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];      } /* end of individual */
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */    }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++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
         for(i=(int)agemin; i <= (int)agemax+3; i++){            for (j=1;j<=nlstate+ndeath;j++){
           for(jk=1; jk <=nlstate ; jk++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
               pp[jk] += freq[jk][m][i];            }
           }          for(d=0; d<dh[mi][i]; d++){
           for(jk=1; jk <=nlstate ; jk++){            newm=savm;
             for(m=-1, pos=0; m <=0 ; m++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             pos += freq[jk][m][i];            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){          if( s2 > nlstate){ 
                probs[i][jk][j1]= pp[jk]/pos;            lli=log(out[s1][s2] - savm[s1][s2]);
              }          }else{
            }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
          }          }
                    ipmx +=1;
         }          sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
          } /* end of wave */
        } /* end of individual */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   free_vector(pp,1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 }  /* End of Freq */        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
 /************* Waves Concatenation ***************/            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 {            }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          for(d=0; d<dh[mi][i]; d++){
      Death is a valid wave (if date is known).            newm=savm;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            for (kk=1; kk<=cptcovage;kk++) {
      and mw[mi+1][i]. dh depends on stepm.              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      */            }
           
   int i, mi, m;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      double sum=0., jmean=0.;*/            savm=oldm;
             oldm=newm;
   int j, k=0,jk, ju, jl;          } /* end mult */
   double sum=0.;        
   jmin=1e+5;          s1=s[mw[mi][i]][i];
   jmax=-1;          s2=s[mw[mi+1][i]][i];
   jmean=0.;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   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)    } /* End of if */
         break;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       else    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         m++;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     }/* end while */    return -l;
     if (s[m][i] > nlstate){  }
       mi++;     /* Death is another wave */  
       /* if(mi==0)  never been interviewed correctly before death */  /*************** log-likelihood *************/
          /* Only death is a correct wave */  double funcone( double *x)
       mw[mi][i]=m;  {
     }    /* Same as likeli but slower because of a lot of printf and if */
     int i, ii, j, k, mi, d, kk;
     wav[i]=mi;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     if(mi==0)    double **out;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    double lli; /* Individual log likelihood */
   }    double llt;
     int s1, s2;
   for(i=1; i<=imx; i++){    double bbh, survp;
     for(mi=1; mi<wav[i];mi++){    /*extern weight */
       if (stepm <=0)    /* We are differentiating ll according to initial status */
         dh[mi][i]=1;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       else{    /*for(i=1;i<imx;i++) 
         if (s[mw[mi+1][i]][i] > nlstate) {      printf(" %d\n",s[4][i]);
           if (agedc[i] < 2*AGESUP) {    */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    cov[1]=1.;
           if(j==0) j=1;  /* Survives at least one month after exam */  
           k=k+1;    for(k=1; k<=nlstate; k++) ll[k]=0.;
           if (j >= jmax) jmax=j;  
           if (j <= jmin) jmin=j;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           sum=sum+j;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      for(mi=1; mi<= wav[i]-1; mi++){
           }        for (ii=1;ii<=nlstate+ndeath;ii++)
         }          for (j=1;j<=nlstate+ndeath;j++){
         else{            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           k=k+1;          }
           if (j >= jmax) jmax=j;        for(d=0; d<dh[mi][i]; d++){
           else if (j <= jmin)jmin=j;          newm=savm;
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           sum=sum+j;          for (kk=1; kk<=cptcovage;kk++) {
         }            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         jk= j/stepm;          }
         jl= j -jk*stepm;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         ju= j -(jk+1)*stepm;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if(jl <= -ju)          savm=oldm;
           dh[mi][i]=jk;          oldm=newm;
         else        } /* end mult */
           dh[mi][i]=jk+1;        
         if(dh[mi][i]==0)        s1=s[mw[mi][i]][i];
           dh[mi][i]=1; /* At least one step */        s2=s[mw[mi+1][i]][i];
       }        bbh=(double)bh[mi][i]/(double)stepm; 
     }        /* bias is positive if real duration
   }         * is higher than the multiple of stepm and negative otherwise.
   jmean=sum/k;         */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        if( s2 > nlstate && (mle <5) ){  /* Jackson */
  }          lli=log(out[s1][s2] - savm[s1][s2]);
 /*********** Tricode ****************************/        } else if (mle==1){
 void tricode(int *Tvar, int **nbcode, int imx)          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 {        } else if(mle==2){
   int Ndum[20],ij=1, k, j, i;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   int cptcode=0;        } else if(mle==3){  /* exponential inter-extrapolation */
   cptcoveff=0;          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
          } else if (mle==4){  /* mle=4 no inter-extrapolation */
   for (k=0; k<19; k++) Ndum[k]=0;          lli=log(out[s1][s2]); /* Original formula */
   for (k=1; k<=7; k++) ncodemax[k]=0;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
           lli=log(out[s1][s2]); /* Original formula */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        } /* End of if */
     for (i=1; i<=imx; i++) {        ipmx +=1;
       ij=(int)(covar[Tvar[j]][i]);        sw += weight[i];
       Ndum[ij]++;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  /*       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 (ij > cptcode) cptcode=ij;        if(globpr){
     }          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
    %10.6f %10.6f %10.6f ", \
     for (i=0; i<=cptcode; i++) {                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       if(Ndum[i]!=0) ncodemax[j]++;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     ij=1;            llt +=ll[k]*gipmx/gsw;
             fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
     for (i=1; i<=ncodemax[j]; i++) {          fprintf(ficresilk," %10.6f\n", -llt);
       for (k=0; k<=19; k++) {        }
         if (Ndum[k] != 0) {      } /* end of wave */
           nbcode[Tvar[j]][ij]=k;    } /* end of individual */
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           ij++;    /* 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 */
         if (ij > ncodemax[j]) break;    if(globpr==0){ /* First time we count the contributions and weights */
       }        gipmx=ipmx;
     }      gsw=sw;
   }      }
     return -l;
  for (k=0; k<19; k++) Ndum[k]=0;  }
   
  for (i=1; i<=ncovmodel-2; i++) {  
       ij=Tvar[i];  /*************** function likelione ***********/
       Ndum[ij]++;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     }  {
     /* This routine should help understanding what is done with 
  ij=1;       the selection of individuals/waves and
  for (i=1; i<=10; i++) {       to check the exact contribution to the likelihood.
    if((Ndum[i]!=0) && (i<=ncovcol)){       Plotting could be done.
      Tvaraff[ij]=i;     */
      ij++;    int k;
    }  
  }    if(*globpri !=0){ /* Just counts and sums, no printings */
        strcpy(fileresilk,"ilk"); 
     cptcoveff=ij-1;      strcat(fileresilk,fileres);
 }      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", fileresilk);
 /*********** Health Expectancies ****************/        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
 {      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   /* Health expectancies */      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   int i, j, nhstepm, hstepm, h, nstepm;      for(k=1; k<=nlstate; k++) 
   double age, agelim, hf;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   double ***p3mat;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
      }
   fprintf(ficreseij,"# Health expectancies\n");  
   fprintf(ficreseij,"# Age");    *fretone=(*funcone)(p);
   for(i=1; i<=nlstate;i++)    if(*globpri !=0){
     for(j=1; j<=nlstate;j++)      fclose(ficresilk);
       fprintf(ficreseij," %1d-%1d",i,j);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   fprintf(ficreseij,"\n");      fflush(fichtm); 
     } 
   if(estepm < stepm){    return;
     printf ("Problem %d lower than %d\n",estepm, stepm);  }
   }  
   else  hstepm=estepm;    
   /* We compute the life expectancy from trapezoids spaced every estepm months  /*********** Maximum Likelihood Estimation ***************/
    * This is mainly to measure the difference between two models: for example  
    * if stepm=24 months pijx are given only every 2 years and by summing them  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
    * we are calculating an estimate of the Life Expectancy assuming a linear  {
    * progression inbetween and thus overestimating or underestimating according    int i,j, iter;
    * to the curvature of the survival function. If, for the same date, we    double **xi;
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    double fret;
    * to compare the new estimate of Life expectancy with the same linear    double fretone; /* Only one call to likelihood */
    * hypothesis. A more precise result, taking into account a more precise    /*  char filerespow[FILENAMELENGTH];*/
    * curvature will be obtained if estepm is as small as stepm. */    xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
   /* For example we decided to compute the life expectancy with the smallest unit */      for (j=1;j<=npar;j++)
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        xi[i][j]=(i==j ? 1.0 : 0.0);
      nhstepm is the number of hstepm from age to agelim    printf("Powell\n");  fprintf(ficlog,"Powell\n");
      nstepm is the number of stepm from age to agelin.    strcpy(filerespow,"pow"); 
      Look at hpijx to understand the reason of that which relies in memory size    strcat(filerespow,fileres);
      and note for a fixed period like estepm months */    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      printf("Problem with resultfile: %s\n", filerespow);
      survival function given by stepm (the optimization length). Unfortunately it      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
      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    fprintf(ficrespow,"# Powell\n# iter -2*LL");
      results. So we changed our mind and took the option of the best precision.    for (i=1;i<=nlstate;i++)
   */      for(j=1;j<=nlstate+ndeath;j++)
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     fprintf(ficrespow,"\n");
   agelim=AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    powell(p,xi,npar,ftol,&iter,&fret,func);
     /* nhstepm age range expressed in number of stepm */  
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    fclose(ficrespow);
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     /* if (stepm >= YEARM) hstepm=1;*/    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     /* 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);    /**** Computes Hessian and covariance matrix ***/
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     for(i=1; i<=nlstate;i++)  {
       for(j=1; j<=nlstate;j++)    double  **a,**y,*x,pd;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    double **hess;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    int i, j,jk;
           /* 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]);*/    int *indx;
         }  
     fprintf(ficreseij,"%3.0f",age );    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     for(i=1; i<=nlstate;i++)    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
       for(j=1; j<=nlstate;j++){    void lubksb(double **a, int npar, int *indx, double b[]) ;
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);    void ludcmp(double **a, int npar, int *indx, double *d) ;
       }    double gompertz(double p[]);
     fprintf(ficreseij,"\n");    hess=matrix(1,npar,1,npar);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   }    printf("\nCalculation of the hessian matrix. Wait...\n");
 }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
 /************ Variance ******************/      printf("%d",i);fflush(stdout);
 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, int estepm)      fprintf(ficlog,"%d",i);fflush(ficlog);
 {     
   /* Variance of health expectancies */       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      
   double **newm;      /*  printf(" %f ",p[i]);
   double **dnewm,**doldm;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   int i, j, nhstepm, hstepm, h, nstepm ;    }
   int k, cptcode;    
   double *xp;    for (i=1;i<=npar;i++) {
   double **gp, **gm;      for (j=1;j<=npar;j++)  {
   double ***gradg, ***trgradg;        if (j>i) { 
   double ***p3mat;          printf(".%d%d",i,j);fflush(stdout);
   double age,agelim, hf;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   int theta;          hess[i][j]=hessij(p,delti,i,j,func,npar);
           
    fprintf(ficresvij,"# Covariances of life expectancies\n");          hess[j][i]=hess[i][j];    
   fprintf(ficresvij,"# Age");          /*printf(" %lf ",hess[i][j]);*/
   for(i=1; i<=nlstate;i++)        }
     for(j=1; j<=nlstate;j++)      }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    }
   fprintf(ficresvij,"\n");    printf("\n");
     fprintf(ficlog,"\n");
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   doldm=matrix(1,nlstate,1,nlstate);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
      
   if(estepm < stepm){    a=matrix(1,npar,1,npar);
     printf ("Problem %d lower than %d\n",estepm, stepm);    y=matrix(1,npar,1,npar);
   }    x=vector(1,npar);
   else  hstepm=estepm;      indx=ivector(1,npar);
   /* For example we decided to compute the life expectancy with the smallest unit */    for (i=1;i<=npar;i++)
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
      nhstepm is the number of hstepm from age to agelim    ludcmp(a,npar,indx,&pd);
      nstepm is the number of stepm from age to agelin.  
      Look at hpijx to understand the reason of that which relies in memory size    for (j=1;j<=npar;j++) {
      and note for a fixed period like k years */      for (i=1;i<=npar;i++) x[i]=0;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      x[j]=1;
      survival function given by stepm (the optimization length). Unfortunately it      lubksb(a,npar,indx,x);
      means that if the survival funtion is printed only each two years of age and if      for (i=1;i<=npar;i++){ 
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        matcov[i][j]=x[i];
      results. So we changed our mind and took the option of the best precision.      }
   */    }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  
   agelim = AGESUP;    printf("\n#Hessian matrix#\n");
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    fprintf(ficlog,"\n#Hessian matrix#\n");
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    for (i=1;i<=npar;i++) { 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      for (j=1;j<=npar;j++) { 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        printf("%.3e ",hess[i][j]);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        fprintf(ficlog,"%.3e ",hess[i][j]);
     gp=matrix(0,nhstepm,1,nlstate);      }
     gm=matrix(0,nhstepm,1,nlstate);      printf("\n");
       fprintf(ficlog,"\n");
     for(theta=1; theta <=npar; theta++){    }
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    /* Recompute Inverse */
       }    for (i=1;i<=npar;i++)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    ludcmp(a,npar,indx,&pd);
   
       if (popbased==1) {    /*  printf("\n#Hessian matrix recomputed#\n");
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];    for (j=1;j<=npar;j++) {
       }      for (i=1;i<=npar;i++) x[i]=0;
        x[j]=1;
       for(j=1; j<= nlstate; j++){      lubksb(a,npar,indx,x);
         for(h=0; h<=nhstepm; h++){      for (i=1;i<=npar;i++){ 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        y[i][j]=x[i];
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        printf("%.3e ",y[i][j]);
         }        fprintf(ficlog,"%.3e ",y[i][j]);
       }      }
          printf("\n");
       for(i=1; i<=npar; i++) /* Computes gradient */      fprintf(ficlog,"\n");
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
      free_matrix(a,1,npar,1,npar);
       if (popbased==1) {    free_matrix(y,1,npar,1,npar);
         for(i=1; i<=nlstate;i++)    free_vector(x,1,npar);
           prlim[i][i]=probs[(int)age][i][ij];    free_ivector(indx,1,npar);
       }    free_matrix(hess,1,npar,1,npar);
   
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){  }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  /*************** hessian matrix ****************/
         }  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
       }  {
     int i;
       for(j=1; j<= nlstate; j++)    int l=1, lmax=20;
         for(h=0; h<=nhstepm; h++){    double k1,k2;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    double p2[NPARMAX+1];
         }    double res;
     } /* End theta */    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     double fx;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    int k=0,kmax=10;
     double l1;
     for(h=0; h<=nhstepm; h++)  
       for(j=1; j<=nlstate;j++)    fx=func(x);
         for(theta=1; theta <=npar; theta++)    for (i=1;i<=npar;i++) p2[i]=x[i];
           trgradg[h][j][theta]=gradg[h][theta][j];    for(l=0 ; l <=lmax; l++){
       l1=pow(10,l);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      delts=delt;
     for(i=1;i<=nlstate;i++)      for(k=1 ; k <kmax; k=k+1){
       for(j=1;j<=nlstate;j++)        delt = delta*(l1*k);
         vareij[i][j][(int)age] =0.;        p2[theta]=x[theta] +delt;
         k1=func(p2)-fx;
     for(h=0;h<=nhstepm;h++){        p2[theta]=x[theta]-delt;
       for(k=0;k<=nhstepm;k++){        k2=func(p2)-fx;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        /*res= (k1-2.0*fx+k2)/delt/delt; */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         for(i=1;i<=nlstate;i++)        
           for(j=1;j<=nlstate;j++)  #ifdef DEBUG
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     }  #endif
         /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     fprintf(ficresvij,"%.0f ",age );        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     for(i=1; i<=nlstate;i++)          k=kmax;
       for(j=1; j<=nlstate;j++){        }
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       }          k=kmax; l=lmax*10.;
     fprintf(ficresvij,"\n");        }
     free_matrix(gp,0,nhstepm,1,nlstate);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     free_matrix(gm,0,nhstepm,1,nlstate);          delts=delt;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        }
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
   } /* End age */    delti[theta]=delts;
      return res; 
   free_vector(xp,1,npar);    
   free_matrix(doldm,1,nlstate,1,npar);  }
   free_matrix(dnewm,1,nlstate,1,nlstate);  
   double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 }  {
     int i;
 /************ Variance of prevlim ******************/    int l=1, l1, lmax=20;
 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)    double k1,k2,k3,k4,res,fx;
 {    double p2[NPARMAX+1];
   /* Variance of prevalence limit */    int k;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;    fx=func(x);
   double **dnewm,**doldm;    for (k=1; k<=2; k++) {
   int i, j, nhstepm, hstepm;      for (i=1;i<=npar;i++) p2[i]=x[i];
   int k, cptcode;      p2[thetai]=x[thetai]+delti[thetai]/k;
   double *xp;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double *gp, *gm;      k1=func(p2)-fx;
   double **gradg, **trgradg;    
   double age,agelim;      p2[thetai]=x[thetai]+delti[thetai]/k;
   int theta;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
          k2=func(p2)-fx;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    
   fprintf(ficresvpl,"# Age");      p2[thetai]=x[thetai]-delti[thetai]/k;
   for(i=1; i<=nlstate;i++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       fprintf(ficresvpl," %1d-%1d",i,i);      k3=func(p2)-fx;
   fprintf(ficresvpl,"\n");    
       p2[thetai]=x[thetai]-delti[thetai]/k;
   xp=vector(1,npar);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   dnewm=matrix(1,nlstate,1,npar);      k4=func(p2)-fx;
   doldm=matrix(1,nlstate,1,nlstate);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
    #ifdef DEBUG
   hstepm=1*YEARM; /* Every year of age */      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);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      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);
   agelim = AGESUP;  #endif
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    return res;
     if (stepm >= YEARM) hstepm=1;  }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
     gradg=matrix(1,npar,1,nlstate);  /************** Inverse of matrix **************/
     gp=vector(1,nlstate);  void ludcmp(double **a, int n, int *indx, double *d) 
     gm=vector(1,nlstate);  { 
     int i,imax,j,k; 
     for(theta=1; theta <=npar; theta++){    double big,dum,sum,temp; 
       for(i=1; i<=npar; i++){ /* Computes gradient */    double *vv; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);   
       }    vv=vector(1,n); 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    *d=1.0; 
       for(i=1;i<=nlstate;i++)    for (i=1;i<=n;i++) { 
         gp[i] = prlim[i][i];      big=0.0; 
          for (j=1;j<=n;j++) 
       for(i=1; i<=npar; i++) /* Computes gradient */        if ((temp=fabs(a[i][j])) > big) big=temp; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      vv[i]=1.0/big; 
       for(i=1;i<=nlstate;i++)    } 
         gm[i] = prlim[i][i];    for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
       for(i=1;i<=nlstate;i++)        sum=a[i][j]; 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     } /* End theta */        a[i][j]=sum; 
       } 
     trgradg =matrix(1,nlstate,1,npar);      big=0.0; 
       for (i=j;i<=n;i++) { 
     for(j=1; j<=nlstate;j++)        sum=a[i][j]; 
       for(theta=1; theta <=npar; theta++)        for (k=1;k<j;k++) 
         trgradg[j][theta]=gradg[theta][j];          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
     for(i=1;i<=nlstate;i++)        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       varpl[i][(int)age] =0.;          big=dum; 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          imax=i; 
     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 */      if (j != imax) { 
         for (k=1;k<=n;k++) { 
     fprintf(ficresvpl,"%.0f ",age );          dum=a[imax][k]; 
     for(i=1; i<=nlstate;i++)          a[imax][k]=a[j][k]; 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          a[j][k]=dum; 
     fprintf(ficresvpl,"\n");        } 
     free_vector(gp,1,nlstate);        *d = -(*d); 
     free_vector(gm,1,nlstate);        vv[imax]=vv[j]; 
     free_matrix(gradg,1,npar,1,nlstate);      } 
     free_matrix(trgradg,1,nlstate,1,npar);      indx[j]=imax; 
   } /* End age */      if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
   free_vector(xp,1,npar);        dum=1.0/(a[j][j]); 
   free_matrix(doldm,1,nlstate,1,npar);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   free_matrix(dnewm,1,nlstate,1,nlstate);      } 
     } 
 }    free_vector(vv,1,n);  /* Doesn't work */
   ;
 /************ Variance of one-step probabilities  ******************/  } 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)  
 {  void lubksb(double **a, int n, int *indx, double b[]) 
   int i, j;  { 
   int k=0, cptcode;    int i,ii=0,ip,j; 
   double **dnewm,**doldm;    double sum; 
   double *xp;   
   double *gp, *gm;    for (i=1;i<=n;i++) { 
   double **gradg, **trgradg;      ip=indx[i]; 
   double age,agelim, cov[NCOVMAX];      sum=b[ip]; 
   int theta;      b[ip]=b[i]; 
   char fileresprob[FILENAMELENGTH];      if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   strcpy(fileresprob,"prob");      else if (sum) ii=i; 
   strcat(fileresprob,fileres);      b[i]=sum; 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    } 
     printf("Problem with resultfile: %s\n", fileresprob);    for (i=n;i>=1;i--) { 
   }      sum=b[i]; 
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
        b[i]=sum/a[i][i]; 
     } 
   xp=vector(1,npar);  } 
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));  /************ 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)
   cov[1]=1;  {  /* Some frequencies */
   for (age=bage; age<=fage; age ++){    
     cov[2]=age;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     gradg=matrix(1,npar,1,9);    int first;
     trgradg=matrix(1,9,1,npar);    double ***freq; /* Frequencies */
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    double *pp, **prop;
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    double pos,posprop, k2, dateintsum=0,k2cpt=0;
        FILE *ficresp;
     for(theta=1; theta <=npar; theta++){    char fileresp[FILENAMELENGTH];
       for(i=1; i<=npar; i++)    
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    pp=vector(1,nlstate);
          prop=matrix(1,nlstate,iagemin,iagemax+3);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    strcpy(fileresp,"p");
        strcat(fileresp,fileres);
       k=0;    if((ficresp=fopen(fileresp,"w"))==NULL) {
       for(i=1; i<= (nlstate+ndeath); i++){      printf("Problem with prevalence resultfile: %s\n", fileresp);
         for(j=1; j<=(nlstate+ndeath);j++){      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
            k=k+1;      exit(0);
           gp[k]=pmmij[i][j];    }
         }    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
       }    j1=0;
     
       for(i=1; i<=npar; i++)    j=cptcoveff;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      
     first=1;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  
       k=0;    for(k1=1; k1<=j;k1++){
       for(i=1; i<=(nlstate+ndeath); i++){      for(i1=1; i1<=ncodemax[k1];i1++){
         for(j=1; j<=(nlstate+ndeath);j++){        j1++;
           k=k+1;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           gm[k]=pmmij[i][j];          scanf("%d", i);*/
         }        for (i=-1; i<=nlstate+ndeath; i++)  
       }          for (jk=-1; jk<=nlstate+ndeath; jk++)  
                  for(m=iagemin; m <= iagemax+3; m++)
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)              freq[i][jk][m]=0;
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    
     }      for (i=1; i<=nlstate; i++)  
         for(m=iagemin; m <= iagemax+3; m++)
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          prop[i][m]=0;
       for(theta=1; theta <=npar; theta++)        
       trgradg[j][theta]=gradg[theta][j];        dateintsum=0;
          k2cpt=0;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        for (i=1; i<=imx; i++) {
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          bool=1;
           if  (cptcovn>0) {
      pmij(pmmij,cov,ncovmodel,x,nlstate);            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
      k=0;                bool=0;
      for(i=1; i<=(nlstate+ndeath); i++){          }
        for(j=1; j<=(nlstate+ndeath);j++){          if (bool==1){
          k=k+1;            for(m=firstpass; m<=lastpass; m++){
          gm[k]=pmmij[i][j];              k2=anint[m][i]+(mint[m][i]/12.);
         }              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
      }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                      if(agev[m][i]==1) agev[m][i]=iagemax+2;
      /*printf("\n%d ",(int)age);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){                if (m<lastpass) {
                          freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                   freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));                }
      }*/                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   fprintf(ficresprob,"\n%d ",(int)age);                  dateintsum=dateintsum+k2;
                   k2cpt++;
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){                }
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);                /*}*/
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);            }
   }          }
         }
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));         
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        if  (cptcovn>0) {
 }          fprintf(ficresp, "\n#********** Variable "); 
  free_vector(xp,1,npar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 fclose(ficresprob);          fprintf(ficresp, "**********\n#");
         }
 }        for(i=1; i<=nlstate;i++) 
           fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 /******************* Printing html file ***********/        fprintf(ficresp, "\n");
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \        
  int lastpass, int stepm, int weightopt, char model[],\        for(i=iagemin; i <= iagemax+3; i++){
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \          if(i==iagemax+3){
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\            fprintf(ficlog,"Total");
  char version[], int popforecast, int estepm ){          }else{
   int jj1, k1, i1, cpt;            if(first==1){
   FILE *fichtm;              first=0;
   /*char optionfilehtm[FILENAMELENGTH];*/              printf("See log file for details...\n");
             }
   strcpy(optionfilehtm,optionfile);            fprintf(ficlog,"Age %d", i);
   strcat(optionfilehtm,".htm");          }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          for(jk=1; jk <=nlstate ; jk++){
     printf("Problem with %s \n",optionfilehtm), exit(0);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   }              pp[jk] += freq[jk][m][i]; 
           }
  fprintf(fichtm,"<body> <font size=\"2\">Imach, Version %s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n          for(jk=1; jk <=nlstate ; jk++){
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n            for(m=-1, pos=0; m <=0 ; m++)
 \n              pos += freq[jk][m][i];
 Total number of observations=%d <br>\n            if(pp[jk]>=1.e-10){
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n              if(first==1){
 <hr  size=\"2\" color=\"#EC5E5E\">              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
  <ul><li>Outputs files<br>\n              }
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n            }else{
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n              if(first==1)
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,estepm);            }
           }
  fprintf(fichtm,"\n  
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n          for(jk=1; jk <=nlstate ; jk++){
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n              pp[jk] += freq[jk][m][i];
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);          }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
  if(popforecast==1) fprintf(fichtm,"\n            pos += pp[jk];
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n            posprop += prop[jk][i];
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n          }
         <br>",fileres,fileres,fileres,fileres);          for(jk=1; jk <=nlstate ; jk++){
  else            if(pos>=1.e-5){
    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);              if(first==1)
 fprintf(fichtm," <li>Graphs</li><p>");                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
  m=cptcoveff;            }else{
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}              if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
  jj1=0;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
  for(k1=1; k1<=m;k1++){            }
    for(i1=1; i1<=ncodemax[k1];i1++){            if( i <= iagemax){
        jj1++;              if(pos>=1.e-5){
        if (cptcovn > 0) {                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");                /*probs[i][jk][j1]= pp[jk]/pos;*/
          for (cpt=1; cpt<=cptcoveff;cpt++)                /*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(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);              }
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");              else
        }                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
        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>          for(jk=-1; jk <=nlstate+ndeath; jk++)
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            for(m=-1; m <=nlstate+ndeath; m++)
        }              if(freq[jk][m][i] !=0 ) {
     for(cpt=1; cpt<=nlstate;cpt++) {              if(first==1)
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
 interval) in state (%d): v%s%d%d.gif <br>                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                }
      }          if(i <= iagemax)
      for(cpt=1; cpt<=nlstate;cpt++) {            fprintf(ficresp,"\n");
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>          if(first==1)
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            printf("Others in log...\n");
      }          fprintf(ficlog,"\n");
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        }
 health expectancies in states (1) and (2): e%s%d.gif<br>      }
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    }
 fprintf(fichtm,"\n</body>");    dateintmean=dateintsum/k2cpt; 
    }   
    }    fclose(ficresp);
 fclose(fichtm);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
 }    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
 /******************* Gnuplot file **************/    /* End of Freq */
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  }
   
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;  /************ Prevalence ********************/
   void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   strcpy(optionfilegnuplot,optionfilefiname);  {  
   strcat(optionfilegnuplot,".gp.txt");    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {       in each health status at the date of interview (if between dateprev1 and dateprev2).
     printf("Problem with file %s",optionfilegnuplot);       We still use firstpass and lastpass as another selection.
   }    */
    
 #ifdef windows    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     fprintf(ficgp,"cd \"%s\" \n",pathc);    double ***freq; /* Frequencies */
 #endif    double *pp, **prop;
 m=pow(2,cptcoveff);    double pos,posprop; 
      double  y2; /* in fractional years */
  /* 1eme*/    int iagemin, iagemax;
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {    iagemin= (int) agemin;
     iagemax= (int) agemax;
 #ifdef windows    /*pp=vector(1,nlstate);*/
     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",ageminpar,fage,fileres,k1-1,k1-1);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
 #endif    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
 #ifdef unix    j1=0;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    
 #endif    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
 for (i=1; i<= nlstate ; i ++) {    
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    for(k1=1; k1<=j;k1++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(i1=1; i1<=ncodemax[k1];i1++){
 }        j1++;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);        
     for (i=1; i<= nlstate ; i ++) {        for (i=1; i<=nlstate; i++)  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for(m=iagemin; m <= iagemax+3; m++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");            prop[i][m]=0.0;
 }       
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        for (i=1; i<=imx; i++) { /* Each individual */
      for (i=1; i<= nlstate ; i ++) {          bool=1;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          if  (cptcovn>0) {
   else fprintf(ficgp," \%%*lf (\%%*lf)");            for (z1=1; z1<=cptcoveff; z1++) 
 }                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));                bool=0;
 #ifdef unix          } 
 fprintf(ficgp,"\nset ter gif small size 400,300");          if (bool==1) { 
 #endif            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
    }              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   /*2 eme*/                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   for (k1=1; k1<= m ; k1 ++) {                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);                  /*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];
     for (i=1; i<= nlstate+1 ; i ++) {                  prop[s[m][i]][iagemax+3] += weight[i]; 
       k=2*i;                } 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);              }
       for (j=1; j<= nlstate+1 ; j ++) {            } /* end selection of waves */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }          for(i=iagemin; i <= iagemax+3; i++){  
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);            posprop += prop[jk][i]; 
       for (j=1; j<= nlstate+1 ; j ++) {          } 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
         else fprintf(ficgp," \%%*lf (\%%*lf)");          for(jk=1; jk <=nlstate ; jk++){     
 }              if( i <=  iagemax){ 
       fprintf(ficgp,"\" t\"\" w l 0,");              if(posprop>=1.e-5){ 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);                probs[i][jk][j1]= prop[jk][i]/posprop;
       for (j=1; j<= nlstate+1 ; j ++) {              } 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }/* end jk */ 
 }          }/* end i */ 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      } /* end i1 */
       else fprintf(ficgp,"\" t\"\" w l 0,");    } /* end k1 */
     }    
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   }    /*free_vector(pp,1,nlstate);*/
      free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   /*3eme*/  }  /* End of prevalence */
   
   for (k1=1; k1<= m ; k1 ++) {  /************* Waves Concatenation ***************/
     for (cpt=1; cpt<= nlstate ; cpt ++) {  
       k=2+nlstate*(cpt-1);  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
       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",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);  {
       for (i=1; i< nlstate ; i ++) {    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);       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
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     }       and mw[mi+1][i]. dh depends on stepm.
     }       */
    
   /* CV preval stat */    int i, mi, m;
     for (k1=1; k1<= m ; k1 ++) {    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     for (cpt=1; cpt<nlstate ; cpt ++) {       double sum=0., jmean=0.;*/
       k=3;    int first;
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    int j, k=0,jk, ju, jl;
     double sum=0.;
       for (i=1; i< nlstate ; i ++)    first=0;
         fprintf(ficgp,"+$%d",k+i+1);    jmin=1e+5;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    jmax=-1;
          jmean=0.;
       l=3+(nlstate+ndeath)*cpt;    for(i=1; i<=imx; i++){
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      mi=0;
       for (i=1; i< nlstate ; i ++) {      m=firstpass;
         l=3+(nlstate+ndeath)*cpt;      while(s[m][i] <= nlstate){
         fprintf(ficgp,"+$%d",l+i+1);        if(s[m][i]>=1)
       }          mw[++mi][i]=m;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          if(m >=lastpass)
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          break;
     }        else
   }            m++;
        }/* end while */
   /* proba elementaires */      if (s[m][i] > nlstate){
    for(i=1,jk=1; i <=nlstate; i++){        mi++;     /* Death is another wave */
     for(k=1; k <=(nlstate+ndeath); k++){        /* if(mi==0)  never been interviewed correctly before death */
       if (k != i) {           /* Only death is a correct wave */
         for(j=1; j <=ncovmodel; j++){        mw[mi][i]=m;
              }
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  
           jk++;      wav[i]=mi;
           fprintf(ficgp,"\n");      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);
     }          first=1;
         }
     for(jk=1; jk <=m; jk++) {        if(first==1){
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
    i=1;        }
    for(k2=1; k2<=nlstate; k2++) {      } /* end mi==0 */
      k3=i;    } /* End individuals */
      for(k=1; k<=(nlstate+ndeath); k++) {  
        if (k != k2){    for(i=1; i<=imx; i++){
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      for(mi=1; mi<wav[i];mi++){
 ij=1;        if (stepm <=0)
         for(j=3; j <=ncovmodel; j++) {          dh[mi][i]=1;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        else{
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             ij++;            if (agedc[i] < 2*AGESUP) {
           }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
           else              if(j==0) j=1;  /* Survives at least one month after exam */
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              else if(j<0){
         }                nberr++;
           fprintf(ficgp,")/(1");                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                        j=1; /* Temporary Dangerous patch */
         for(k1=1; k1 <=nlstate; k1++){                  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(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                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]);
 ij=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);
           for(j=3; j <=ncovmodel; j++){              }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              k=k+1;
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);              if (j >= jmax) jmax=j;
             ij++;              if (j <= jmin) jmin=j;
           }              sum=sum+j;
           else              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           }            }
           fprintf(ficgp,")");          }
         }          else{
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
         i=i+ncovmodel;            k=k+1;
        }            if (j >= jmax) jmax=j;
      }            else if (j <= jmin)jmin=j;
    }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
    }            if(j<0){
                  nberr++;
   fclose(ficgp);              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]);
 }  /* end gnuplot */              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]);
             }
             sum=sum+j;
 /*************** Moving average **************/          }
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){          jk= j/stepm;
           jl= j -jk*stepm;
   int i, cpt, cptcod;          ju= j -(jk+1)*stepm;
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       for (i=1; i<=nlstate;i++)            if(jl==0){
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)              dh[mi][i]=jk;
           mobaverage[(int)agedeb][i][cptcod]=0.;              bh[mi][i]=0;
                }else{ /* We want a negative bias in order to only have interpolation ie
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){                    * at the price of an extra matrix product in likelihood */
       for (i=1; i<=nlstate;i++){              dh[mi][i]=jk+1;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              bh[mi][i]=ju;
           for (cpt=0;cpt<=4;cpt++){            }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          }else{
           }            if(jl <= -ju){
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;              dh[mi][i]=jk;
         }              bh[mi][i]=jl;       /* bias is positive if real duration
       }                                   * is higher than the multiple of stepm and negative otherwise.
     }                                   */
                }
 }            else{
               dh[mi][i]=jk+1;
               bh[mi][i]=ju;
 /************** Forecasting ******************/            }
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){            if(dh[mi][i]==0){
                dh[mi][i]=1; /* At least one step */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;              bh[mi][i]=ju; /* At least one step */
   int *popage;              /*  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);*/
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            }
   double *popeffectif,*popcount;          } /* end if mle */
   double ***p3mat;        }
   char fileresf[FILENAMELENGTH];      } /* end wave */
     }
  agelim=AGESUP;    jmean=sum/k;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    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);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);   }
    
    /*********** Tricode ****************************/
   strcpy(fileresf,"f");  void tricode(int *Tvar, int **nbcode, int imx)
   strcat(fileresf,fileres);  {
   if((ficresf=fopen(fileresf,"w"))==NULL) {    
     printf("Problem with forecast resultfile: %s\n", fileresf);    int Ndum[20],ij=1, k, j, i, maxncov=19;
   }    int cptcode=0;
   printf("Computing forecasting: result on file '%s' \n", fileresf);    cptcoveff=0; 
    
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    for (k=0; k<maxncov; k++) Ndum[k]=0;
     for (k=1; k<=7; k++) ncodemax[k]=0;
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     movingaverage(agedeb, fage, ageminpar, mobaverage);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   }                                 modality*/ 
         ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   stepsize=(int) (stepm+YEARM-1)/YEARM;        Ndum[ij]++; /*store the modality */
   if (stepm<=12) stepsize=1;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
          if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   agelim=AGESUP;                                         Tvar[j]. If V=sex and male is 0 and 
                                           female is 1, then  cptcode=1.*/
   hstepm=1;      }
   hstepm=hstepm/stepm;  
   yp1=modf(dateintmean,&yp);      for (i=0; i<=cptcode; i++) {
   anprojmean=yp;        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 */
   yp2=modf((yp1*12),&yp);      }
   mprojmean=yp;  
   yp1=modf((yp2*30.5),&yp);      ij=1; 
   jprojmean=yp;      for (i=1; i<=ncodemax[j]; i++) {
   if(jprojmean==0) jprojmean=1;        for (k=0; k<= maxncov; k++) {
   if(mprojmean==0) jprojmean=1;          if (Ndum[k] != 0) {
              nbcode[Tvar[j]][ij]=k; 
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);            /* 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; */
              
   for(cptcov=1;cptcov<=i2;cptcov++){            ij++;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          }
       k=k+1;          if (ij > ncodemax[j]) break; 
       fprintf(ficresf,"\n#******");        }  
       for(j=1;j<=cptcoveff;j++) {      } 
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    }  
       }  
       fprintf(ficresf,"******\n");   for (k=0; k< maxncov; k++) Ndum[k]=0;
       fprintf(ficresf,"# StartingAge FinalAge");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);   for (i=1; i<=ncovmodel-2; i++) { 
           /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
           ij=Tvar[i];
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {     Ndum[ij]++;
         fprintf(ficresf,"\n");   }
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    
    ij=1;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){   for (i=1; i<= maxncov; i++) {
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);     if((Ndum[i]!=0) && (i<=ncovcol)){
           nhstepm = nhstepm/hstepm;       Tvaraff[ij]=i; /*For printing */
                 ij++;
           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);     
           cptcoveff=ij-1; /*Number of simple covariates*/
           for (h=0; h<=nhstepm; h++){  }
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);  /*********** Health Expectancies ****************/
             }  
             for(j=1; j<=nlstate+ndeath;j++) {  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 )
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                {
                 if (mobilav==1)    /* Health expectancies */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
                 else {    double age, agelim, hf;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    double ***p3mat,***varhe;
                 }    double **dnewm,**doldm;
                    double *xp;
               }    double **gp, **gm;
               if (h==(int)(calagedate+12*cpt)){    double ***gradg, ***trgradg;
                 fprintf(ficresf," %.3f", kk1);    int theta;
                          
               }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
             }    xp=vector(1,npar);
           }    dnewm=matrix(1,nlstate*nlstate,1,npar);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
         }    
       }    fprintf(ficreseij,"# Health expectancies\n");
     }    fprintf(ficreseij,"# Age");
   }    for(i=1; i<=nlstate;i++)
              for(j=1; j<=nlstate;j++)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     fprintf(ficreseij,"\n");
   fclose(ficresf);  
 }    if(estepm < stepm){
 /************** Forecasting ******************/      printf ("Problem %d lower than %d\n",estepm, stepm);
 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){    }
      else  hstepm=estepm;   
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    /* We compute the life expectancy from trapezoids spaced every estepm months
   int *popage;     * This is mainly to measure the difference between two models: for example
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;     * if stepm=24 months pijx are given only every 2 years and by summing them
   double *popeffectif,*popcount;     * we are calculating an estimate of the Life Expectancy assuming a linear 
   double ***p3mat,***tabpop,***tabpopprev;     * progression in between and thus overestimating or underestimating according
   char filerespop[FILENAMELENGTH];     * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * to compare the new estimate of Life expectancy with the same linear 
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * hypothesis. A more precise result, taking into account a more precise
   agelim=AGESUP;     * curvature will be obtained if estepm is as small as stepm. */
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;  
      /* For example we decided to compute the life expectancy with the smallest unit */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         nhstepm is the number of hstepm from age to agelim 
         nstepm is the number of stepm from age to agelin. 
   strcpy(filerespop,"pop");       Look at hpijx to understand the reason of that which relies in memory size
   strcat(filerespop,fileres);       and note for a fixed period like estepm months */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     printf("Problem with forecast resultfile: %s\n", filerespop);       survival function given by stepm (the optimization length). Unfortunately it
   }       means that if the survival funtion is printed only each two years of age and if
   printf("Computing forecasting: result on file '%s' \n", filerespop);       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.
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    agelim=AGESUP;
     movingaverage(agedeb, fage, ageminpar, mobaverage);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   }      /* nhstepm age range expressed in number of stepm */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   stepsize=(int) (stepm+YEARM-1)/YEARM;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   if (stepm<=12) stepsize=1;      /* if (stepm >= YEARM) hstepm=1;*/
        nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   agelim=AGESUP;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   hstepm=1;      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   hstepm=hstepm/stepm;      gm=matrix(0,nhstepm,1,nlstate*nlstate);
    
   if (popforecast==1) {      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     if((ficpop=fopen(popfile,"r"))==NULL) {         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       printf("Problem with population file : %s\n",popfile);exit(0);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     }   
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     popcount=vector(0,AGESUP);  
          /* Computing  Variances of health expectancies */
     i=1;    
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;       for(theta=1; theta <=npar; theta++){
            for(i=1; i<=npar; i++){ 
     imx=i;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        }
   }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     
   for(cptcov=1;cptcov<=i2;cptcov++){        cptj=0;
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        for(j=1; j<= nlstate; j++){
       k=k+1;          for(i=1; i<=nlstate; i++){
       fprintf(ficrespop,"\n#******");            cptj=cptj+1;
       for(j=1;j<=cptcoveff;j++) {            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       }            }
       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(i=1; i<=npar; i++) 
       for (cpt=0; cpt<=0;cpt++) {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        cptj=0;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        for(j=1; j<= nlstate; j++){
           nhstepm = nhstepm/hstepm;          for(i=1;i<=nlstate;i++){
                      cptj=cptj+1;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
                    }
           for (h=0; h<=nhstepm; h++){          }
             if (h==(int) (calagedate+YEARM*cpt)) {        }
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        for(j=1; j<= nlstate*nlstate; j++)
             }          for(h=0; h<=nhstepm-1; h++){
             for(j=1; j<=nlstate+ndeath;j++) {            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
               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];  /* End theta */
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
                 }  
               }       for(h=0; h<=nhstepm-1; h++)
               if (h==(int)(calagedate+12*cpt)){        for(j=1; j<=nlstate*nlstate;j++)
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          for(theta=1; theta <=npar; theta++)
                   /*fprintf(ficrespop," %.3f", kk1);            trgradg[h][j][theta]=gradg[h][theta][j];
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/       
               }  
             }       for(i=1;i<=nlstate*nlstate;i++)
             for(i=1; i<=nlstate;i++){        for(j=1;j<=nlstate*nlstate;j++)
               kk1=0.;          varhe[i][j][(int)age] =0.;
                 for(j=1; j<=nlstate;j++){  
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];       printf("%d|",(int)age);fflush(stdout);
                 }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];       for(h=0;h<=nhstepm-1;h++){
             }        for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);          for(i=1;i<=nlstate*nlstate;i++)
           }            for(j=1;j<=nlstate*nlstate;j++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         }        }
       }      }
        /* Computing expectancies */
   /******/      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);              eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){            
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  /* 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]);*/
           nhstepm = nhstepm/hstepm;  
                    }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;      fprintf(ficreseij,"%3.0f",age );
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        cptj=0;
           for (h=0; h<=nhstepm; h++){      for(i=1; i<=nlstate;i++)
             if (h==(int) (calagedate+YEARM*cpt)) {        for(j=1; j<=nlstate;j++){
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          cptj++;
             }          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
             for(j=1; j<=nlstate+ndeath;j++) {        }
               kk1=0.;kk2=0;      fprintf(ficreseij,"\n");
               for(i=1; i<=nlstate;i++) {                   
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];          free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
               }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
             }      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
           }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
         }    printf("\n");
       }    fprintf(ficlog,"\n");
    }  
   }    free_vector(xp,1,npar);
      free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   if (popforecast==1) {  }
     free_ivector(popage,0,AGESUP);  
     free_vector(popeffectif,0,AGESUP);  /************ Variance ******************/
     free_vector(popcount,0,AGESUP);  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
   }  {
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* Variance of health expectancies */
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   fclose(ficrespop);    /* double **newm;*/
 }    double **dnewm,**doldm;
     double **dnewmp,**doldmp;
 /***********************************************/    int i, j, nhstepm, hstepm, h, nstepm ;
 /**************** Main Program *****************/    int k, cptcode;
 /***********************************************/    double *xp;
     double **gp, **gm;  /* for var eij */
 int main(int argc, char *argv[])    double ***gradg, ***trgradg; /*for var eij */
 {    double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   double agedeb, agefin,hf;    double ***p3mat;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    double age,agelim, hf;
     double ***mobaverage;
   double fret;    int theta;
   double **xi,tmp,delta;    char digit[4];
     char digitp[25];
   double dum; /* Dummy variable */  
   double ***p3mat;    char fileresprobmorprev[FILENAMELENGTH];
   int *indx;  
   char line[MAXLINE], linepar[MAXLINE];    if(popbased==1){
   char title[MAXLINE];      if(mobilav!=0)
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];        strcpy(digitp,"-populbased-mobilav-");
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];      else strcpy(digitp,"-populbased-nomobil-");
      }
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    else 
       strcpy(digitp,"-stablbased-");
   char filerest[FILENAMELENGTH];  
   char fileregp[FILENAMELENGTH];    if (mobilav!=0) {
   char popfile[FILENAMELENGTH];      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   int firstobs=1, lastobs=10;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   int sdeb, sfin; /* Status at beginning and end */        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   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,**adl,*tab;    strcpy(fileresprobmorprev,"prmorprev"); 
   int mobilav=0,popforecast=0;    sprintf(digit,"%-d",ij);
   int hstepm, nhstepm;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   double bage, fage, age, agelim, agebase;    strcat(fileresprobmorprev,fileres);
   double ftolpl=FTOL;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   double **prlim;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   double *severity;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   double ***param; /* Matrix of parameters */    }
   double  *p;    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   double **matcov; /* Matrix of covariance */    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   double ***delti3; /* Scale */    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);
   double *delti; /* Scale */    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   double ***eij, ***vareij;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   double **varpl; /* Variances of prevalence limits by age */      fprintf(ficresprobmorprev," p.%-d SE",j);
   double *epj, vepp;      for(i=1; i<=nlstate;i++)
   double kk1, kk2;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    }  
      fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
   char version[80]="Imach version 0.8a, March 2002, INED-EUROREVES ";    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");
   char *alph[]={"a","a","b","c","d","e"}, str[4];    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   char z[1]="c", occ;  
 #include <sys/time.h>    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");
 #include <time.h>    fprintf(ficresvij,"# Age");
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
   /* long total_usecs;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   struct timeval start_time, end_time;    fprintf(ficresvij,"\n");
    
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    xp=vector(1,npar);
   getcwd(pathcd, size);    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
   printf("\n%s",version);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   if(argc <=1){    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     printf("\nEnter the parameter file name: ");  
     scanf("%s",pathtot);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   }    gpp=vector(nlstate+1,nlstate+ndeath);
   else{    gmp=vector(nlstate+1,nlstate+ndeath);
     strcpy(pathtot,argv[1]);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   }    
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    if(estepm < stepm){
   /*cygwin_split_path(pathtot,path,optionfile);      printf ("Problem %d lower than %d\n",estepm, stepm);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    }
   /* cutv(path,optionfile,pathtot,'\\');*/    else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);       nhstepm is the number of hstepm from age to agelim 
   chdir(path);       nstepm is the number of stepm from age to agelin. 
   replace(pathc,path);       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
 /*-------- arguments in the command line --------*/    /* 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
   strcpy(fileres,"r");       means that if the survival funtion is printed every two years of age and if
   strcat(fileres, optionfilefiname);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   strcat(fileres,".txt");    /* Other files have txt extension */       results. So we changed our mind and took the option of the best precision.
     */
   /*---------arguments file --------*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     printf("Problem with optionfile %s\n",optionfile);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     goto end;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   strcpy(filereso,"o");      gp=matrix(0,nhstepm,1,nlstate);
   strcat(filereso,fileres);      gm=matrix(0,nhstepm,1,nlstate);
   if((ficparo=fopen(filereso,"w"))==NULL) {  
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  
   }      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   /* Reads comments: lines beginning with '#' */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   while((c=getc(ficpar))=='#' && c!= EOF){        }
     ungetc(c,ficpar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     fgets(line, MAXLINE, ficpar);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     puts(line);  
     fputs(line,ficparo);        if (popbased==1) {
   }          if(mobilav ==0){
   ungetc(c,ficpar);            for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
   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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);          }else{ /* mobilav */ 
   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);            for(i=1; i<=nlstate;i++)
   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);              prlim[i][i]=mobaverage[(int)age][i][ij];
 while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);    
     puts(line);        for(j=1; j<= nlstate; j++){
     fputs(line,ficparo);          for(h=0; h<=nhstepm; h++){
   }            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   ungetc(c,ficpar);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
            }
            }
   covar=matrix(0,NCOVMAX,1,n);        /* This for computing probability of death (h=1 means
   cptcovn=0;           computed over hstepm matrices product = hstepm*stepm months) 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;           as a weighted average of prlim.
         */
   ncovmodel=2+cptcovn;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */          for(i=1,gpp[j]=0.; i<= nlstate; i++)
              gpp[j] += prlim[i][i]*p3mat[i][j][1];
   /* Read guess parameters */        }    
   /* Reads comments: lines beginning with '#' */        /* end probability of death */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     fgets(line, MAXLINE, ficpar);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     puts(line);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     fputs(line,ficparo);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   }   
   ungetc(c,ficpar);        if (popbased==1) {
            if(mobilav ==0){
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            for(i=1; i<=nlstate;i++)
     for(i=1; i <=nlstate; i++)              prlim[i][i]=probs[(int)age][i][ij];
     for(j=1; j <=nlstate+ndeath-1; j++){          }else{ /* mobilav */ 
       fscanf(ficpar,"%1d%1d",&i1,&j1);            for(i=1; i<=nlstate;i++)
       fprintf(ficparo,"%1d%1d",i1,j1);              prlim[i][i]=mobaverage[(int)age][i][ij];
       printf("%1d%1d",i,j);          }
       for(k=1; k<=ncovmodel;k++){        }
         fscanf(ficpar," %lf",&param[i][j][k]);  
         printf(" %lf",param[i][j][k]);        for(j=1; j<= nlstate; j++){
         fprintf(ficparo," %lf",param[i][j][k]);          for(h=0; h<=nhstepm; h++){
       }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
       fscanf(ficpar,"\n");              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
       printf("\n");          }
       fprintf(ficparo,"\n");        }
     }        /* This for computing probability of death (h=1 means
             computed over hstepm matrices product = hstepm*stepm months) 
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;           as a weighted average of prlim.
         */
   p=param[1][1];        for(j=nlstate+1;j<=nlstate+ndeath;j++){
            for(i=1,gmp[j]=0.; i<= nlstate; i++)
   /* Reads comments: lines beginning with '#' */           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   while((c=getc(ficpar))=='#' && c!= EOF){        }    
     ungetc(c,ficpar);        /* end probability of death */
     fgets(line, MAXLINE, ficpar);  
     puts(line);        for(j=1; j<= nlstate; j++) /* vareij */
     fputs(line,ficparo);          for(h=0; h<=nhstepm; h++){
   }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   ungetc(c,ficpar);          }
   
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   for(i=1; i <=nlstate; i++){        }
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);      } /* End theta */
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar,"%le",&delti3[i][j][k]);      for(h=0; h<=nhstepm; h++) /* veij */
         printf(" %le",delti3[i][j][k]);        for(j=1; j<=nlstate;j++)
         fprintf(ficparo," %le",delti3[i][j][k]);          for(theta=1; theta <=npar; theta++)
       }            trgradg[h][j][theta]=gradg[h][theta][j];
       fscanf(ficpar,"\n");  
       printf("\n");      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       fprintf(ficparo,"\n");        for(theta=1; theta <=npar; theta++)
     }          trgradgp[j][theta]=gradgp[theta][j];
   }    
   delti=delti3[1][1];  
        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   /* Reads comments: lines beginning with '#' */      for(i=1;i<=nlstate;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){        for(j=1;j<=nlstate;j++)
     ungetc(c,ficpar);          vareij[i][j][(int)age] =0.;
     fgets(line, MAXLINE, ficpar);  
     puts(line);      for(h=0;h<=nhstepm;h++){
     fputs(line,ficparo);        for(k=0;k<=nhstepm;k++){
   }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   ungetc(c,ficpar);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
            for(i=1;i<=nlstate;i++)
   matcov=matrix(1,npar,1,npar);            for(j=1;j<=nlstate;j++)
   for(i=1; i <=npar; i++){              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     fscanf(ficpar,"%s",&str);        }
     printf("%s",str);      }
     fprintf(ficparo,"%s",str);    
     for(j=1; j <=i; j++){      /* pptj */
       fscanf(ficpar," %le",&matcov[i][j]);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       printf(" %.5le",matcov[i][j]);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       fprintf(ficparo," %.5le",matcov[i][j]);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
     }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     fscanf(ficpar,"\n");          varppt[j][i]=doldmp[j][i];
     printf("\n");      /* end ppptj */
     fprintf(ficparo,"\n");      /*  x centered again */
   }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   for(i=1; i <=npar; i++)      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     for(j=i+1;j<=npar;j++)   
       matcov[i][j]=matcov[j][i];      if (popbased==1) {
            if(mobilav ==0){
   printf("\n");          for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
     /*-------- Rewriting paramater file ----------*/          for(i=1; i<=nlstate;i++)
      strcpy(rfileres,"r");    /* "Rparameterfile */            prlim[i][i]=mobaverage[(int)age][i][ij];
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        }
      strcat(rfileres,".");    /* */      }
      strcat(rfileres,optionfilext);    /* Other files have txt extension */               
     if((ficres =fopen(rfileres,"w"))==NULL) {      /* This for computing probability of death (h=1 means
       printf("Problem writing new parameter file: %s\n", fileres);goto end;         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     }         as a weighted average of prlim.
     fprintf(ficres,"#%s\n",version);      */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
     /*-------- data file ----------*/        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     if((fic=fopen(datafile,"r"))==NULL)    {          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       printf("Problem with datafile: %s\n", datafile);goto end;      }    
     }      /* end probability of death */
   
     n= lastobs;      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     severity = vector(1,maxwav);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     outcome=imatrix(1,maxwav+1,1,n);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     num=ivector(1,n);        for(i=1; i<=nlstate;i++){
     moisnais=vector(1,n);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     annais=vector(1,n);        }
     moisdc=vector(1,n);      } 
     andc=vector(1,n);      fprintf(ficresprobmorprev,"\n");
     agedc=vector(1,n);  
     cod=ivector(1,n);      fprintf(ficresvij,"%.0f ",age );
     weight=vector(1,n);      for(i=1; i<=nlstate;i++)
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        for(j=1; j<=nlstate;j++){
     mint=matrix(1,maxwav,1,n);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     anint=matrix(1,maxwav,1,n);        }
     s=imatrix(1,maxwav+1,1,n);      fprintf(ficresvij,"\n");
     adl=imatrix(1,maxwav+1,1,n);          free_matrix(gp,0,nhstepm,1,nlstate);
     tab=ivector(1,NCOVMAX);      free_matrix(gm,0,nhstepm,1,nlstate);
     ncodemax=ivector(1,8);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     i=1;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     while (fgets(line, MAXLINE, fic) != NULL)    {    } /* End age */
       if ((i >= firstobs) && (i <=lastobs)) {    free_vector(gpp,nlstate+1,nlstate+ndeath);
            free_vector(gmp,nlstate+1,nlstate+ndeath);
         for (j=maxwav;j>=1;j--){    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           strcpy(line,stra);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
         }  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
          /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    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));
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    /*  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);
         for (j=ncovcol;j>=1;j--){  */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
         }    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
         num[i]=atol(stra);  
            free_vector(xp,1,npar);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    free_matrix(doldm,1,nlstate,1,nlstate);
           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;}*/    free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         i=i+1;    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);
     /* printf("ii=%d", ij);    fclose(ficresprobmorprev);
        scanf("%d",i);*/    fflush(ficgp);
   imx=i-1; /* Number of individuals */    fflush(fichtm); 
   }  /* end varevsij */
   /* for (i=1; i<=imx; i++){  
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;  /************ Variance of prevlim ******************/
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;  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)
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;  {
     }*/    /* Variance of prevalence limit */
      /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   /* for (i=1; i<=imx; i++){    double **newm;
      if (s[4][i]==9)  s[4][i]=-1;    double **dnewm,**doldm;
      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]));}    int i, j, nhstepm, hstepm;
   */    int k, cptcode;
      double *xp;
   /* Calculation of the number of parameter from char model*/    double *gp, *gm;
   Tvar=ivector(1,15);    double **gradg, **trgradg;
   Tprod=ivector(1,15);    double age,agelim;
   Tvaraff=ivector(1,15);    int theta;
   Tvard=imatrix(1,15,1,2);     
   Tage=ivector(1,15);          fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
        fprintf(ficresvpl,"# Age");
   if (strlen(model) >1){    for(i=1; i<=nlstate;i++)
     j=0, j1=0, k1=1, k2=1;        fprintf(ficresvpl," %1d-%1d",i,i);
     j=nbocc(model,'+');    fprintf(ficresvpl,"\n");
     j1=nbocc(model,'*');  
     cptcovn=j+1;    xp=vector(1,npar);
     cptcovprod=j1;    dnewm=matrix(1,nlstate,1,npar);
        doldm=matrix(1,nlstate,1,nlstate);
     strcpy(modelsav,model);    
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    hstepm=1*YEARM; /* Every year of age */
       printf("Error. Non available option model=%s ",model);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
       goto end;    agelim = AGESUP;
     }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
          nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     for(i=(j+1); i>=1;i--){      if (stepm >= YEARM) hstepm=1;
       cutv(stra,strb,modelsav,'+');      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      gradg=matrix(1,npar,1,nlstate);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      gp=vector(1,nlstate);
       /*scanf("%d",i);*/      gm=vector(1,nlstate);
       if (strchr(strb,'*')) {  
         cutv(strd,strc,strb,'*');      for(theta=1; theta <=npar; theta++){
         if (strcmp(strc,"age")==0) {        for(i=1; i<=npar; i++){ /* Computes gradient */
           cptcovprod--;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           cutv(strb,stre,strd,'V');        }
           Tvar[i]=atoi(stre);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           cptcovage++;        for(i=1;i<=nlstate;i++)
             Tage[cptcovage]=i;          gp[i] = prlim[i][i];
             /*printf("stre=%s ", stre);*/      
         }        for(i=1; i<=npar; i++) /* Computes gradient */
         else if (strcmp(strd,"age")==0) {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           cptcovprod--;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           cutv(strb,stre,strc,'V');        for(i=1;i<=nlstate;i++)
           Tvar[i]=atoi(stre);          gm[i] = prlim[i][i];
           cptcovage++;  
           Tage[cptcovage]=i;        for(i=1;i<=nlstate;i++)
         }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         else {      } /* End theta */
           cutv(strb,stre,strc,'V');  
           Tvar[i]=ncovcol+k1;      trgradg =matrix(1,nlstate,1,npar);
           cutv(strb,strc,strd,'V');  
           Tprod[k1]=i;      for(j=1; j<=nlstate;j++)
           Tvard[k1][1]=atoi(strc);        for(theta=1; theta <=npar; theta++)
           Tvard[k1][2]=atoi(stre);          trgradg[j][theta]=gradg[theta][j];
           Tvar[cptcovn+k2]=Tvard[k1][1];  
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      for(i=1;i<=nlstate;i++)
           for (k=1; k<=lastobs;k++)        varpl[i][(int)age] =0.;
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
           k1++;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
           k2=k2+2;      for(i=1;i<=nlstate;i++)
         }        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
       }  
       else {      fprintf(ficresvpl,"%.0f ",age );
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      for(i=1; i<=nlstate;i++)
        /*  scanf("%d",i);*/        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       cutv(strd,strc,strb,'V');      fprintf(ficresvpl,"\n");
       Tvar[i]=atoi(strc);      free_vector(gp,1,nlstate);
       }      free_vector(gm,1,nlstate);
       strcpy(modelsav,stra);        free_matrix(gradg,1,npar,1,nlstate);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      free_matrix(trgradg,1,nlstate,1,npar);
         scanf("%d",i);*/    } /* End age */
     }  
 }    free_vector(xp,1,npar);
      free_matrix(doldm,1,nlstate,1,npar);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    free_matrix(dnewm,1,nlstate,1,nlstate);
   printf("cptcovprod=%d ", cptcovprod);  
   scanf("%d ",i);*/  }
     fclose(fic);  
   /************ Variance of one-step probabilities  ******************/
     /*  if(mle==1){*/  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
     if (weightopt != 1) { /* Maximisation without weights*/  {
       for(i=1;i<=n;i++) weight[i]=1.0;    int i, j=0,  i1, k1, l1, t, tj;
     }    int k2, l2, j1,  z1;
     /*-calculation of age at interview from date of interview and age at death -*/    int k=0,l, cptcode;
     agev=matrix(1,maxwav,1,imx);    int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     for (i=1; i<=imx; i++) {    double **dnewm,**doldm;
       for(m=2; (m<= maxwav); m++) {    double *xp;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    double *gp, *gm;
          anint[m][i]=9999;    double **gradg, **trgradg;
          s[m][i]=-1;    double **mu;
        }    double age,agelim, cov[NCOVMAX];
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
       }    int theta;
     }    char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     for (i=1; i<=imx; i++)  {    char fileresprobcor[FILENAMELENGTH];
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  
       for(m=1; (m<= maxwav); m++){    double ***varpij;
         if(s[m][i] >0){  
           if (s[m][i] >= nlstate+1) {    strcpy(fileresprob,"prob"); 
             if(agedc[i]>0)    strcat(fileresprob,fileres);
               if(moisdc[i]!=99 && andc[i]!=9999)    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
                 agev[m][i]=agedc[i];      printf("Problem with resultfile: %s\n", fileresprob);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
            else {    }
               if (andc[i]!=9999){    strcpy(fileresprobcov,"probcov"); 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    strcat(fileresprobcov,fileres);
               agev[m][i]=-1;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
               }      printf("Problem with resultfile: %s\n", fileresprobcov);
             }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
           }    }
           else if(s[m][i] !=9){ /* Should no more exist */    strcpy(fileresprobcor,"probcor"); 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    strcat(fileresprobcor,fileres);
             if(mint[m][i]==99 || anint[m][i]==9999)    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
               agev[m][i]=1;      printf("Problem with resultfile: %s\n", fileresprobcor);
             else if(agev[m][i] <agemin){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
               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);*/    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
             }    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
             else if(agev[m][i] >agemax){    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
               agemax=agev[m][i];    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    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);
             /*agev[m][i]=anint[m][i]-annais[i];*/    
             /*   agev[m][i] = age[i]+2*m;*/    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
           }    fprintf(ficresprob,"# Age");
           else { /* =9 */    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
             agev[m][i]=1;    fprintf(ficresprobcov,"# Age");
             s[m][i]=-1;    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
           }    fprintf(ficresprobcov,"# Age");
         }  
         else /*= 0 Unknown */  
           agev[m][i]=1;    for(i=1; i<=nlstate;i++)
       }      for(j=1; j<=(nlstate+ndeath);j++){
            fprintf(ficresprob," p%1d-%1d (SE)",i,j);
     }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
     for (i=1; i<=imx; i++)  {        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       for(m=1; (m<= maxwav); m++){      }  
         if (s[m][i] > (nlstate+ndeath)) {   /* fprintf(ficresprob,"\n");
           printf("Error: Wrong value in nlstate or ndeath\n");      fprintf(ficresprobcov,"\n");
           goto end;    fprintf(ficresprobcor,"\n");
         }   */
       }   xp=vector(1,npar);
     }    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     free_vector(severity,1,maxwav);    first=1;
     free_imatrix(outcome,1,maxwav+1,1,n);    fprintf(ficgp,"\n# Routine varprob");
     free_vector(moisnais,1,n);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     free_vector(annais,1,n);    fprintf(fichtm,"\n");
     /* free_matrix(mint,1,maxwav,1,n);  
        free_matrix(anint,1,maxwav,1,n);*/    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     free_vector(moisdc,1,n);    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     free_vector(andc,1,n);    file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
      and drawn. It helps understanding how is the covariance between two incidences.\
     wav=ivector(1,imx);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    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. \
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
      would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
     /* Concatenates waves */  standard deviations wide on each axis. <br>\
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
       Tcode=ivector(1,100);  
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    cov[1]=1;
       ncodemax[1]=1;    tj=cptcoveff;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
          j1=0;
    codtab=imatrix(1,100,1,10);    for(t=1; t<=tj;t++){
    h=0;      for(i1=1; i1<=ncodemax[t];i1++){ 
    m=pow(2,cptcoveff);        j1++;
          if  (cptcovn>0) {
    for(k=1;k<=cptcoveff; k++){          fprintf(ficresprob, "\n#********** Variable "); 
      for(i=1; i <=(m/pow(2,k));i++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
        for(j=1; j <= ncodemax[k]; j++){          fprintf(ficresprob, "**********\n#\n");
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          fprintf(ficresprobcov, "\n#********** Variable "); 
            h++;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;          fprintf(ficresprobcov, "**********\n#\n");
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/          
          }          fprintf(ficgp, "\n#********** Variable "); 
        }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      }          fprintf(ficgp, "**********\n#\n");
    }          
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);          
       codtab[1][2]=1;codtab[2][2]=2; */          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
    /* for(i=1; i <=m ;i++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       for(k=1; k <=cptcovn; k++){          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);          
       }          fprintf(ficresprobcor, "\n#********** Variable ");    
       printf("\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       }          fprintf(ficresprobcor, "**********\n#");    
       scanf("%d",i);*/        }
            
    /* Calculates basic frequencies. Computes observed prevalence at single age        for (age=bage; age<=fage; age ++){ 
        and prints on file fileres'p'. */          cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
                cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
              }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for (k=1; k<=cptcovprod;k++)
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
                trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     /* For Powell, parameters are in a vector p[] starting at p[1]          gp=vector(1,(nlstate)*(nlstate+ndeath));
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          gm=vector(1,(nlstate)*(nlstate+ndeath));
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      
           for(theta=1; theta <=npar; theta++){
     if(mle==1){            for(i=1; i<=npar; i++)
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
     }            
                pmij(pmmij,cov,ncovmodel,xp,nlstate);
     /*--------- 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);            k=0;
              for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
    jk=1;                k=k+1;
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");                gp[k]=pmmij[i][j];
    printf("# 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)            for(i=1; i<=npar; i++)
          {              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
            printf("%d%d ",i,k);      
            fprintf(ficres,"%1d%1d ",i,k);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
            for(j=1; j <=ncovmodel; j++){            k=0;
              printf("%f ",p[jk]);            for(i=1; i<=(nlstate); i++){
              fprintf(ficres,"%f ",p[jk]);              for(j=1; j<=(nlstate+ndeath);j++){
              jk++;                k=k+1;
            }                gm[k]=pmmij[i][j];
            printf("\n");              }
            fprintf(ficres,"\n");            }
          }       
      }            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
    }              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
  if(mle==1){          }
     /* Computing hessian and covariance matrix */  
     ftolhess=ftol; /* Usually correct */          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     hesscov(matcov, p, npar, delti, ftolhess, func);            for(theta=1; theta <=npar; theta++)
  }              trgradg[j][theta]=gradg[theta][j];
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");          
     printf("# Scales (for hessian or gradient estimation)\n");          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
      for(i=1,jk=1; i <=nlstate; i++){          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
       for(j=1; j <=nlstate+ndeath; j++){          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         if (j!=i) {          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           fprintf(ficres,"%1d%1d",i,j);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           printf("%1d%1d",i,j);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           for(k=1; k<=ncovmodel;k++){  
             printf(" %.5e",delti[jk]);          pmij(pmmij,cov,ncovmodel,x,nlstate);
             fprintf(ficres," %.5e",delti[jk]);          
             jk++;          k=0;
           }          for(i=1; i<=(nlstate); i++){
           printf("\n");            for(j=1; j<=(nlstate+ndeath);j++){
           fprintf(ficres,"\n");              k=k+1;
         }              mu[k][(int) age]=pmmij[i][j];
       }            }
      }          }
              for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     k=1;            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
     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");              varpij[i][j][(int)age] = doldm[i][j];
     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");  
     for(i=1;i<=npar;i++){          /*printf("\n%d ",(int)age);
       /*  if (k>nlstate) k=1;            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       i1=(i-1)/(ncovmodel*nlstate)+1;            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       printf("%s%d%d",alph[k],i1,tab[i]);*/            }*/
       fprintf(ficres,"%3d",i);  
       printf("%3d",i);          fprintf(ficresprob,"\n%d ",(int)age);
       for(j=1; j<=i;j++){          fprintf(ficresprobcov,"\n%d ",(int)age);
         fprintf(ficres," %.5e",matcov[i][j]);          fprintf(ficresprobcor,"\n%d ",(int)age);
         printf(" %.5e",matcov[i][j]);  
       }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
       fprintf(ficres,"\n");            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       printf("\n");          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       k++;            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     }            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
              }
     while((c=getc(ficpar))=='#' && c!= EOF){          i=0;
       ungetc(c,ficpar);          for (k=1; k<=(nlstate);k++){
       fgets(line, MAXLINE, ficpar);            for (l=1; l<=(nlstate+ndeath);l++){ 
       puts(line);              i=i++;
       fputs(line,ficparo);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     }              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     ungetc(c,ficpar);              for (j=1; j<=i;j++){
     estepm=0;                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     if (estepm==0 || estepm < stepm) estepm=stepm;              }
     if (fage <= 2) {            }
       bage = ageminpar;          }/* end of loop for state */
       fage = agemaxpar;        } /* end of loop for age */
     }  
            /* Confidence intervalle of pij  */
     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(ficgp,"\nset noparametric;unset label");
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);          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");
     while((c=getc(ficpar))=='#' && c!= EOF){          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);
     ungetc(c,ficpar);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     fgets(line, MAXLINE, ficpar);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     puts(line);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     fputs(line,ficparo);        */
   }  
   ungetc(c,ficpar);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
          first1=1;
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        for (k2=1; k2<=(nlstate);k2++){
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            if(l2==k2) continue;
                  j=(k2-1)*(nlstate+ndeath)+l2;
   while((c=getc(ficpar))=='#' && c!= EOF){            for (k1=1; k1<=(nlstate);k1++){
     ungetc(c,ficpar);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     fgets(line, MAXLINE, ficpar);                if(l1==k1) continue;
     puts(line);                i=(k1-1)*(nlstate+ndeath)+l1;
     fputs(line,ficparo);                if(i<=j) continue;
   }                for (age=bage; age<=fage; age ++){ 
   ungetc(c,ficpar);                  if ((int)age %5==0){
                      v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;                    mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
   fscanf(ficpar,"pop_based=%d\n",&popbased);                    c12=cv12/sqrt(v1*v2);
   fprintf(ficparo,"pop_based=%d\n",popbased);                      /* Computing eigen value of matrix of covariance */
   fprintf(ficres,"pop_based=%d\n",popbased);                      lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                      lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   while((c=getc(ficpar))=='#' && c!= EOF){                    /* Eigen vectors */
     ungetc(c,ficpar);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     fgets(line, MAXLINE, ficpar);                    /*v21=sqrt(1.-v11*v11); *//* error */
     puts(line);                    v21=(lc1-v1)/cv12*v11;
     fputs(line,ficparo);                    v12=-v21;
   }                    v22=v11;
   ungetc(c,ficpar);                    tnalp=v21/v11;
                     if(first1==1){
   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);                      first1=0;
 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);                      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(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);                    }
                     fprintf(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*/
 while((c=getc(ficpar))=='#' && c!= EOF){                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     ungetc(c,ficpar);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     fgets(line, MAXLINE, ficpar);                    if(first==1){
     puts(line);                      first=0;
     fputs(line,ficparo);                      fprintf(ficgp,"\nset parametric;unset label");
   }                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
   ungetc(c,ficpar);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                      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);
 /*------------ gnuplot -------------*/                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                        fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
 /*------------ free_vector  -------------*/                      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",\
  chdir(path);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                                mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
  free_ivector(wav,1,imx);                    }else{
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);                      first=0;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                        fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
  free_ivector(num,1,n);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
  free_vector(agedc,1,n);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
  /*free_matrix(covar,1,NCOVMAX,1,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",\
  fclose(ficparo);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
  fclose(ficres);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
 /*--------- index.htm --------*/                  } /* age mod 5 */
                 } /* end loop age */
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
                } /*l12 */
   /*--------------- Prevalence limit --------------*/            } /* k12 */
            } /*l1 */
   strcpy(filerespl,"pl");        }/* k1 */
   strcat(filerespl,fileres);      } /* loop covariates */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    }
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   }    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    free_vector(xp,1,npar);
   fprintf(ficrespl,"#Prevalence limit\n");    fclose(ficresprob);
   fprintf(ficrespl,"#Age ");    fclose(ficresprobcov);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    fclose(ficresprobcor);
   fprintf(ficrespl,"\n");    fflush(ficgp);
      fflush(fichtmcov);
   prlim=matrix(1,nlstate,1,nlstate);  }
   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 */  /******************* Printing html file ***********/
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                    int lastpass, int stepm, int weightopt, char model[],\
   k=0;                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   agebase=ageminpar;                    int popforecast, int estepm ,\
   agelim=agemaxpar;                    double jprev1, double mprev1,double anprev1, \
   ftolpl=1.e-10;                    double jprev2, double mprev2,double anprev2){
   i1=cptcoveff;    int jj1, k1, i1, cpt;
   if (cptcovn < 1){i1=1;}  
      fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
   for(cptcov=1;cptcov<=i1;cptcov++){   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
         k=k+1;     fprintf(fichtm,"\
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
         fprintf(ficrespl,"\n#******");             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
         for(j=1;j<=cptcoveff;j++)     fprintf(fichtm,"\
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
         fprintf(ficrespl,"******\n");             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
             fprintf(fichtm,"\
         for (age=agebase; age<=agelim; age++){   - Life expectancies by age and initial health status (estepm=%2d months): \
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);     <a href=\"%s\">%s</a> <br>\n</li>",
           fprintf(ficrespl,"%.0f",age );             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
           for(i=1; i<=nlstate;i++)  
           fprintf(ficrespl," %.5f", prlim[i][i]);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
           fprintf(ficrespl,"\n");  
         }   m=cptcoveff;
       }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     }  
   fclose(ficrespl);   jj1=0;
    for(k1=1; k1<=m;k1++){
   /*------------- h Pij x at various ages ------------*/     for(i1=1; i1<=ncodemax[k1];i1++){
         jj1++;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);       if (cptcovn > 0) {
   if((ficrespij=fopen(filerespij,"w"))==NULL) {         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;         for (cpt=1; cpt<=cptcoveff;cpt++) 
   }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   printf("Computing pij: result on file '%s' \n", filerespij);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         }
   stepsize=(int) (stepm+YEARM-1)/YEARM;       /* Pij */
   /*if (stepm<=24) stepsize=2;*/       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);     
   agelim=AGESUP;       /* Quasi-incidences */
   hstepm=stepsize*YEARM; /* Every year of age */       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
    <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
   k=0;         /* Stable prevalence in each health state */
   for(cptcov=1;cptcov<=i1;cptcov++){         for(cpt=1; cpt<nlstate;cpt++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
       k=k+1;  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
         fprintf(ficrespij,"\n#****** ");         }
         for(j=1;j<=cptcoveff;j++)       for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
         fprintf(ficrespij,"******\n");  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
               }
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */     } /* end i1 */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */   }/* End k1 */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */   fprintf(fichtm,"</ul>");
           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(fichtm,"\
           fprintf(ficrespij,"# Age");  \n<br><li><h4> Result files (second order: variances)</h4>\n\
           for(i=1; i<=nlstate;i++)   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %1d-%1d",i,j);   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
           fprintf(ficrespij,"\n");           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
           for (h=0; h<=nhstepm; h++){   fprintf(fichtm,"\
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
             for(i=1; i<=nlstate;i++)           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
               for(j=1; j<=nlstate+ndeath;j++)  
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);   fprintf(fichtm,"\
             fprintf(ficrespij,"\n");   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
           }           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   fprintf(fichtm,"\
           fprintf(ficrespij,"\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"));
     }   fprintf(fichtm,"\
   }   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/   fprintf(fichtm,"\
    - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
   fclose(ficrespij);           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*---------- Forecasting ------------------*/  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   if((stepm == 1) && (strcmp(model,".")==0)){  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);  /*      <br>",fileres,fileres,fileres,fileres); */
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  /*  else  */
     free_matrix(mint,1,maxwav,1,n);  /*    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); */
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);   fflush(fichtm);
     free_vector(weight,1,n);}   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   else{  
     erreur=108;   m=cptcoveff;
     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);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   }  
     jj1=0;
    for(k1=1; k1<=m;k1++){
   /*---------- Health expectancies and variances ------------*/     for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
   strcpy(filerest,"t");       if (cptcovn > 0) {
   strcat(filerest,fileres);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   if((ficrest=fopen(filerest,"w"))==NULL) {         for (cpt=1; cpt<=cptcoveff;cpt++) 
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   printf("Computing Total LEs with variances: file '%s' \n", filerest);       }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   strcpy(filerese,"e");  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   strcat(filerese,fileres);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
   if((ficreseij=fopen(filerese,"w"))==NULL) {       }
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   }  health expectancies in states (1) and (2): %s%d.png<br>\
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
  strcpy(fileresv,"v");   }/* End k1 */
   strcat(fileresv,fileres);   fprintf(fichtm,"</ul>");
   if((ficresvij=fopen(fileresv,"w"))==NULL) {   fflush(fichtm);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  }
   }  
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  /******************* 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(ficrest,"\n#****** ");  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
       for(j=1;j<=cptcoveff;j++)  /*     printf("Problem with file %s",optionfilegnuplot); */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
       fprintf(ficrest,"******\n");  /*   } */
   
       fprintf(ficreseij,"\n#****** ");    /*#ifdef windows */
       for(j=1;j<=cptcoveff;j++)    fprintf(ficgp,"cd \"%s\" \n",pathc);
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      /*#endif */
       fprintf(ficreseij,"******\n");    m=pow(2,cptcoveff);
   
       fprintf(ficresvij,"\n#****** ");    strcpy(dirfileres,optionfilefiname);
       for(j=1;j<=cptcoveff;j++)    strcpy(optfileres,"vpl");
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   /* 1eme*/
       fprintf(ficresvij,"******\n");    for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
       oldm=oldms;savm=savms;       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);         fprintf(ficgp,"set xlabel \"Age\" \n\
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  set ylabel \"Probability\" \n\
       oldm=oldms;savm=savms;  set ter png small\n\
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);  set size 0.65,0.65\n\
      plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
         for (i=1; i<= nlstate ; i ++) {
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       fprintf(ficrest,"\n");       }
        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);
       epj=vector(1,nlstate+1);       for (i=1; i<= nlstate ; i ++) {
       for(age=bage; age <=fage ;age++){         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);         else fprintf(ficgp," \%%*lf (\%%*lf)");
         if (popbased==1) {       } 
           for(i=1; i<=nlstate;i++)       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
             prlim[i][i]=probs[(int)age][i][k];       for (i=1; i<= nlstate ; i ++) {
         }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
                 else fprintf(ficgp," \%%*lf (\%%*lf)");
         fprintf(ficrest," %4.0f",age);       }  
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
           for(i=1, epj[j]=0.;i <=nlstate;i++) {     }
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    }
           }    /*2 eme*/
           epj[nlstate+1] +=epj[j];    
         }    for (k1=1; k1<= m ; k1 ++) { 
         for(i=1, vepp=0.;i <=nlstate;i++)      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
           for(j=1;j <=nlstate;j++)      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
             vepp += vareij[i][j][(int)age];      
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));      for (i=1; i<= nlstate+1 ; i ++) {
         for(j=1;j <=nlstate;j++){        k=2*i;
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         }        for (j=1; j<= nlstate+1 ; j ++) {
         fprintf(ficrest,"\n");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       }          else fprintf(ficgp," \%%*lf (\%%*lf)");
     }        }   
   }        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   fclose(ficreseij);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   fclose(ficresvij);        for (j=1; j<= nlstate+1 ; j ++) {
   fclose(ficrest);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   fclose(ficpar);          else fprintf(ficgp," \%%*lf (\%%*lf)");
   free_vector(epj,1,nlstate+1);        }   
          fprintf(ficgp,"\" t\"\" w l 0,");
   /*------- Variance limit prevalence------*/          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 ++) {
   strcpy(fileresvpl,"vpl");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   strcat(fileresvpl,fileres);          else fprintf(ficgp," \%%*lf (\%%*lf)");
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        }   
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
     exit(0);        else fprintf(ficgp,"\" t\"\" w l 0,");
   }      }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    }
     
   k=0;    /*3eme*/
   for(cptcov=1;cptcov<=i1;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    for (k1=1; k1<= m ; k1 ++) { 
       k=k+1;      for (cpt=1; cpt<= nlstate ; cpt ++) {
       fprintf(ficresvpl,"\n#****** ");        k=2+nlstate*(2*cpt-2);
       for(j=1;j<=cptcoveff;j++)        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficgp,"set ter png small\n\
       fprintf(ficresvpl,"******\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);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
       oldm=oldms;savm=savms;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          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);
   fclose(ficresvpl);          
         */
   /*---------- End : free ----------------*/        for (i=1; i< nlstate ; i ++) {
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          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);
            
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        } 
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      }
      }
      
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    /* CV preval stable (period) */
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    for (k1=1; k1<= m ; k1 ++) { 
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      for (cpt=1; cpt<=nlstate ; cpt ++) {
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        k=3;
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
   free_matrix(matcov,1,npar,1,npar);        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   free_vector(delti,1,npar);  set ter png small\nset size 0.65,0.65\n\
   free_matrix(agev,1,maxwav,1,imx);  unset log y\n\
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
   if(erreur >0)        for (i=1; i< nlstate ; i ++)
     printf("End of Imach with error or warning %d\n",erreur);          fprintf(ficgp,"+$%d",k+i+1);
   else   printf("End of Imach\n");        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        
          l=3+(nlstate+ndeath)*cpt;
   /* 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);*/        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
   /*printf("Total time was %d uSec.\n", total_usecs);*/        for (i=1; i< nlstate ; i ++) {
   /*------ End -----------*/          l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
  end:        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
 #ifdef windows      } 
   /* chdir(pathcd);*/    }  
 #endif    
  /*system("wgnuplot graph.plt");*/    /* proba elementaires */
  /*system("../gp37mgw/wgnuplot graph.plt");*/    for(i=1,jk=1; i <=nlstate; i++){
  /*system("cd ../gp37mgw");*/      for(k=1; k <=(nlstate+ndeath); k++){
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        if (k != i) {
  strcpy(plotcmd,GNUPLOTPROGRAM);          for(j=1; j <=ncovmodel; j++){
  strcat(plotcmd," ");            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
  strcat(plotcmd,optionfilegnuplot);            jk++; 
  system(plotcmd);            fprintf(ficgp,"\n");
           }
 #ifdef windows        }
   while (z[0] != 'q') {      }
     /* chdir(path); */     }
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");  
     scanf("%s",z);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
     if (z[0] == 'c') system("./imach");       for(jk=1; jk <=m; jk++) {
     else if (z[0] == 'e') system(optionfilehtm);         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
     else if (z[0] == 'g') system(plotcmd);         if (ng==2)
     else if (z[0] == 'q') exit(0);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   }         else
 #endif           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=1; 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=0;i<=imx-1 ; i++)
       {
         if (cens[i]==1 & wav[i]>1)
           A=-x[1]/(x[2])*
             (exp(x[2]/YEARM*(agecens[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)));
         
         if (cens[i]==0 & wav[i]>1)
           A=-x[1]/(x[2])*
                (exp(x[2]/YEARM*(agedc[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)))
             +log(x[1]/YEARM)+x[2]/YEARM*(agedc[i]*12-agegomp*12)+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=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (j=1; j<=lastpass; j++)
           if (s[j][i]>nlstate) {
             dcwave[i]=j;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];agecens[i]=1.; 
           if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
           cens[i]=1;
           
           if (ageexmed[i]<1) cens[i]=-1;
           if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
   
       p[1]=0.1; p[2]=0.1;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow-mort"); 
     strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
     /*  for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     */
     fprintf(ficrespow,"\n");
   
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM,delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov);
     } /* Endof if mle==-3 */
   
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficrespl,"#Stable prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
   
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /*---------- Health expectancies and variances ------------*/
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total LEs with variances: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficreseij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
           }
   
    
           fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficreseij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of stable prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocaltime at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
     strcpy(plotcmd,"\"");
     strcat(plotcmd,pathimach);
     strcat(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd,"\"");
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     if((outcmd=system(plotcmd)) != 0){
       printf(" Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.36  
changed lines
  Added in v.1.101


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