Diff for /imach/src/imach.c between versions 1.44 and 1.104

version 1.44, 2002/05/24 13:01:48 version 1.104, 2005/09/30 16:11:43
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.104  2005/09/30 16:11:43  lievre
      (Module): sump fixed, loop imx fixed, and simplifications.
   This program computes Healthy Life Expectancies from    (Module): If the status is missing at the last wave but we know
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    that the person is alive, then we can code his/her status as -2
   first survey ("cross") where individuals from different ages are    (instead of missing=-1 in earlier versions) and his/her
   interviewed on their health status or degree of disability (in the    contributions to the likelihood is 1 - Prob of dying from last
   case of a health survey which is our main interest) -2- at least a    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   second wave of interviews ("longitudinal") which measure each change    the healthy state at last known wave). Version is 0.98
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.103  2005/09/30 15:54:49  lievre
   model. More health states you consider, more time is necessary to reach the    (Module): sump fixed, loop imx fixed, and simplifications.
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.102  2004/09/15 17:31:30  brouard
   probability to be observed in state j at the second wave    Add the possibility to read data file including tab characters.
   conditional to be observed in state i at the first wave. Therefore  
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Revision 1.101  2004/09/15 10:38:38  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    Fix on curr_time
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.100  2004/07/12 18:29:06  brouard
   you to do it.  More covariates you add, slower the    Add version for Mac OS X. Just define UNIX in Makefile
   convergence.  
     Revision 1.99  2004/06/05 08:57:40  brouard
   The advantage of this computer programme, compared to a simple    *** empty log message ***
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.98  2004/05/16 15:05:56  brouard
   intermediate interview, the information is lost, but taken into    New version 0.97 . First attempt to estimate force of mortality
   account using an interpolation or extrapolation.      directly from the data i.e. without the need of knowing the health
     state at each age, but using a Gompertz model: log u =a + b*age .
   hPijx is the probability to be observed in state i at age x+h    This is the basic analysis of mortality and should be done before any
   conditional to the observed state i at age x. The delay 'h' can be    other analysis, in order to test if the mortality estimated from the
   split into an exact number (nh*stepm) of unobserved intermediate    cross-longitudinal survey is different from the mortality estimated
   states. This elementary transition (by month or quarter trimester,    from other sources like vital statistic data.
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    The same imach parameter file can be used but the option for mle should be -3.
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Agnès, who wrote this part of the code, tried to keep most of the
     former routines in order to include the new code within the former code.
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    The output is very simple: only an estimate of the intercept and of
      the slope with 95% confident intervals.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Current limitations:
   This software have been partly granted by Euro-REVES, a concerted action    A) Even if you enter covariates, i.e. with the
   from the European Union.    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   It is copyrighted identically to a GNU software product, ie programme and    B) There is no computation of Life Expectancy nor Life Table.
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Revision 1.97  2004/02/20 13:25:42  lievre
   **********************************************************************/    Version 0.96d. Population forecasting command line is (temporarily)
      suppressed.
 #include <math.h>  
 #include <stdio.h>    Revision 1.96  2003/07/15 15:38:55  brouard
 #include <stdlib.h>    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #include <unistd.h>    rewritten within the same printf. Workaround: many printfs.
   
 #define MAXLINE 256    Revision 1.95  2003/07/08 07:54:34  brouard
 #define GNUPLOTPROGRAM "gnuplot"    * imach.c (Repository):
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    (Repository): Using imachwizard code to output a more meaningful covariance
 #define FILENAMELENGTH 80    matrix (cov(a12,c31) instead of numbers.
 /*#define DEBUG*/  
 #define windows    Revision 1.94  2003/06/27 13:00:02  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Just cleaning
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.93  2003/06/25 16:33:55  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    (Module): On windows (cygwin) function asctime_r doesn't
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    exist so I changed back to asctime which exists.
     (Module): Version 0.96b
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.92  2003/06/25 16:30:45  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    (Module): On windows (cygwin) function asctime_r doesn't
 #define NCOVMAX 8 /* Maximum number of covariates */    exist so I changed back to asctime which exists.
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.91  2003/06/25 15:30:29  brouard
 #define AGESUP 130    * imach.c (Repository): Duplicated warning errors corrected.
 #define AGEBASE 40    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
 int erreur; /* Error number */    concerning matrix of covariance. It has extension -cov.htm.
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.90  2003/06/24 12:34:15  brouard
 int npar=NPARMAX;    (Module): Some bugs corrected for windows. Also, when
 int nlstate=2; /* Number of live states */    mle=-1 a template is output in file "or"mypar.txt with the design
 int ndeath=1; /* Number of dead states */    of the covariance matrix to be input.
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.89  2003/06/24 12:30:52  brouard
     (Module): Some bugs corrected for windows. Also, when
 int *wav; /* Number of waves for this individuual 0 is possible */    mle=-1 a template is output in file "or"mypar.txt with the design
 int maxwav; /* Maxim number of waves */    of the covariance matrix to be input.
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.88  2003/06/23 17:54:56  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Revision 1.87  2003/06/18 12:26:01  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Version 0.96
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Revision 1.86  2003/06/17 20:04:08  brouard
 FILE *ficgp,*ficresprob,*ficpop;    (Module): Change position of html and gnuplot routines and added
 FILE *ficreseij;    routine fileappend.
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.85  2003/06/17 13:12:43  brouard
   char fileresv[FILENAMELENGTH];    * imach.c (Repository): Check when date of death was earlier that
  FILE  *ficresvpl;    current date of interview. It may happen when the death was just
   char fileresvpl[FILENAMELENGTH];    prior to the death. In this case, dh was negative and likelihood
     was wrong (infinity). We still send an "Error" but patch by
 #define NR_END 1    assuming that the date of death was just one stepm after the
 #define FREE_ARG char*    interview.
 #define FTOL 1.0e-10    (Repository): Because some people have very long ID (first column)
     we changed int to long in num[] and we added a new lvector for
 #define NRANSI    memory allocation. But we also truncated to 8 characters (left
 #define ITMAX 200    truncation)
     (Repository): No more line truncation errors.
 #define TOL 2.0e-4  
     Revision 1.84  2003/06/13 21:44:43  brouard
 #define CGOLD 0.3819660    * imach.c (Repository): Replace "freqsummary" at a correct
 #define ZEPS 1.0e-10    place. It differs from routine "prevalence" which may be called
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    many times. Probs is memory consuming and must be used with
     parcimony.
 #define GOLD 1.618034    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.82  2003/06/05 15:57:20  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Add log in  imach.c and  fullversion number is now printed.
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  */
 #define rint(a) floor(a+0.5)  /*
      Interpolated Markov Chain
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Short summary of the programme:
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    
     This program computes Healthy Life Expectancies from
 int imx;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 int stepm;    first survey ("cross") where individuals from different ages are
 /* Stepm, step in month: minimum step interpolation*/    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
 int estepm;    second wave of interviews ("longitudinal") which measure each change
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
 int m,nb;    model. More health states you consider, more time is necessary to reach the
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Maximum Likelihood of the parameters involved in the model.  The
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    simplest model is the multinomial logistic model where pij is the
 double **pmmij, ***probs, ***mobaverage;    probability to be observed in state j at the second wave
 double dateintmean=0;    conditional to be observed in state i at the first wave. Therefore
     the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 double *weight;    'age' is age and 'sex' is a covariate. If you want to have a more
 int **s; /* Status */    complex model than "constant and age", you should modify the program
 double *agedc, **covar, idx;    where the markup *Covariates have to be included here again* invites
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    you to do it.  More covariates you add, slower the
     convergence.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    The advantage of this computer programme, compared to a simple
     multinomial logistic model, is clear when the delay between waves is not
 /**************** split *************************/    identical for each individual. Also, if a individual missed an
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    intermediate interview, the information is lost, but taken into
 {    account using an interpolation or extrapolation.  
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    hPijx is the probability to be observed in state i at age x+h
     conditional to the observed state i at age x. The delay 'h' can be
    l1 = strlen( path );                 /* length of path */    split into an exact number (nh*stepm) of unobserved intermediate
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    states. This elementary transition (by month, quarter,
 #ifdef windows    semester or year) is modelled as a multinomial logistic.  The hPx
    s = strrchr( path, '\\' );           /* find last / */    matrix is simply the matrix product of nh*stepm elementary matrices
 #else    and the contribution of each individual to the likelihood is simply
    s = strrchr( path, '/' );            /* find last / */    hPijx.
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */    Also this programme outputs the covariance matrix of the parameters but also
 #if     defined(__bsd__)                /* get current working directory */    of the life expectancies. It also computes the stable prevalence. 
       extern char       *getwd( );    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
       if ( getwd( dirc ) == NULL ) {             Institut national d'études démographiques, Paris.
 #else    This software have been partly granted by Euro-REVES, a concerted action
       extern char       *getcwd( );    from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    software can be distributed freely for non commercial use. Latest version
 #endif    can be accessed at http://euroreves.ined.fr/imach .
          return( GLOCK_ERROR_GETCWD );  
       }    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
       strcpy( name, path );             /* we've got it */    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
    } else {                             /* strip direcotry from path */    
       s++;                              /* after this, the filename */    **********************************************************************/
       l2 = strlen( s );                 /* length of filename */  /*
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    main
       strcpy( name, s );                /* save file name */    read parameterfile
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    read datafile
       dirc[l1-l2] = 0;                  /* add zero */    concatwav
    }    freqsummary
    l1 = strlen( dirc );                 /* length of directory */    if (mle >= 1)
 #ifdef windows      mlikeli
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    print results files
 #else    if mle==1 
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }       computes hessian
 #endif    read end of parameter file: agemin, agemax, bage, fage, estepm
    s = strrchr( name, '.' );            /* find last / */        begin-prev-date,...
    s++;    open gnuplot file
    strcpy(ext,s);                       /* save extension */    open html file
    l1= strlen( name);    stable prevalence
    l2= strlen( s)+1;     for age prevalim()
    strncpy( finame, name, l1-l2);    h Pij x
    finame[l1-l2]= 0;    variance of p varprob
    return( 0 );                         /* we're done */    forecasting if prevfcast==1 prevforecast call prevalence()
 }    health expectancies
     Variance-covariance of DFLE
     prevalence()
 /******************************************/     movingaverage()
     varevsij() 
 void replace(char *s, char*t)    if popbased==1 varevsij(,popbased)
 {    total life expectancies
   int i;    Variance of stable prevalence
   int lg=20;   end
   i=0;  */
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';   
   }  #include <math.h>
 }  #include <stdio.h>
   #include <stdlib.h>
 int nbocc(char *s, char occ)  #include <unistd.h>
 {  
   int i,j=0;  /* #include <sys/time.h> */
   int lg=20;  #include <time.h>
   i=0;  #include "timeval.h"
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {  /* #include <libintl.h> */
   if  (s[i] == occ ) j++;  /* #define _(String) gettext (String) */
   }  
   return j;  #define MAXLINE 256
 }  #define GNUPLOTPROGRAM "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 void cutv(char *u,char *v, char*t, char occ)  #define FILENAMELENGTH 132
 {  /*#define DEBUG*/
   int i,lg,j,p=0;  /*#define windows*/
   i=0;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   for(j=0; j<=strlen(t)-1; j++) {  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   lg=strlen(t);  
   for(j=0; j<p; j++) {  #define NINTERVMAX 8
     (u[j] = t[j]);  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   }  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
      u[p]='\0';  #define NCOVMAX 8 /* Maximum number of covariates */
   #define MAXN 20000
    for(j=0; j<= lg; j++) {  #define YEARM 12. /* Number of months per year */
     if (j>=(p+1))(v[j-p-1] = t[j]);  #define AGESUP 130
   }  #define AGEBASE 40
 }  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   #ifdef UNIX
 /********************** nrerror ********************/  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
 void nrerror(char error_text[])  #else
 {  #define DIRSEPARATOR '\\'
   fprintf(stderr,"ERREUR ...\n");  #define ODIRSEPARATOR '/'
   fprintf(stderr,"%s\n",error_text);  #endif
   exit(1);  
 }  /* $Id$ */
 /*********************** vector *******************/  /* $State$ */
 double *vector(int nl, int nh)  
 {  char version[]="Imach version 0.98, September 2005, INED-EUROREVES ";
   double *v;  char fullversion[]="$Revision$ $Date$"; 
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   if (!v) nrerror("allocation failure in vector");  int nvar;
   return v-nl+NR_END;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 }  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
 /************************ free vector ******************/  int ndeath=1; /* Number of dead states */
 void free_vector(double*v, int nl, int nh)  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 {  int popbased=0;
   free((FREE_ARG)(v+nl-NR_END));  
 }  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav; /* Maxim number of waves */
 /************************ivector *******************************/  int jmin, jmax; /* min, max spacing between 2 waves */
 int *ivector(long nl,long nh)  int gipmx, gsw; /* Global variables on the number of contributions 
 {                     to the likelihood and the sum of weights (done by funcone)*/
   int *v;  int mle, weightopt;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   if (!v) nrerror("allocation failure in ivector");  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 ivector **************************/  double **oldm, **newm, **savm; /* Working pointers to matrices */
 void free_ivector(int *v, long nl, long 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 */
 /******************* imatrix *******************************/  long ipmx; /* Number of contributions */
 int **imatrix(long nrl, long nrh, long ncl, long nch)  double sw; /* Sum of weights */
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  char filerespow[FILENAMELENGTH];
 {  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  FILE *ficresilk;
   int **m;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
    FILE *ficresprobmorprev;
   /* allocate pointers to rows */  FILE *fichtm, *fichtmcov; /* Html File */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  FILE *ficreseij;
   if (!m) nrerror("allocation failure 1 in matrix()");  char filerese[FILENAMELENGTH];
   m += NR_END;  FILE  *ficresvij;
   m -= nrl;  char fileresv[FILENAMELENGTH];
    FILE  *ficresvpl;
    char fileresvpl[FILENAMELENGTH];
   /* allocate rows and set pointers to them */  char title[MAXLINE];
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   m[nrl] += NR_END;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   m[nrl] -= ncl;  char command[FILENAMELENGTH];
    int  outcmd=0;
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   /* return pointer to array of pointers to rows */  
   return m;  char filelog[FILENAMELENGTH]; /* Log file */
 }  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
 /****************** free_imatrix *************************/  char popfile[FILENAMELENGTH];
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 {  struct timezone tzp;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  extern int gettimeofday();
   free((FREE_ARG) (m+nrl-NR_END));  struct tm tmg, tm, tmf, *gmtime(), *localtime();
 }  long time_value;
   extern long time();
 /******************* matrix *******************************/  char strcurr[80], strfor[80];
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {  #define NR_END 1
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  #define FREE_ARG char*
   double **m;  #define FTOL 1.0e-10
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define NRANSI 
   if (!m) nrerror("allocation failure 1 in matrix()");  #define ITMAX 200 
   m += NR_END;  
   m -= nrl;  #define TOL 2.0e-4 
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define CGOLD 0.3819660 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define ZEPS 1.0e-10 
   m[nrl] += NR_END;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   m[nrl] -= ncl;  
   #define GOLD 1.618034 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define GLIMIT 100.0 
   return m;  #define TINY 1.0e-20 
 }  
   static double maxarg1,maxarg2;
 /*************************free matrix ************************/  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 {    
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   free((FREE_ARG)(m+nrl-NR_END));  #define rint(a) floor(a+0.5)
 }  
   static double sqrarg;
 /******************* ma3x *******************************/  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 {  int agegomp= AGEGOMP;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  int imx; 
   int stepm=1;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  /* Stepm, step in month: minimum step interpolation*/
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  int estepm;
   m -= nrl;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int m,nb;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  long *num;
   m[nrl] += NR_END;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   m[nrl] -= ncl;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  double *ageexmed,*agecens;
   double dateintmean=0;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  double *weight;
   m[nrl][ncl] += NR_END;  int **s; /* Status */
   m[nrl][ncl] -= nll;  double *agedc, **covar, idx;
   for (j=ncl+1; j<=nch; j++)  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
     m[nrl][j]=m[nrl][j-1]+nlay;  
    double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   for (i=nrl+1; i<=nrh; i++) {  double ftolhess; /* Tolerance for computing hessian */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  /**************** split *************************/
       m[i][j]=m[i][j-1]+nlay;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   }  {
   return m;    /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
 }       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     */ 
 /*************************free ma3x ************************/    char  *ss;                            /* pointer */
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    int   l1, l2;                         /* length counters */
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    l1 = strlen(path );                   /* length of path */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   free((FREE_ARG)(m+nrl-NR_END));    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 }    if ( ss == NULL ) {                   /* no directory, so use current */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 /***************** f1dim *************************/        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 extern int ncom;      /* get current working directory */
 extern double *pcom,*xicom;      /*    extern  char* getcwd ( char *buf , int len);*/
 extern double (*nrfunc)(double []);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
          return( GLOCK_ERROR_GETCWD );
 double f1dim(double x)      }
 {      strcpy( name, path );               /* we've got it */
   int j;    } else {                              /* strip direcotry from path */
   double f;      ss++;                               /* after this, the filename */
   double *xt;      l2 = strlen( ss );                  /* length of filename */
        if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   xt=vector(1,ncom);      strcpy( name, ss );         /* save file name */
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   f=(*nrfunc)(xt);      dirc[l1-l2] = 0;                    /* add zero */
   free_vector(xt,1,ncom);    }
   return f;    l1 = strlen( dirc );                  /* length of directory */
 }    /*#ifdef windows
     if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 /*****************brent *************************/  #else
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 {  #endif
   int iter;    */
   double a,b,d,etemp;    ss = strrchr( name, '.' );            /* find last / */
   double fu,fv,fw,fx;    if (ss >0){
   double ftemp;      ss++;
   double p,q,r,tol1,tol2,u,v,w,x,xm;      strcpy(ext,ss);                     /* save extension */
   double e=0.0;      l1= strlen( name);
        l2= strlen(ss)+1;
   a=(ax < cx ? ax : cx);      strncpy( finame, name, l1-l2);
   b=(ax > cx ? ax : cx);      finame[l1-l2]= 0;
   x=w=v=bx;    }
   fw=fv=fx=(*f)(x);    return( 0 );                          /* we're done */
   for (iter=1;iter<=ITMAX;iter++) {  }
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  /******************************************/
     printf(".");fflush(stdout);  
 #ifdef DEBUG  void replace_back_to_slash(char *s, char*t)
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  {
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    int i;
 #endif    int lg=0;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    i=0;
       *xmin=x;    lg=strlen(t);
       return fx;    for(i=0; i<= lg; i++) {
     }      (s[i] = t[i]);
     ftemp=fu;      if (t[i]== '\\') s[i]='/';
     if (fabs(e) > tol1) {    }
       r=(x-w)*(fx-fv);  }
       q=(x-v)*(fx-fw);  
       p=(x-v)*q-(x-w)*r;  int nbocc(char *s, char occ)
       q=2.0*(q-r);  {
       if (q > 0.0) p = -p;    int i,j=0;
       q=fabs(q);    int lg=20;
       etemp=e;    i=0;
       e=d;    lg=strlen(s);
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    for(i=0; i<= lg; i++) {
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    if  (s[i] == occ ) j++;
       else {    }
         d=p/q;    return j;
         u=x+d;  }
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  void cutv(char *u,char *v, char*t, char occ)
       }  {
     } else {    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
     }       gives u="abcedf" and v="ghi2j" */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    int i,lg,j,p=0;
     fu=(*f)(u);    i=0;
     if (fu <= fx) {    for(j=0; j<=strlen(t)-1; j++) {
       if (u >= x) a=x; else b=x;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
       SHFT(v,w,x,u)    }
         SHFT(fv,fw,fx,fu)  
         } else {    lg=strlen(t);
           if (u < x) a=u; else b=u;    for(j=0; j<p; j++) {
           if (fu <= fw || w == x) {      (u[j] = t[j]);
             v=w;    }
             w=u;       u[p]='\0';
             fv=fw;  
             fw=fu;     for(j=0; j<= lg; j++) {
           } else if (fu <= fv || v == x || v == w) {      if (j>=(p+1))(v[j-p-1] = t[j]);
             v=u;    }
             fv=fu;  }
           }  
         }  /********************** nrerror ********************/
   }  
   nrerror("Too many iterations in brent");  void nrerror(char error_text[])
   *xmin=x;  {
   return fx;    fprintf(stderr,"ERREUR ...\n");
 }    fprintf(stderr,"%s\n",error_text);
     exit(EXIT_FAILURE);
 /****************** mnbrak ***********************/  }
   /*********************** vector *******************/
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  double *vector(int nl, int nh)
             double (*func)(double))  {
 {    double *v;
   double ulim,u,r,q, dum;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   double fu;    if (!v) nrerror("allocation failure in vector");
      return v-nl+NR_END;
   *fa=(*func)(*ax);  }
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  /************************ free vector ******************/
     SHFT(dum,*ax,*bx,dum)  void free_vector(double*v, int nl, int nh)
       SHFT(dum,*fb,*fa,dum)  {
       }    free((FREE_ARG)(v+nl-NR_END));
   *cx=(*bx)+GOLD*(*bx-*ax);  }
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  /************************ivector *******************************/
     r=(*bx-*ax)*(*fb-*fc);  int *ivector(long nl,long nh)
     q=(*bx-*cx)*(*fb-*fa);  {
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    int *v;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     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 ivector **************************/
       if (fu < *fc) {  void free_ivector(int *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;  /************************lvector *******************************/
       fu=(*func)(u);  long *lvector(long nl,long nh)
     } else {  {
       u=(*cx)+GOLD*(*cx-*bx);    long *v;
       fu=(*func)(u);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     }    if (!v) nrerror("allocation failure in ivector");
     SHFT(*ax,*bx,*cx,u)    return v-nl+NR_END;
       SHFT(*fa,*fb,*fc,fu)  }
       }  
 }  /******************free lvector **************************/
   void free_lvector(long *v, long nl, long nh)
 /*************** linmin ************************/  {
     free((FREE_ARG)(v+nl-NR_END));
 int ncom;  }
 double *pcom,*xicom;  
 double (*nrfunc)(double []);  /******************* imatrix *******************************/
    int **imatrix(long nrl, long nrh, long ncl, long nch) 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 {  { 
   double brent(double ax, double bx, double cx,    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
                double (*f)(double), double tol, double *xmin);    int **m; 
   double f1dim(double x);    
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    /* allocate pointers to rows */ 
               double *fc, double (*func)(double));    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   int j;    if (!m) nrerror("allocation failure 1 in matrix()"); 
   double xx,xmin,bx,ax;    m += NR_END; 
   double fx,fb,fa;    m -= nrl; 
      
   ncom=n;    
   pcom=vector(1,n);    /* allocate rows and set pointers to them */ 
   xicom=vector(1,n);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   nrfunc=func;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   for (j=1;j<=n;j++) {    m[nrl] += NR_END; 
     pcom[j]=p[j];    m[nrl] -= ncl; 
     xicom[j]=xi[j];    
   }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   ax=0.0;    
   xx=1.0;    /* return pointer to array of pointers to rows */ 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    return m; 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  } 
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  /****************** free_imatrix *************************/
 #endif  void free_imatrix(m,nrl,nrh,ncl,nch)
   for (j=1;j<=n;j++) {        int **m;
     xi[j] *= xmin;        long nch,ncl,nrh,nrl; 
     p[j] += xi[j];       /* free an int matrix allocated by imatrix() */ 
   }  { 
   free_vector(xicom,1,n);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   free_vector(pcom,1,n);    free((FREE_ARG) (m+nrl-NR_END)); 
 }  } 
   
 /*************** powell ************************/  /******************* matrix *******************************/
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  double **matrix(long nrl, long nrh, long ncl, long nch)
             double (*func)(double []))  {
 {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   void linmin(double p[], double xi[], int n, double *fret,    double **m;
               double (*func)(double []));  
   int i,ibig,j;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double del,t,*pt,*ptt,*xit;    if (!m) nrerror("allocation failure 1 in matrix()");
   double fp,fptt;    m += NR_END;
   double *xits;    m -= nrl;
   pt=vector(1,n);  
   ptt=vector(1,n);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   xit=vector(1,n);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   xits=vector(1,n);    m[nrl] += NR_END;
   *fret=(*func)(p);    m[nrl] -= ncl;
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     fp=(*fret);    return m;
     ibig=0;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     del=0.0;     */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  }
     for (i=1;i<=n;i++)  
       printf(" %d %.12f",i, p[i]);  /*************************free matrix ************************/
     printf("\n");  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     for (i=1;i<=n;i++) {  {
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       fptt=(*fret);    free((FREE_ARG)(m+nrl-NR_END));
 #ifdef DEBUG  }
       printf("fret=%lf \n",*fret);  
 #endif  /******************* ma3x *******************************/
       printf("%d",i);fflush(stdout);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       linmin(p,xit,n,fret,func);  {
       if (fabs(fptt-(*fret)) > del) {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
         del=fabs(fptt-(*fret));    double ***m;
         ibig=i;  
       }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 #ifdef DEBUG    if (!m) nrerror("allocation failure 1 in matrix()");
       printf("%d %.12e",i,(*fret));    m += NR_END;
       for (j=1;j<=n;j++) {    m -= nrl;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       for(j=1;j<=n;j++)    m[nrl] += NR_END;
         printf(" p=%.12e",p[j]);    m[nrl] -= ncl;
       printf("\n");  
 #endif    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 #ifdef DEBUG    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       int k[2],l;    m[nrl][ncl] += NR_END;
       k[0]=1;    m[nrl][ncl] -= nll;
       k[1]=-1;    for (j=ncl+1; j<=nch; j++) 
       printf("Max: %.12e",(*func)(p));      m[nrl][j]=m[nrl][j-1]+nlay;
       for (j=1;j<=n;j++)    
         printf(" %.12e",p[j]);    for (i=nrl+1; i<=nrh; i++) {
       printf("\n");      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       for(l=0;l<=1;l++) {      for (j=ncl+1; j<=nch; j++) 
         for (j=1;j<=n;j++) {        m[i][j]=m[i][j-1]+nlay;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    }
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    return m; 
         }    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       }    */
 #endif  }
   
   /*************************free ma3x ************************/
       free_vector(xit,1,n);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       free_vector(xits,1,n);  {
       free_vector(ptt,1,n);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       free_vector(pt,1,n);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       return;    free((FREE_ARG)(m+nrl-NR_END));
     }  }
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  
     for (j=1;j<=n;j++) {  /*************** function subdirf ***********/
       ptt[j]=2.0*p[j]-pt[j];  char *subdirf(char fileres[])
       xit[j]=p[j]-pt[j];  {
       pt[j]=p[j];    /* Caution optionfilefiname is hidden */
     }    strcpy(tmpout,optionfilefiname);
     fptt=(*func)(ptt);    strcat(tmpout,"/"); /* Add to the right */
     if (fptt < fp) {    strcat(tmpout,fileres);
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    return tmpout;
       if (t < 0.0) {  }
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {  /*************** function subdirf2 ***********/
           xi[j][ibig]=xi[j][n];  char *subdirf2(char fileres[], char *preop)
           xi[j][n]=xit[j];  {
         }    
 #ifdef DEBUG    /* Caution optionfilefiname is hidden */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    strcpy(tmpout,optionfilefiname);
         for(j=1;j<=n;j++)    strcat(tmpout,"/");
           printf(" %.12e",xit[j]);    strcat(tmpout,preop);
         printf("\n");    strcat(tmpout,fileres);
 #endif    return tmpout;
       }  }
     }  
   }  /*************** function subdirf3 ***********/
 }  char *subdirf3(char fileres[], char *preop, char *preop2)
   {
 /**** Prevalence limit ****************/    
     /* Caution optionfilefiname is hidden */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    strcpy(tmpout,optionfilefiname);
 {    strcat(tmpout,"/");
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    strcat(tmpout,preop);
      matrix by transitions matrix until convergence is reached */    strcat(tmpout,preop2);
     strcat(tmpout,fileres);
   int i, ii,j,k;    return tmpout;
   double min, max, maxmin, maxmax,sumnew=0.;  }
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();  /***************** f1dim *************************/
   double **newm;  extern int ncom; 
   double agefin, delaymax=50 ; /* Max number of years to converge */  extern double *pcom,*xicom;
   extern double (*nrfunc)(double []); 
   for (ii=1;ii<=nlstate+ndeath;ii++)   
     for (j=1;j<=nlstate+ndeath;j++){  double f1dim(double x) 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  { 
     }    int j; 
     double f;
    cov[1]=1.;    double *xt; 
     
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    xt=vector(1,ncom); 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     newm=savm;    f=(*nrfunc)(xt); 
     /* Covariates have to be included here again */    free_vector(xt,1,ncom); 
      cov[2]=agefin;    return f; 
    } 
       for (k=1; k<=cptcovn;k++) {  
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  /*****************brent *************************/
         /*      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]]);*/  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       }  { 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    int iter; 
       for (k=1; k<=cptcovprod;k++)    double a,b,d,etemp;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    double fu,fv,fw,fx;
     double ftemp;
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    double e=0.0; 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/   
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    a=(ax < cx ? ax : cx); 
     b=(ax > cx ? ax : cx); 
     savm=oldm;    x=w=v=bx; 
     oldm=newm;    fw=fv=fx=(*f)(x); 
     maxmax=0.;    for (iter=1;iter<=ITMAX;iter++) { 
     for(j=1;j<=nlstate;j++){      xm=0.5*(a+b); 
       min=1.;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       max=0.;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       for(i=1; i<=nlstate; i++) {      printf(".");fflush(stdout);
         sumnew=0;      fprintf(ficlog,".");fflush(ficlog);
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  #ifdef DEBUG
         prlim[i][j]= newm[i][j]/(1-sumnew);      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);
         max=FMAX(max,prlim[i][j]);      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
         min=FMIN(min,prlim[i][j]);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       }  #endif
       maxmin=max-min;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       maxmax=FMAX(maxmax,maxmin);        *xmin=x; 
     }        return fx; 
     if(maxmax < ftolpl){      } 
       return prlim;      ftemp=fu;
     }      if (fabs(e) > tol1) { 
   }        r=(x-w)*(fx-fv); 
 }        q=(x-v)*(fx-fw); 
         p=(x-v)*q-(x-w)*r; 
 /*************** transition probabilities ***************/        q=2.0*(q-r); 
         if (q > 0.0) p = -p; 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        q=fabs(q); 
 {        etemp=e; 
   double s1, s2;        e=d; 
   /*double t34;*/        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   int i,j,j1, nc, ii, jj;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         else { 
     for(i=1; i<= nlstate; i++){          d=p/q; 
     for(j=1; j<i;j++){          u=x+d; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          if (u-a < tol2 || b-u < tol2) 
         /*s2 += param[i][j][nc]*cov[nc];*/            d=SIGN(tol1,xm-x); 
         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);*/      } else { 
       }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       ps[i][j]=s2;      } 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     }      fu=(*f)(u); 
     for(j=i+1; j<=nlstate+ndeath;j++){      if (fu <= fx) { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        if (u >= x) a=x; else b=x; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        SHFT(v,w,x,u) 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/          SHFT(fv,fw,fx,fu) 
       }          } else { 
       ps[i][j]=s2;            if (u < x) a=u; else b=u; 
     }            if (fu <= fw || w == x) { 
   }              v=w; 
     /*ps[3][2]=1;*/              w=u; 
               fv=fw; 
   for(i=1; i<= nlstate; i++){              fw=fu; 
      s1=0;            } else if (fu <= fv || v == x || v == w) { 
     for(j=1; j<i; j++)              v=u; 
       s1+=exp(ps[i][j]);              fv=fu; 
     for(j=i+1; j<=nlstate+ndeath; j++)            } 
       s1+=exp(ps[i][j]);          } 
     ps[i][i]=1./(s1+1.);    } 
     for(j=1; j<i; j++)    nrerror("Too many iterations in brent"); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    *xmin=x; 
     for(j=i+1; j<=nlstate+ndeath; j++)    return fx; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];  } 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  
   } /* end i */  /****************** mnbrak ***********************/
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     for(jj=1; jj<= nlstate+ndeath; jj++){              double (*func)(double)) 
       ps[ii][jj]=0;  { 
       ps[ii][ii]=1;    double ulim,u,r,q, dum;
     }    double fu; 
   }   
     *fa=(*func)(*ax); 
     *fb=(*func)(*bx); 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    if (*fb > *fa) { 
     for(jj=1; jj<= nlstate+ndeath; jj++){      SHFT(dum,*ax,*bx,dum) 
      printf("%lf ",ps[ii][jj]);        SHFT(dum,*fb,*fa,dum) 
    }        } 
     printf("\n ");    *cx=(*bx)+GOLD*(*bx-*ax); 
     }    *fc=(*func)(*cx); 
     printf("\n ");printf("%lf ",cov[2]);*/    while (*fb > *fc) { 
 /*      r=(*bx-*ax)*(*fb-*fc); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      q=(*bx-*cx)*(*fb-*fa); 
   goto end;*/      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     return ps;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 }      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if ((*bx-u)*(u-*cx) > 0.0) { 
 /**************** Product of 2 matrices ******************/        fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        fu=(*func)(u); 
 {        if (fu < *fc) { 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */            SHFT(*fb,*fc,fu,(*func)(u)) 
   /* in, b, out are matrice of pointers which should have been initialized            } 
      before: only the contents of out is modified. The function returns      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
      a pointer to pointers identical to out */        u=ulim; 
   long i, j, k;        fu=(*func)(u); 
   for(i=nrl; i<= nrh; i++)      } else { 
     for(k=ncolol; k<=ncoloh; k++)        u=(*cx)+GOLD*(*cx-*bx); 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        fu=(*func)(u); 
         out[i][k] +=in[i][j]*b[j][k];      } 
       SHFT(*ax,*bx,*cx,u) 
   return out;        SHFT(*fa,*fb,*fc,fu) 
 }        } 
   } 
   
 /************* Higher Matrix Product ***************/  /*************** linmin ************************/
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  int ncom; 
 {  double *pcom,*xicom;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  double (*nrfunc)(double []); 
      duration (i.e. until   
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  { 
      (typically every 2 years instead of every month which is too big).    double brent(double ax, double bx, double cx, 
      Model is determined by parameters x and covariates have to be                 double (*f)(double), double tol, double *xmin); 
      included manually here.    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
      */                double *fc, double (*func)(double)); 
     int j; 
   int i, j, d, h, k;    double xx,xmin,bx,ax; 
   double **out, cov[NCOVMAX];    double fx,fb,fa;
   double **newm;   
     ncom=n; 
   /* Hstepm could be zero and should return the unit matrix */    pcom=vector(1,n); 
   for (i=1;i<=nlstate+ndeath;i++)    xicom=vector(1,n); 
     for (j=1;j<=nlstate+ndeath;j++){    nrfunc=func; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);    for (j=1;j<=n;j++) { 
       po[i][j][0]=(i==j ? 1.0 : 0.0);      pcom[j]=p[j]; 
     }      xicom[j]=xi[j]; 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    } 
   for(h=1; h <=nhstepm; h++){    ax=0.0; 
     for(d=1; d <=hstepm; d++){    xx=1.0; 
       newm=savm;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       /* Covariates have to be included here again */    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       cov[1]=1.;  #ifdef DEBUG
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       for (k=1; k<=cptcovage;k++)  #endif
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    for (j=1;j<=n;j++) { 
       for (k=1; k<=cptcovprod;k++)      xi[j] *= xmin; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      p[j] += xi[j]; 
     } 
     free_vector(xicom,1,n); 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    free_vector(pcom,1,n); 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  } 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  char *asc_diff_time(long time_sec, char ascdiff[])
       savm=oldm;  {
       oldm=newm;    long sec_left, days, hours, minutes;
     }    days = (time_sec) / (60*60*24);
     for(i=1; i<=nlstate+ndeath; i++)    sec_left = (time_sec) % (60*60*24);
       for(j=1;j<=nlstate+ndeath;j++) {    hours = (sec_left) / (60*60) ;
         po[i][j][h]=newm[i][j];    sec_left = (sec_left) %(60*60);
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    minutes = (sec_left) /60;
          */    sec_left = (sec_left) % (60);
       }    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   } /* end h */    return ascdiff;
   return po;  }
 }  
   /*************** powell ************************/
   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 /*************** log-likelihood *************/              double (*func)(double [])) 
 double func( double *x)  { 
 {    void linmin(double p[], double xi[], int n, double *fret, 
   int i, ii, j, k, mi, d, kk;                double (*func)(double [])); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    int i,ibig,j; 
   double **out;    double del,t,*pt,*ptt,*xit;
   double sw; /* Sum of weights */    double fp,fptt;
   double lli; /* Individual log likelihood */    double *xits;
   long ipmx;    int niterf, itmp;
   /*extern weight */  
   /* We are differentiating ll according to initial status */    pt=vector(1,n); 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    ptt=vector(1,n); 
   /*for(i=1;i<imx;i++)    xit=vector(1,n); 
     printf(" %d\n",s[4][i]);    xits=vector(1,n); 
   */    *fret=(*func)(p); 
   cov[1]=1.;    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
   for(k=1; k<=nlstate; k++) ll[k]=0.;      fp=(*fret); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      ibig=0; 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      del=0.0; 
     for(mi=1; mi<= wav[i]-1; mi++){      last_time=curr_time;
       for (ii=1;ii<=nlstate+ndeath;ii++)      (void) gettimeofday(&curr_time,&tzp);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
       for(d=0; d<dh[mi][i]; d++){      /*    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);
         newm=savm;      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      */
         for (kk=1; kk<=cptcovage;kk++) {     for (i=1;i<=n;i++) {
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        printf(" %d %.12f",i, p[i]);
         }        fprintf(ficlog," %d %.12lf",i, p[i]);
                fprintf(ficrespow," %.12lf", p[i]);
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      }
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      printf("\n");
         savm=oldm;      fprintf(ficlog,"\n");
         oldm=newm;      fprintf(ficrespow,"\n");fflush(ficrespow);
              if(*iter <=3){
                tm = *localtime(&curr_time.tv_sec);
       } /* end mult */        strcpy(strcurr,asctime(&tm));
        /*       asctime_r(&tm,strcurr); */
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        forecast_time=curr_time; 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        itmp = strlen(strcurr);
       ipmx +=1;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
       sw += weight[i];          strcurr[itmp-1]='\0';
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     } /* end of wave */        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   } /* end of individual */        for(niterf=10;niterf<=30;niterf+=10){
           forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];          tmf = *localtime(&forecast_time.tv_sec);
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  /*      asctime_r(&tmf,strfor); */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */          strcpy(strfor,asctime(&tmf));
   return -l;          itmp = strlen(strfor);
 }          if(strfor[itmp-1]=='\n')
           strfor[itmp-1]='\0';
           printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
 /*********** Maximum Likelihood Estimation ***************/          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);
         }
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      }
 {      for (i=1;i<=n;i++) { 
   int i,j, iter;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   double **xi,*delti;        fptt=(*fret); 
   double fret;  #ifdef DEBUG
   xi=matrix(1,npar,1,npar);        printf("fret=%lf \n",*fret);
   for (i=1;i<=npar;i++)        fprintf(ficlog,"fret=%lf \n",*fret);
     for (j=1;j<=npar;j++)  #endif
       xi[i][j]=(i==j ? 1.0 : 0.0);        printf("%d",i);fflush(stdout);
   printf("Powell\n");        fprintf(ficlog,"%d",i);fflush(ficlog);
   powell(p,xi,npar,ftol,&iter,&fret,func);        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          del=fabs(fptt-(*fret)); 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));          ibig=i; 
         } 
 }  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
 /**** Computes Hessian and covariance matrix ***/        fprintf(ficlog,"%d %.12e",i,(*fret));
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        for (j=1;j<=n;j++) {
 {          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   double  **a,**y,*x,pd;          printf(" x(%d)=%.12e",j,xit[j]);
   double **hess;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   int i, j,jk;        }
   int *indx;        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
   double hessii(double p[], double delta, int theta, double delti[]);          fprintf(ficlog," p=%.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");
   #endif
   hess=matrix(1,npar,1,npar);      } 
       if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   printf("\nCalculation of the hessian matrix. Wait...\n");  #ifdef DEBUG
   for (i=1;i<=npar;i++){        int k[2],l;
     printf("%d",i);fflush(stdout);        k[0]=1;
     hess[i][i]=hessii(p,ftolhess,i,delti);        k[1]=-1;
     /*printf(" %f ",p[i]);*/        printf("Max: %.12e",(*func)(p));
     /*printf(" %lf ",hess[i][i]);*/        fprintf(ficlog,"Max: %.12e",(*func)(p));
   }        for (j=1;j<=n;j++) {
            printf(" %.12e",p[j]);
   for (i=1;i<=npar;i++) {          fprintf(ficlog," %.12e",p[j]);
     for (j=1;j<=npar;j++)  {        }
       if (j>i) {        printf("\n");
         printf(".%d%d",i,j);fflush(stdout);        fprintf(ficlog,"\n");
         hess[i][j]=hessij(p,delti,i,j);        for(l=0;l<=1;l++) {
         hess[j][i]=hess[i][j];              for (j=1;j<=n;j++) {
         /*printf(" %lf ",hess[i][j]);*/            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       }            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   }          }
   printf("\n");          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        }
    #endif
   a=matrix(1,npar,1,npar);  
   y=matrix(1,npar,1,npar);  
   x=vector(1,npar);        free_vector(xit,1,n); 
   indx=ivector(1,npar);        free_vector(xits,1,n); 
   for (i=1;i<=npar;i++)        free_vector(ptt,1,n); 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        free_vector(pt,1,n); 
   ludcmp(a,npar,indx,&pd);        return; 
       } 
   for (j=1;j<=npar;j++) {      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     for (i=1;i<=npar;i++) x[i]=0;      for (j=1;j<=n;j++) { 
     x[j]=1;        ptt[j]=2.0*p[j]-pt[j]; 
     lubksb(a,npar,indx,x);        xit[j]=p[j]-pt[j]; 
     for (i=1;i<=npar;i++){        pt[j]=p[j]; 
       matcov[i][j]=x[i];      } 
     }      fptt=(*func)(ptt); 
   }      if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   printf("\n#Hessian matrix#\n");        if (t < 0.0) { 
   for (i=1;i<=npar;i++) {          linmin(p,xit,n,fret,func); 
     for (j=1;j<=npar;j++) {          for (j=1;j<=n;j++) { 
       printf("%.3e ",hess[i][j]);            xi[j][ibig]=xi[j][n]; 
     }            xi[j][n]=xit[j]; 
     printf("\n");          }
   }  #ifdef DEBUG
           printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   /* Recompute Inverse */          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   for (i=1;i<=npar;i++)          for(j=1;j<=n;j++){
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];            printf(" %.12e",xit[j]);
   ludcmp(a,npar,indx,&pd);            fprintf(ficlog," %.12e",xit[j]);
           }
   /*  printf("\n#Hessian matrix recomputed#\n");          printf("\n");
           fprintf(ficlog,"\n");
   for (j=1;j<=npar;j++) {  #endif
     for (i=1;i<=npar;i++) x[i]=0;        }
     x[j]=1;      } 
     lubksb(a,npar,indx,x);    } 
     for (i=1;i<=npar;i++){  } 
       y[i][j]=x[i];  
       printf("%.3e ",y[i][j]);  /**** Prevalence limit (stable prevalence)  ****************/
     }  
     printf("\n");  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   }  {
   */    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
        matrix by transitions matrix until convergence is reached */
   free_matrix(a,1,npar,1,npar);  
   free_matrix(y,1,npar,1,npar);    int i, ii,j,k;
   free_vector(x,1,npar);    double min, max, maxmin, maxmax,sumnew=0.;
   free_ivector(indx,1,npar);    double **matprod2();
   free_matrix(hess,1,npar,1,npar);    double **out, cov[NCOVMAX], **pmij();
     double **newm;
     double agefin, delaymax=50 ; /* Max number of years to converge */
 }  
     for (ii=1;ii<=nlstate+ndeath;ii++)
 /*************** hessian matrix ****************/      for (j=1;j<=nlstate+ndeath;j++){
 double hessii( double x[], double delta, int theta, double delti[])        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 {      }
   int i;  
   int l=1, lmax=20;     cov[1]=1.;
   double k1,k2;   
   double p2[NPARMAX+1];   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   double res;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      newm=savm;
   double fx;      /* Covariates have to be included here again */
   int k=0,kmax=10;       cov[2]=agefin;
   double l1;    
         for (k=1; k<=cptcovn;k++) {
   fx=func(x);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   for (i=1;i<=npar;i++) p2[i]=x[i];          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
   for(l=0 ; l <=lmax; l++){        }
     l1=pow(10,l);        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     delts=delt;        for (k=1; k<=cptcovprod;k++)
     for(k=1 ; k <kmax; k=k+1){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       delt = delta*(l1*k);  
       p2[theta]=x[theta] +delt;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       k1=func(p2)-fx;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       p2[theta]=x[theta]-delt;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       k2=func(p2)-fx;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       /*res= (k1-2.0*fx+k2)/delt/delt; */  
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      savm=oldm;
            oldm=newm;
 #ifdef DEBUG      maxmax=0.;
       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);      for(j=1;j<=nlstate;j++){
 #endif        min=1.;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        max=0.;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        for(i=1; i<=nlstate; i++) {
         k=kmax;          sumnew=0;
       }          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          prlim[i][j]= newm[i][j]/(1-sumnew);
         k=kmax; l=lmax*10.;          max=FMAX(max,prlim[i][j]);
       }          min=FMIN(min,prlim[i][j]);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        }
         delts=delt;        maxmin=max-min;
       }        maxmax=FMAX(maxmax,maxmin);
     }      }
   }      if(maxmax < ftolpl){
   delti[theta]=delts;        return prlim;
   return res;      }
      }
 }  }
   
 double hessij( double x[], double delti[], int thetai,int thetaj)  /*************** transition probabilities ***************/ 
 {  
   int i;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   int l=1, l1, lmax=20;  {
   double k1,k2,k3,k4,res,fx;    double s1, s2;
   double p2[NPARMAX+1];    /*double t34;*/
   int k;    int i,j,j1, nc, ii, jj;
   
   fx=func(x);      for(i=1; i<= nlstate; i++){
   for (k=1; k<=2; k++) {        for(j=1; j<i;j++){
     for (i=1;i<=npar;i++) p2[i]=x[i];          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     p2[thetai]=x[thetai]+delti[thetai]/k;            /*s2 += param[i][j][nc]*cov[nc];*/
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     k1=func(p2)-fx;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
            }
     p2[thetai]=x[thetai]+delti[thetai]/k;          ps[i][j]=s2;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
     k2=func(p2)-fx;        }
          for(j=i+1; j<=nlstate+ndeath;j++){
     p2[thetai]=x[thetai]-delti[thetai]/k;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     k3=func(p2)-fx;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
            }
     p2[thetai]=x[thetai]-delti[thetai]/k;          ps[i][j]=s2;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        }
     k4=func(p2)-fx;      }
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      /*ps[3][2]=1;*/
 #ifdef DEBUG      
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);      for(i=1; i<= nlstate; i++){
 #endif        s1=0;
   }        for(j=1; j<i; j++)
   return res;          s1+=exp(ps[i][j]);
 }        for(j=i+1; j<=nlstate+ndeath; j++)
           s1+=exp(ps[i][j]);
 /************** Inverse of matrix **************/        ps[i][i]=1./(s1+1.);
 void ludcmp(double **a, int n, int *indx, double *d)        for(j=1; j<i; j++)
 {          ps[i][j]= exp(ps[i][j])*ps[i][i];
   int i,imax,j,k;        for(j=i+1; j<=nlstate+ndeath; j++)
   double big,dum,sum,temp;          ps[i][j]= exp(ps[i][j])*ps[i][i];
   double *vv;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
        } /* end i */
   vv=vector(1,n);      
   *d=1.0;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   for (i=1;i<=n;i++) {        for(jj=1; jj<= nlstate+ndeath; jj++){
     big=0.0;          ps[ii][jj]=0;
     for (j=1;j<=n;j++)          ps[ii][ii]=1;
       if ((temp=fabs(a[i][j])) > big) big=temp;        }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      }
     vv[i]=1.0/big;      
   }  
   for (j=1;j<=n;j++) {  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
     for (i=1;i<j;i++) {  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
       sum=a[i][j];  /*         printf("ddd %lf ",ps[ii][jj]); */
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  /*       } */
       a[i][j]=sum;  /*       printf("\n "); */
     }  /*        } */
     big=0.0;  /*        printf("\n ");printf("%lf ",cov[2]); */
     for (i=j;i<=n;i++) {         /*
       sum=a[i][j];        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       for (k=1;k<j;k++)        goto end;*/
         sum -= a[i][k]*a[k][j];      return ps;
       a[i][j]=sum;  }
       if ( (dum=vv[i]*fabs(sum)) >= big) {  
         big=dum;  /**************** Product of 2 matrices ******************/
         imax=i;  
       }  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     }  {
     if (j != imax) {    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       for (k=1;k<=n;k++) {       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         dum=a[imax][k];    /* in, b, out are matrice of pointers which should have been initialized 
         a[imax][k]=a[j][k];       before: only the contents of out is modified. The function returns
         a[j][k]=dum;       a pointer to pointers identical to out */
       }    long i, j, k;
       *d = -(*d);    for(i=nrl; i<= nrh; i++)
       vv[imax]=vv[j];      for(k=ncolol; k<=ncoloh; k++)
     }        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     indx[j]=imax;          out[i][k] +=in[i][j]*b[j][k];
     if (a[j][j] == 0.0) a[j][j]=TINY;  
     if (j != n) {    return out;
       dum=1.0/(a[j][j]);  }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }  
   }  /************* Higher Matrix Product ***************/
   free_vector(vv,1,n);  /* Doesn't work */  
 ;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
 }  {
     /* Computes the transition matrix starting at age 'age' over 
 void lubksb(double **a, int n, int *indx, double b[])       'nhstepm*hstepm*stepm' months (i.e. until
 {       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   int i,ii=0,ip,j;       nhstepm*hstepm matrices. 
   double sum;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         (typically every 2 years instead of every month which is too big 
   for (i=1;i<=n;i++) {       for the memory).
     ip=indx[i];       Model is determined by parameters x and covariates have to be 
     sum=b[ip];       included manually here. 
     b[ip]=b[i];  
     if (ii)       */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  
     else if (sum) ii=i;    int i, j, d, h, k;
     b[i]=sum;    double **out, cov[NCOVMAX];
   }    double **newm;
   for (i=n;i>=1;i--) {  
     sum=b[i];    /* Hstepm could be zero and should return the unit matrix */
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    for (i=1;i<=nlstate+ndeath;i++)
     b[i]=sum/a[i][i];      for (j=1;j<=nlstate+ndeath;j++){
   }        oldm[i][j]=(i==j ? 1.0 : 0.0);
 }        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
 /************ Frequencies ********************/    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 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)    for(h=1; h <=nhstepm; h++){
 {  /* Some frequencies */      for(d=1; d <=hstepm; d++){
          newm=savm;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        /* Covariates have to be included here again */
   double ***freq; /* Frequencies */        cov[1]=1.;
   double *pp;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   double pos, k2, dateintsum=0,k2cpt=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   FILE *ficresp;        for (k=1; k<=cptcovage;k++)
   char fileresp[FILENAMELENGTH];          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
          for (k=1; k<=cptcovprod;k++)
   pp=vector(1,nlstate);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   strcpy(fileresp,"p");  
   strcat(fileresp,fileres);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   if((ficresp=fopen(fileresp,"w"))==NULL) {        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     printf("Problem with prevalence resultfile: %s\n", fileresp);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     exit(0);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   }        savm=oldm;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        oldm=newm;
   j1=0;      }
        for(i=1; i<=nlstate+ndeath; i++)
   j=cptcoveff;        for(j=1;j<=nlstate+ndeath;j++) {
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          po[i][j][h]=newm[i][j];
            /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   for(k1=1; k1<=j;k1++){           */
     for(i1=1; i1<=ncodemax[k1];i1++){        }
       j1++;    } /* end h */
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    return po;
         scanf("%d", i);*/  }
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)    
           for(m=agemin; m <= agemax+3; m++)  /*************** log-likelihood *************/
             freq[i][jk][m]=0;  double func( double *x)
        {
       dateintsum=0;    int i, ii, j, k, mi, d, kk;
       k2cpt=0;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       for (i=1; i<=imx; i++) {    double **out;
         bool=1;    double sw; /* Sum of weights */
         if  (cptcovn>0) {    double lli; /* Individual log likelihood */
           for (z1=1; z1<=cptcoveff; z1++)    int s1, s2;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    double bbh, survp;
               bool=0;    long ipmx;
         }    /*extern weight */
         if (bool==1) {    /* We are differentiating ll according to initial status */
           for(m=firstpass; m<=lastpass; m++){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
             k2=anint[m][i]+(mint[m][i]/12.);    /*for(i=1;i<imx;i++) 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      printf(" %d\n",s[4][i]);
               if(agev[m][i]==0) agev[m][i]=agemax+1;    */
               if(agev[m][i]==1) agev[m][i]=agemax+2;    cov[1]=1.;
               if (m<lastpass) {  
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    for(k=1; k<=nlstate; k++) ll[k]=0.;
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  
               }    if(mle==1){
                    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                 dateintsum=dateintsum+k2;        for(mi=1; mi<= wav[i]-1; mi++){
                 k2cpt++;          for (ii=1;ii<=nlstate+ndeath;ii++)
               }            for (j=1;j<=nlstate+ndeath;j++){
             }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            }
       }          for(d=0; d<dh[mi][i]; d++){
                    newm=savm;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
       if  (cptcovn>0) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         fprintf(ficresp, "\n#********** Variable ");            }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         fprintf(ficresp, "**********\n#");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
       for(i=1; i<=nlstate;i++)            oldm=newm;
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          } /* end mult */
       fprintf(ficresp, "\n");        
                /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       for(i=(int)agemin; i <= (int)agemax+3; i++){          /* But now since version 0.9 we anticipate for bias at large stepm.
         if(i==(int)agemax+3)           * If stepm is larger than one month (smallest stepm) and if the exact delay 
           printf("Total");           * (in months) between two waves is not a multiple of stepm, we rounded to 
         else           * the nearest (and in case of equal distance, to the lowest) interval but now
           printf("Age %d", i);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         for(jk=1; jk <=nlstate ; jk++){           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)           * probability in order to take into account the bias as a fraction of the way
             pp[jk] += freq[jk][m][i];           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
         }           * -stepm/2 to stepm/2 .
         for(jk=1; jk <=nlstate ; jk++){           * For stepm=1 the results are the same as for previous versions of Imach.
           for(m=-1, pos=0; m <=0 ; m++)           * For stepm > 1 the results are less biased than in previous versions. 
             pos += freq[jk][m][i];           */
           if(pp[jk]>=1.e-10)          s1=s[mw[mi][i]][i];
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          s2=s[mw[mi+1][i]][i];
           else          bbh=(double)bh[mi][i]/(double)stepm; 
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          /* bias bh is positive if real duration
         }           * is higher than the multiple of stepm and negative otherwise.
            */
         for(jk=1; jk <=nlstate ; jk++){          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          if( s2 > nlstate){ 
             pp[jk] += freq[jk][m][i];            /* i.e. if s2 is a death state and if the date of death is known 
         }               then the contribution to the likelihood is the probability to 
                die between last step unit time and current  step unit time, 
         for(jk=1,pos=0; jk <=nlstate ; jk++)               which is also equal to probability to die before dh 
           pos += pp[jk];               minus probability to die before dh-stepm . 
         for(jk=1; jk <=nlstate ; jk++){               In version up to 0.92 likelihood was computed
           if(pos>=1.e-5)          as if date of death was unknown. Death was treated as any other
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          health state: the date of the interview describes the actual state
           else          and not the date of a change in health state. The former idea was
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          to consider that at each interview the state was recorded
           if( i <= (int) agemax){          (healthy, disable or death) and IMaCh was corrected; but when we
             if(pos>=1.e-5){          introduced the exact date of death then we should have modified
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          the contribution of an exact death to the likelihood. This new
               probs[i][jk][j1]= pp[jk]/pos;          contribution is smaller and very dependent of the step unit
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          stepm. It is no more the probability to die between last interview
             }          and month of death but the probability to survive from last
             else          interview up to one month before death multiplied by the
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          probability to die within a month. Thanks to Chris
           }          Jackson for correcting this bug.  Former versions increased
         }          mortality artificially. The bad side is that we add another loop
                  which slows down the processing. The difference can be up to 10%
         for(jk=-1; jk <=nlstate+ndeath; jk++)          lower mortality.
           for(m=-1; m <=nlstate+ndeath; m++)            */
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            lli=log(out[s1][s2] - savm[s1][s2]);
         if(i <= (int) agemax)  
           fprintf(ficresp,"\n");  
         printf("\n");          } else if  (s2==-2) {
       }            for (j=1,survp=0. ; j<=nlstate; j++) 
     }              survp += out[s1][j];
   }            lli= survp;
   dateintmean=dateintsum/k2cpt;          }
    
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          else{
   free_vector(pp,1,nlstate);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
              /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   /* End of Freq */          } 
 }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
 /************ Prevalence ********************/          /*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); */
 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)          ipmx +=1;
 {  /* Some frequencies */          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        } /* end of wave */
   double ***freq; /* Frequencies */      } /* end of individual */
   double *pp;    }  else if(mle==2){
   double pos, k2;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   pp=vector(1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   j1=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
   j=cptcoveff;          for(d=0; d<=dh[mi][i]; d++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for(k1=1; k1<=j;k1++){            for (kk=1; kk<=cptcovage;kk++) {
     for(i1=1; i1<=ncodemax[k1];i1++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       j1++;            }
                  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for (i=-1; i<=nlstate+ndeath; i++)                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         for (jk=-1; jk<=nlstate+ndeath; jk++)              savm=oldm;
           for(m=agemin; m <= agemax+3; m++)            oldm=newm;
             freq[i][jk][m]=0;          } /* end mult */
              
       for (i=1; i<=imx; i++) {          s1=s[mw[mi][i]][i];
         bool=1;          s2=s[mw[mi+1][i]][i];
         if  (cptcovn>0) {          bbh=(double)bh[mi][i]/(double)stepm; 
           for (z1=1; z1<=cptcoveff; z1++)          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 (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          ipmx +=1;
               bool=0;          sw += weight[i];
         }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         if (bool==1) {        } /* end of wave */
           for(m=firstpass; m<=lastpass; m++){      } /* end of individual */
             k2=anint[m][i]+(mint[m][i]/12.);    }  else if(mle==3){  /* exponential inter-extrapolation */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
               if(agev[m][i]==0) agev[m][i]=agemax+1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
               if(agev[m][i]==1) agev[m][i]=agemax+2;        for(mi=1; mi<= wav[i]-1; mi++){
               if (m<lastpass) {          for (ii=1;ii<=nlstate+ndeath;ii++)
                 if (calagedate>0)            for (j=1;j<=nlstate+ndeath;j++){
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                 else              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];            }
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];          for(d=0; d<dh[mi][i]; d++){
               }            newm=savm;
             }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           }            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
       for(i=(int)agemin; i <= (int)agemax+3; i++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for(jk=1; jk <=nlstate ; jk++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            savm=oldm;
             pp[jk] += freq[jk][m][i];            oldm=newm;
         }          } /* end mult */
         for(jk=1; jk <=nlstate ; jk++){        
           for(m=-1, pos=0; m <=0 ; m++)          s1=s[mw[mi][i]][i];
             pos += freq[jk][m][i];          s2=s[mw[mi+1][i]][i];
         }          bbh=(double)bh[mi][i]/(double)stepm; 
                  lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         for(jk=1; jk <=nlstate ; jk++){          ipmx +=1;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          sw += weight[i];
             pp[jk] += freq[jk][m][i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         }        } /* end of wave */
              } /* end of individual */
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    }else if (mle==4){  /* ml=4 no inter-extrapolation */
              for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for(jk=1; jk <=nlstate ; jk++){            for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           if( i <= (int) agemax){        for(mi=1; mi<= wav[i]-1; mi++){
             if(pos>=1.e-5){          for (ii=1;ii<=nlstate+ndeath;ii++)
               probs[i][jk][j1]= pp[jk]/pos;            for (j=1;j<=nlstate+ndeath;j++){
             }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            }
                  for(d=0; d<dh[mi][i]; d++){
       }            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          
   free_vector(pp,1,nlstate);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }  /* End of Freq */            savm=oldm;
             oldm=newm;
 /************* Waves Concatenation ***************/          } /* end mult */
         
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          s1=s[mw[mi][i]][i];
 {          s2=s[mw[mi+1][i]][i];
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          if( s2 > nlstate){ 
      Death is a valid wave (if date is known).            lli=log(out[s1][s2] - savm[s1][s2]);
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          }else{
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
      and mw[mi+1][i]. dh depends on stepm.          }
      */          ipmx +=1;
           sw += weight[i];
   int i, mi, m;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
      double sum=0., jmean=0.;*/        } /* end of wave */
       } /* end of individual */
   int j, k=0,jk, ju, jl;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   double sum=0.;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   jmin=1e+5;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   jmax=-1;        for(mi=1; mi<= wav[i]-1; mi++){
   jmean=0.;          for (ii=1;ii<=nlstate+ndeath;ii++)
   for(i=1; i<=imx; i++){            for (j=1;j<=nlstate+ndeath;j++){
     mi=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     m=firstpass;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     while(s[m][i] <= nlstate){            }
       if(s[m][i]>=1)          for(d=0; d<dh[mi][i]; d++){
         mw[++mi][i]=m;            newm=savm;
       if(m >=lastpass)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         break;            for (kk=1; kk<=cptcovage;kk++) {
       else              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         m++;            }
     }/* end while */          
     if (s[m][i] > nlstate){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       mi++;     /* Death is another wave */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       /* if(mi==0)  never been interviewed correctly before death */            savm=oldm;
          /* Only death is a correct wave */            oldm=newm;
       mw[mi][i]=m;          } /* end mult */
     }        
           s1=s[mw[mi][i]][i];
     wav[i]=mi;          s2=s[mw[mi+1][i]][i];
     if(mi==0)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          ipmx +=1;
   }          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for(i=1; i<=imx; i++){          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
     for(mi=1; mi<wav[i];mi++){        } /* end of wave */
       if (stepm <=0)      } /* end of individual */
         dh[mi][i]=1;    } /* End of if */
       else{    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         if (s[mw[mi+1][i]][i] > nlstate) {    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           if (agedc[i] < 2*AGESUP) {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    return -l;
           if(j==0) j=1;  /* Survives at least one month after exam */  }
           k=k+1;  
           if (j >= jmax) jmax=j;  /*************** log-likelihood *************/
           if (j <= jmin) jmin=j;  double funcone( double *x)
           sum=sum+j;  {
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    /* Same as likeli but slower because of a lot of printf and if */
           }    int i, ii, j, k, mi, d, kk;
         }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         else{    double **out;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    double lli; /* Individual log likelihood */
           k=k+1;    double llt;
           if (j >= jmax) jmax=j;    int s1, s2;
           else if (j <= jmin)jmin=j;    double bbh, survp;
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    /*extern weight */
           sum=sum+j;    /* We are differentiating ll according to initial status */
         }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         jk= j/stepm;    /*for(i=1;i<imx;i++) 
         jl= j -jk*stepm;      printf(" %d\n",s[4][i]);
         ju= j -(jk+1)*stepm;    */
         if(jl <= -ju)    cov[1]=1.;
           dh[mi][i]=jk;  
         else    for(k=1; k<=nlstate; k++) ll[k]=0.;
           dh[mi][i]=jk+1;  
         if(dh[mi][i]==0)    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           dh[mi][i]=1; /* At least one step */      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       }      for(mi=1; mi<= wav[i]-1; mi++){
     }        for (ii=1;ii<=nlstate+ndeath;ii++)
   }          for (j=1;j<=nlstate+ndeath;j++){
   jmean=sum/k;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
  }          }
 /*********** Tricode ****************************/        for(d=0; d<dh[mi][i]; d++){
 void tricode(int *Tvar, int **nbcode, int imx)          newm=savm;
 {          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int Ndum[20],ij=1, k, j, i;          for (kk=1; kk<=cptcovage;kk++) {
   int cptcode=0;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   cptcoveff=0;          }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for (k=0; k<19; k++) Ndum[k]=0;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (k=1; k<=7; k++) ncodemax[k]=0;          savm=oldm;
           oldm=newm;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        } /* end mult */
     for (i=1; i<=imx; i++) {        
       ij=(int)(covar[Tvar[j]][i]);        s1=s[mw[mi][i]][i];
       Ndum[ij]++;        s2=s[mw[mi+1][i]][i];
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        bbh=(double)bh[mi][i]/(double)stepm; 
       if (ij > cptcode) cptcode=ij;        /* bias is positive if real duration
     }         * is higher than the multiple of stepm and negative otherwise.
          */
     for (i=0; i<=cptcode; i++) {        if( s2 > nlstate && (mle <5) ){  /* Jackson */
       if(Ndum[i]!=0) ncodemax[j]++;          lli=log(out[s1][s2] - savm[s1][s2]);
     }        } else if (mle==1){
     ij=1;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     for (i=1; i<=ncodemax[j]; i++) {        } else if(mle==3){  /* exponential inter-extrapolation */
       for (k=0; k<=19; k++) {          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 */
         if (Ndum[k] != 0) {        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           nbcode[Tvar[j]][ij]=k;          lli=log(out[s1][s2]); /* Original formula */
                  } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
           ij++;          lli=log(out[s1][s2]); /* Original formula */
         }        } /* End of if */
         if (ij > ncodemax[j]) break;        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]); */
         if(globpr){
  for (k=0; k<19; k++) Ndum[k]=0;          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
    %10.6f %10.6f %10.6f ", \
  for (i=1; i<=ncovmodel-2; i++) {                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       ij=Tvar[i];                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
       Ndum[ij]++;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     }            llt +=ll[k]*gipmx/gsw;
             fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
  ij=1;          }
  for (i=1; i<=10; i++) {          fprintf(ficresilk," %10.6f\n", -llt);
    if((Ndum[i]!=0) && (i<=ncovcol)){        }
      Tvaraff[ij]=i;      } /* end of wave */
      ij++;    } /* end of individual */
    }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
  }    /* 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 */
     cptcoveff=ij-1;    if(globpr==0){ /* First time we count the contributions and weights */
 }      gipmx=ipmx;
       gsw=sw;
 /*********** Health Expectancies ****************/    }
     return -l;
 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 )  }
   
 {  
   /* Health expectancies */  /*************** function likelione ***********/
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   double age, agelim, hf;  {
   double ***p3mat,***varhe;    /* This routine should help understanding what is done with 
   double **dnewm,**doldm;       the selection of individuals/waves and
   double *xp;       to check the exact contribution to the likelihood.
   double **gp, **gm;       Plotting could be done.
   double ***gradg, ***trgradg;     */
   int theta;    int k;
   
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    if(*globpri !=0){ /* Just counts and sums, no printings */
   xp=vector(1,npar);      strcpy(fileresilk,"ilk"); 
   dnewm=matrix(1,nlstate*2,1,npar);      strcat(fileresilk,fileres);
   doldm=matrix(1,nlstate*2,1,nlstate*2);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
          printf("Problem with resultfile: %s\n", fileresilk);
   fprintf(ficreseij,"# Health expectancies\n");        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   fprintf(ficreseij,"# Age");      }
   for(i=1; i<=nlstate;i++)      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
     for(j=1; j<=nlstate;j++)      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       fprintf(ficreseij," %1d-%1d (SE)",i,j);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   fprintf(ficreseij,"\n");      for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   if(estepm < stepm){      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     printf ("Problem %d lower than %d\n",estepm, stepm);    }
   }  
   else  hstepm=estepm;      *fretone=(*funcone)(p);
   /* We compute the life expectancy from trapezoids spaced every estepm months    if(*globpri !=0){
    * This is mainly to measure the difference between two models: for example      fclose(ficresilk);
    * if stepm=24 months pijx are given only every 2 years and by summing them      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
    * we are calculating an estimate of the Life Expectancy assuming a linear      fflush(fichtm); 
    * progression inbetween and thus overestimating or underestimating according    } 
    * to the curvature of the survival function. If, for the same date, we    return;
    * estimate the model with stepm=1 month, we can keep estepm to 24 months  }
    * to compare the new estimate of Life expectancy with the same linear  
    * hypothesis. A more precise result, taking into account a more precise  
    * curvature will be obtained if estepm is as small as stepm. */  /*********** Maximum Likelihood Estimation ***************/
   
   /* For example we decided to compute the life expectancy with the smallest unit */  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.  {
      nhstepm is the number of hstepm from age to agelim    int i,j, iter;
      nstepm is the number of stepm from age to agelin.    double **xi;
      Look at hpijx to understand the reason of that which relies in memory size    double fret;
      and note for a fixed period like estepm months */    double fretone; /* Only one call to likelihood */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    /*  char filerespow[FILENAMELENGTH];*/
      survival function given by stepm (the optimization length). Unfortunately it    xi=matrix(1,npar,1,npar);
      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      for (j=1;j<=npar;j++)
      results. So we changed our mind and took the option of the best precision.        xi[i][j]=(i==j ? 1.0 : 0.0);
   */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    strcpy(filerespow,"pow"); 
     strcat(filerespow,fileres);
   agelim=AGESUP;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      printf("Problem with resultfile: %s\n", filerespow);
     /* nhstepm age range expressed in number of stepm */      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    }
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     /* if (stepm >= YEARM) hstepm=1;*/    for (i=1;i<=nlstate;i++)
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      for(j=1;j<=nlstate+ndeath;j++)
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    fprintf(ficrespow,"\n");
     gp=matrix(0,nhstepm,1,nlstate*2);  
     gm=matrix(0,nhstepm,1,nlstate*2);    powell(p,xi,npar,ftol,&iter,&fret,func);
   
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    fclose(ficrespow);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
      fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  }
   
     /* Computing Variances of health expectancies */  /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
      for(theta=1; theta <=npar; theta++){  {
       for(i=1; i<=npar; i++){    double  **a,**y,*x,pd;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double **hess;
       }    int i, j,jk;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      int *indx;
    
       cptj=0;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
       for(j=1; j<= nlstate; j++){    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
         for(i=1; i<=nlstate; i++){    void lubksb(double **a, int npar, int *indx, double b[]) ;
           cptj=cptj+1;    void ludcmp(double **a, int npar, int *indx, double *d) ;
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    double gompertz(double p[]);
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    hess=matrix(1,npar,1,npar);
           }  
         }    printf("\nCalculation of the hessian matrix. Wait...\n");
       }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
          for (i=1;i<=npar;i++){
            printf("%d",i);fflush(stdout);
       for(i=1; i<=npar; i++)      fprintf(ficlog,"%d",i);fflush(ficlog);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);     
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);         hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
            
       cptj=0;      /*  printf(" %f ",p[i]);
       for(j=1; j<= nlstate; j++){          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
         for(i=1;i<=nlstate;i++){    }
           cptj=cptj+1;    
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    for (i=1;i<=npar;i++) {
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      for (j=1;j<=npar;j++)  {
           }        if (j>i) { 
         }          printf(".%d%d",i,j);fflush(stdout);
       }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
                hess[i][j]=hessij(p,delti,i,j,func,npar);
              
           hess[j][i]=hess[i][j];    
       for(j=1; j<= nlstate*2; j++)          /*printf(" %lf ",hess[i][j]);*/
         for(h=0; h<=nhstepm-1; h++){        }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      }
         }    }
     printf("\n");
      }    fprintf(ficlog,"\n");
      
 /* End theta */    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    
     a=matrix(1,npar,1,npar);
      for(h=0; h<=nhstepm-1; h++)    y=matrix(1,npar,1,npar);
       for(j=1; j<=nlstate*2;j++)    x=vector(1,npar);
         for(theta=1; theta <=npar; theta++)    indx=ivector(1,npar);
         trgradg[h][j][theta]=gradg[h][theta][j];    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     ludcmp(a,npar,indx,&pd);
      for(i=1;i<=nlstate*2;i++)  
       for(j=1;j<=nlstate*2;j++)    for (j=1;j<=npar;j++) {
         varhe[i][j][(int)age] =0.;      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
      printf("%d|",(int)age);fflush(stdout);      lubksb(a,npar,indx,x);
     for(h=0;h<=nhstepm-1;h++){      for (i=1;i<=npar;i++){ 
       for(k=0;k<=nhstepm-1;k++){        matcov[i][j]=x[i];
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);      }
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);    }
         for(i=1;i<=nlstate*2;i++)  
           for(j=1;j<=nlstate*2;j++)    printf("\n#Hessian matrix#\n");
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    fprintf(ficlog,"\n#Hessian matrix#\n");
       }    for (i=1;i<=npar;i++) { 
     }      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
              fprintf(ficlog,"%.3e ",hess[i][j]);
     /* Computing expectancies */      }
     for(i=1; i<=nlstate;i++)      printf("\n");
       for(j=1; j<=nlstate;j++)      fprintf(ficlog,"\n");
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    }
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;  
              /* Recompute Inverse */
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         }    ludcmp(a,npar,indx,&pd);
   
     fprintf(ficreseij,"%3.0f",age );    /*  printf("\n#Hessian matrix recomputed#\n");
     cptj=0;  
     for(i=1; i<=nlstate;i++)    for (j=1;j<=npar;j++) {
       for(j=1; j<=nlstate;j++){      for (i=1;i<=npar;i++) x[i]=0;
         cptj++;      x[j]=1;
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      lubksb(a,npar,indx,x);
       }      for (i=1;i<=npar;i++){ 
     fprintf(ficreseij,"\n");        y[i][j]=x[i];
            printf("%.3e ",y[i][j]);
     free_matrix(gm,0,nhstepm,1,nlstate*2);        fprintf(ficlog,"%.3e ",y[i][j]);
     free_matrix(gp,0,nhstepm,1,nlstate*2);      }
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);      printf("\n");
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);      fprintf(ficlog,"\n");
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
   }    */
   free_vector(xp,1,npar);  
   free_matrix(dnewm,1,nlstate*2,1,npar);    free_matrix(a,1,npar,1,npar);
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);    free_matrix(y,1,npar,1,npar);
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);    free_vector(x,1,npar);
 }    free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
 /************ Variance ******************/  
 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)  
 {  }
   /* Variance of health expectancies */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  /*************** hessian matrix ****************/
   double **newm;  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   double **dnewm,**doldm;  {
   int i, j, nhstepm, hstepm, h, nstepm ;    int i;
   int k, cptcode;    int l=1, lmax=20;
   double *xp;    double k1,k2;
   double **gp, **gm;    double p2[NPARMAX+1];
   double ***gradg, ***trgradg;    double res;
   double ***p3mat;    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   double age,agelim, hf;    double fx;
   int theta;    int k=0,kmax=10;
     double l1;
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");  
   fprintf(ficresvij,"# Age");    fx=func(x);
   for(i=1; i<=nlstate;i++)    for (i=1;i<=npar;i++) p2[i]=x[i];
     for(j=1; j<=nlstate;j++)    for(l=0 ; l <=lmax; l++){
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      l1=pow(10,l);
   fprintf(ficresvij,"\n");      delts=delt;
       for(k=1 ; k <kmax; k=k+1){
   xp=vector(1,npar);        delt = delta*(l1*k);
   dnewm=matrix(1,nlstate,1,npar);        p2[theta]=x[theta] +delt;
   doldm=matrix(1,nlstate,1,nlstate);        k1=func(p2)-fx;
          p2[theta]=x[theta]-delt;
   if(estepm < stepm){        k2=func(p2)-fx;
     printf ("Problem %d lower than %d\n",estepm, stepm);        /*res= (k1-2.0*fx+k2)/delt/delt; */
   }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   else  hstepm=estepm;          
   /* For example we decided to compute the life expectancy with the smallest unit */  #ifdef DEBUG
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        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);
      nhstepm is the number of hstepm from age to agelim        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);
      nstepm is the number of stepm from age to agelin.  #endif
      Look at hpijx to understand the reason of that which relies in memory size        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
      and note for a fixed period like k years */        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          k=kmax;
      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        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          k=kmax; l=lmax*10.;
      results. So we changed our mind and took the option of the best precision.        }
   */        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          delts=delt;
   agelim = AGESUP;        }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      }
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    }
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    delti[theta]=delts;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    return res; 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    
     gp=matrix(0,nhstepm,1,nlstate);  }
     gm=matrix(0,nhstepm,1,nlstate);  
   double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     for(theta=1; theta <=npar; theta++){  {
       for(i=1; i<=npar; i++){ /* Computes gradient */    int i;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    int l=1, l1, lmax=20;
       }    double k1,k2,k3,k4,res,fx;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      double p2[NPARMAX+1];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int k;
   
       if (popbased==1) {    fx=func(x);
         for(i=1; i<=nlstate;i++)    for (k=1; k<=2; k++) {
           prlim[i][i]=probs[(int)age][i][ij];      for (i=1;i<=npar;i++) p2[i]=x[i];
       }      p2[thetai]=x[thetai]+delti[thetai]/k;
        p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       for(j=1; j<= nlstate; j++){      k1=func(p2)-fx;
         for(h=0; h<=nhstepm; h++){    
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      p2[thetai]=x[thetai]+delti[thetai]/k;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         }      k2=func(p2)-fx;
       }    
          p2[thetai]=x[thetai]-delti[thetai]/k;
       for(i=1; i<=npar; i++) /* Computes gradient */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      k3=func(p2)-fx;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      p2[thetai]=x[thetai]-delti[thetai]/k;
        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       if (popbased==1) {      k4=func(p2)-fx;
         for(i=1; i<=nlstate;i++)      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
           prlim[i][i]=probs[(int)age][i][ij];  #ifdef DEBUG
       }      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       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);
       for(j=1; j<= nlstate; j++){  #endif
         for(h=0; h<=nhstepm; h++){    }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    return res;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  }
         }  
       }  /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
       for(j=1; j<= nlstate; j++)  { 
         for(h=0; h<=nhstepm; h++){    int i,imax,j,k; 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    double big,dum,sum,temp; 
         }    double *vv; 
     } /* End theta */   
     vv=vector(1,n); 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    *d=1.0; 
     for (i=1;i<=n;i++) { 
     for(h=0; h<=nhstepm; h++)      big=0.0; 
       for(j=1; j<=nlstate;j++)      for (j=1;j<=n;j++) 
         for(theta=1; theta <=npar; theta++)        if ((temp=fabs(a[i][j])) > big) big=temp; 
           trgradg[h][j][theta]=gradg[h][theta][j];      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    } 
     for(i=1;i<=nlstate;i++)    for (j=1;j<=n;j++) { 
       for(j=1;j<=nlstate;j++)      for (i=1;i<j;i++) { 
         vareij[i][j][(int)age] =0.;        sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     for(h=0;h<=nhstepm;h++){        a[i][j]=sum; 
       for(k=0;k<=nhstepm;k++){      } 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      big=0.0; 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      for (i=j;i<=n;i++) { 
         for(i=1;i<=nlstate;i++)        sum=a[i][j]; 
           for(j=1;j<=nlstate;j++)        for (k=1;k<j;k++) 
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          sum -= a[i][k]*a[k][j]; 
       }        a[i][j]=sum; 
     }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
     fprintf(ficresvij,"%.0f ",age );          imax=i; 
     for(i=1; i<=nlstate;i++)        } 
       for(j=1; j<=nlstate;j++){      } 
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);      if (j != imax) { 
       }        for (k=1;k<=n;k++) { 
     fprintf(ficresvij,"\n");          dum=a[imax][k]; 
     free_matrix(gp,0,nhstepm,1,nlstate);          a[imax][k]=a[j][k]; 
     free_matrix(gm,0,nhstepm,1,nlstate);          a[j][k]=dum; 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        } 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        *d = -(*d); 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        vv[imax]=vv[j]; 
   } /* End age */      } 
        indx[j]=imax; 
   free_vector(xp,1,npar);      if (a[j][j] == 0.0) a[j][j]=TINY; 
   free_matrix(doldm,1,nlstate,1,npar);      if (j != n) { 
   free_matrix(dnewm,1,nlstate,1,nlstate);        dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
 }      } 
     } 
 /************ Variance of prevlim ******************/    free_vector(vv,1,n);  /* Doesn't work */
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)  ;
 {  } 
   /* Variance of prevalence limit */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  void lubksb(double **a, int n, int *indx, double b[]) 
   double **newm;  { 
   double **dnewm,**doldm;    int i,ii=0,ip,j; 
   int i, j, nhstepm, hstepm;    double sum; 
   int k, cptcode;   
   double *xp;    for (i=1;i<=n;i++) { 
   double *gp, *gm;      ip=indx[i]; 
   double **gradg, **trgradg;      sum=b[ip]; 
   double age,agelim;      b[ip]=b[i]; 
   int theta;      if (ii) 
            for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");      else if (sum) ii=i; 
   fprintf(ficresvpl,"# Age");      b[i]=sum; 
   for(i=1; i<=nlstate;i++)    } 
       fprintf(ficresvpl," %1d-%1d",i,i);    for (i=n;i>=1;i--) { 
   fprintf(ficresvpl,"\n");      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   xp=vector(1,npar);      b[i]=sum/a[i][i]; 
   dnewm=matrix(1,nlstate,1,npar);    } 
   doldm=matrix(1,nlstate,1,nlstate);  } 
    
   hstepm=1*YEARM; /* Every year of age */  /************ Frequencies ********************/
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  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)
   agelim = AGESUP;  {  /* Some frequencies */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     if (stepm >= YEARM) hstepm=1;    int first;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    double ***freq; /* Frequencies */
     gradg=matrix(1,npar,1,nlstate);    double *pp, **prop;
     gp=vector(1,nlstate);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     gm=vector(1,nlstate);    FILE *ficresp;
     char fileresp[FILENAMELENGTH];
     for(theta=1; theta <=npar; theta++){    
       for(i=1; i<=npar; i++){ /* Computes gradient */    pp=vector(1,nlstate);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    prop=matrix(1,nlstate,iagemin,iagemax+3);
       }    strcpy(fileresp,"p");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    strcat(fileresp,fileres);
       for(i=1;i<=nlstate;i++)    if((ficresp=fopen(fileresp,"w"))==NULL) {
         gp[i] = prlim[i][i];      printf("Problem with prevalence resultfile: %s\n", fileresp);
          fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       for(i=1; i<=npar; i++) /* Computes gradient */      exit(0);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    freq= ma3x(-2,nlstate+ndeath,-2,nlstate+ndeath,iagemin,iagemax+3);
       for(i=1;i<=nlstate;i++)    j1=0;
         gm[i] = prlim[i][i];    
     j=cptcoveff;
       for(i=1;i<=nlstate;i++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  
     } /* End theta */    first=1;
   
     trgradg =matrix(1,nlstate,1,npar);    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
     for(j=1; j<=nlstate;j++)        j1++;
       for(theta=1; theta <=npar; theta++)        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         trgradg[j][theta]=gradg[theta][j];          scanf("%d", i);*/
         for (i=-2; i<=nlstate+ndeath; i++)  
     for(i=1;i<=nlstate;i++)          for (jk=-2; jk<=nlstate+ndeath; jk++)  
       varpl[i][(int)age] =0.;            for(m=iagemin; m <= iagemax+3; m++)
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);              freq[i][jk][m]=0;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  
     for(i=1;i<=nlstate;i++)      for (i=1; i<=nlstate; i++)  
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
     fprintf(ficresvpl,"%.0f ",age );        
     for(i=1; i<=nlstate;i++)        dateintsum=0;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        k2cpt=0;
     fprintf(ficresvpl,"\n");        for (i=1; i<=imx; i++) {
     free_vector(gp,1,nlstate);          bool=1;
     free_vector(gm,1,nlstate);          if  (cptcovn>0) {
     free_matrix(gradg,1,npar,1,nlstate);            for (z1=1; z1<=cptcoveff; z1++) 
     free_matrix(trgradg,1,nlstate,1,npar);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   } /* End age */                bool=0;
           }
   free_vector(xp,1,npar);          if (bool==1){
   free_matrix(doldm,1,nlstate,1,npar);            for(m=firstpass; m<=lastpass; m++){
   free_matrix(dnewm,1,nlstate,1,nlstate);              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;
 /************ Variance of one-step probabilities  ******************/                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)                if (m<lastpass) {
 {                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   int i, j, i1, k1, j1, z1;                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   int k=0, cptcode;                }
   double **dnewm,**doldm;                
   double *xp;                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   double *gp, *gm;                  dateintsum=dateintsum+k2;
   double **gradg, **trgradg;                  k2cpt++;
   double age,agelim, cov[NCOVMAX];                }
   int theta;                /*}*/
   char fileresprob[FILENAMELENGTH];            }
           }
   strcpy(fileresprob,"prob");        }
   strcat(fileresprob,fileres);         
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     printf("Problem with resultfile: %s\n", fileresprob);  
   }        if  (cptcovn>0) {
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);          fprintf(ficresp, "\n#********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");          fprintf(ficresp, "**********\n#");
   fprintf(ficresprob,"# Age");        }
   for(i=1; i<=nlstate;i++)        for(i=1; i<=nlstate;i++) 
     for(j=1; j<=(nlstate+ndeath);j++)          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);        fprintf(ficresp, "\n");
         
         for(i=iagemin; i <= iagemax+3; i++){
   fprintf(ficresprob,"\n");          if(i==iagemax+3){
             fprintf(ficlog,"Total");
           }else{
   xp=vector(1,npar);            if(first==1){
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              first=0;
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));              printf("See log file for details...\n");
              }
   cov[1]=1;            fprintf(ficlog,"Age %d", i);
   j=cptcoveff;          }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          for(jk=1; jk <=nlstate ; jk++){
   j1=0;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   for(k1=1; k1<=1;k1++){              pp[jk] += freq[jk][m][i]; 
     for(i1=1; i1<=ncodemax[k1];i1++){          }
     j1++;          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
     if  (cptcovn>0) {              pos += freq[jk][m][i];
       fprintf(ficresprob, "\n#********** Variable ");            if(pp[jk]>=1.e-10){
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);              if(first==1){
       fprintf(ficresprob, "**********\n#");              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     }              }
                  fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       for (age=bage; age<=fage; age ++){            }else{
         cov[2]=age;              if(first==1)
         for (k=1; k<=cptcovn;k++) {                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                      }
         }          }
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
         for (k=1; k<=cptcovprod;k++)          for(jk=1; jk <=nlstate ; jk++){
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
                      pp[jk] += freq[jk][m][i];
         gradg=matrix(1,npar,1,9);          }       
         trgradg=matrix(1,9,1,npar);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            pos += pp[jk];
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            posprop += prop[jk][i];
              }
         for(theta=1; theta <=npar; theta++){          for(jk=1; jk <=nlstate ; jk++){
           for(i=1; i<=npar; i++)            if(pos>=1.e-5){
             xp[i] = x[i] + (i==theta ?delti[theta]:0);              if(first==1)
                          printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                      }else{
           k=0;              if(first==1)
           for(i=1; i<= (nlstate+ndeath); i++){                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             for(j=1; j<=(nlstate+ndeath);j++){              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               k=k+1;            }
               gp[k]=pmmij[i][j];            if( i <= iagemax){
             }              if(pos>=1.e-5){
           }                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                          /*probs[i][jk][j1]= pp[jk]/pos;*/
           for(i=1; i<=npar; i++)                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
             xp[i] = x[i] - (i==theta ?delti[theta]:0);              }
                  else
           pmij(pmmij,cov,ncovmodel,xp,nlstate);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
           k=0;            }
           for(i=1; i<=(nlstate+ndeath); i++){          }
             for(j=1; j<=(nlstate+ndeath);j++){          
               k=k+1;          for(jk=-1; jk <=nlstate+ndeath; jk++)
               gm[k]=pmmij[i][j];            for(m=-1; m <=nlstate+ndeath; m++)
             }              if(freq[jk][m][i] !=0 ) {
           }              if(first==1)
                      printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                }
         }          if(i <= iagemax)
             fprintf(ficresp,"\n");
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          if(first==1)
           for(theta=1; theta <=npar; theta++)            printf("Others in log...\n");
             trgradg[j][theta]=gradg[theta][j];          fprintf(ficlog,"\n");
                }
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      }
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    }
            dateintmean=dateintsum/k2cpt; 
         pmij(pmmij,cov,ncovmodel,x,nlstate);   
            fclose(ficresp);
         k=0;    free_ma3x(freq,-2,nlstate+ndeath,-2,nlstate+ndeath, iagemin, iagemax+3);
         for(i=1; i<=(nlstate+ndeath); i++){    free_vector(pp,1,nlstate);
           for(j=1; j<=(nlstate+ndeath);j++){    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
             k=k+1;    /* End of Freq */
             gm[k]=pmmij[i][j];  }
           }  
         }  /************ 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)
      /*printf("\n%d ",(int)age);  {  
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));       in each health status at the date of interview (if between dateprev1 and dateprev2).
      }*/       We still use firstpass and lastpass as another selection.
     */
         fprintf(ficresprob,"\n%d ",(int)age);   
     int i, m, jk, k1, i1, j1, bool, z1,z2,j;
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)    double ***freq; /* Frequencies */
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));    double *pp, **prop;
      double pos,posprop; 
       }    double  y2; /* in fractional years */
     }    int iagemin, iagemax;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    iagemin= (int) agemin;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    iagemax= (int) agemax;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    /*pp=vector(1,nlstate);*/
   }    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   free_vector(xp,1,npar);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   fclose(ficresprob);    j1=0;
      
 }    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
 /******************* Printing html file ***********/    
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    for(k1=1; k1<=j;k1++){
                   int lastpass, int stepm, int weightopt, char model[],\      for(i1=1; i1<=ncodemax[k1];i1++){
                   int imx,int jmin, int jmax, double jmeanint,char optionfile[], \        j1++;
                   char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\        
                   char version[], int popforecast, int estepm ,/* \ */        for (i=1; i<=nlstate; i++)  
                   double jprev1, double mprev1,double anprev1, \          for(m=iagemin; m <= iagemax+3; m++)
                   double jprev2, double mprev2,double anprev2){            prop[i][m]=0.0;
   int jj1, k1, i1, cpt;       
   FILE *fichtm;        for (i=1; i<=imx; i++) { /* Each individual */
   /*char optionfilehtm[FILENAMELENGTH];*/          bool=1;
           if  (cptcovn>0) {
   strcpy(optionfilehtm,optionfile);            for (z1=1; z1<=cptcoveff; z1++) 
   strcat(optionfilehtm,".htm");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {                bool=0;
     printf("Problem with %s \n",optionfilehtm), exit(0);          } 
   }          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
 \n                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 Total number of observations=%d <br>\n                if(agev[m][i]==1) agev[m][i]=iagemax+2;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n                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); 
 <hr  size=\"2\" color=\"#EC5E5E\">                if (s[m][i]>0 && s[m][i]<=nlstate) { 
  <ul><li>Parameter files<br>\n                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);                  prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n              }
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n            } /* end selection of waves */
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n          }
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n        }
  - Life expectancies by age and initial health status (estepm=%2d months):        for(i=iagemin; i <= iagemax+3; i++){  
    <a href=\"e%s\">e%s</a> <br>\n</li>", \          
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n          } 
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n  
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n          for(jk=1; jk <=nlstate ; jk++){     
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n            if( i <=  iagemax){ 
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n              if(posprop>=1.e-5){ 
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);                probs[i][jk][j1]= prop[jk][i]/posprop;
               } 
  if(popforecast==1) fprintf(fichtm,"\n            } 
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n          }/* end jk */ 
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n        }/* end i */ 
         <br>",fileres,fileres,fileres,fileres);      } /* end i1 */
  else    } /* end k1 */
    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);    
 fprintf(fichtm," <li>Graphs</li><p>");    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     /*free_vector(pp,1,nlstate);*/
  m=cptcoveff;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  }  /* End of prevalence */
   
  jj1=0;  /************* Waves Concatenation ***************/
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){  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)
        jj1++;  {
        if (cptcovn > 0) {    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");       Death is a valid wave (if date is known).
          for (cpt=1; cpt<=cptcoveff;cpt++)       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");       and mw[mi+1][i]. dh depends on stepm.
        }       */
        /* Pij */  
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>    int i, mi, m;
 <img src=\"pe%s%d1.png\">",strtok(optionfile, "."),jj1,stepm,strtok(optionfile, "."),jj1);        /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        /* Quasi-incidences */       double sum=0., jmean=0.;*/
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>    int first;
 <img src=\"pe%s%d2.png\">",strtok(optionfile, "."),jj1,stepm,strtok(optionfile, "."),jj1);        int j, k=0,jk, ju, jl;
        /* Stable prevalence in each health state */    double sum=0.;
        for(cpt=1; cpt<nlstate;cpt++){    first=0;
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    jmin=1e+5;
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    jmax=-1;
        }    jmean=0.;
     for(cpt=1; cpt<=nlstate;cpt++) {    for(i=1; i<=imx; i++){
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      mi=0;
 interval) in state (%d): v%s%d%d.png <br>      m=firstpass;
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        while(s[m][i] <= nlstate){
      }        if(s[m][i]>=1 || s[m][i]==-2)
      for(cpt=1; cpt<=nlstate;cpt++) {          mw[++mi][i]=m;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>        if(m >=lastpass)
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          break;
      }        else
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          m++;
 health expectancies in states (1) and (2): e%s%d.png<br>      }/* end while */
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      if (s[m][i] > nlstate){
 fprintf(fichtm,"\n</body>");        mi++;     /* Death is another wave */
    }        /* if(mi==0)  never been interviewed correctly before death */
    }           /* Only death is a correct wave */
 fclose(fichtm);        mw[mi][i]=m;
 }      }
   
 /******************* Gnuplot file **************/      wav[i]=mi;
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){      if(mi==0){
         nbwarn++;
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        if(first==0){
   int ng;          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   strcpy(optionfilegnuplot,optionfilefiname);          first=1;
   strcat(optionfilegnuplot,".gp.txt");        }
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        if(first==1){
     printf("Problem with file %s",optionfilegnuplot);          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
   }        }
       } /* end mi==0 */
 #ifdef windows    } /* End individuals */
     fprintf(ficgp,"cd \"%s\" \n",pathc);  
 #endif    for(i=1; i<=imx; i++){
 m=pow(2,cptcoveff);      for(mi=1; mi<wav[i];mi++){
          if (stepm <=0)
  /* 1eme*/          dh[mi][i]=1;
   for (cpt=1; cpt<= nlstate ; cpt ++) {        else{
    for (k1=1; k1<= m ; k1 ++) {          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             if (agedc[i] < 2*AGESUP) {
 #ifdef windows              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);              if(j==0) j=1;  /* Survives at least one month after exam */
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);              else if(j<0){
 #endif                nberr++;
 #ifdef unix                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]);
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);                j=1; /* Temporary Dangerous patch */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);                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);
 #endif                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
 for (i=1; i<= nlstate ; i ++) {              }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              k=k+1;
   else fprintf(ficgp," \%%*lf (\%%*lf)");              if (j >= jmax) jmax=j;
 }              if (j <= jmin) jmin=j;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);              sum=sum+j;
     for (i=1; i<= nlstate ; i ++) {              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");            }
 }          }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          else{
      for (i=1; i<= nlstate ; i ++) {            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }              k=k+1;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));            if (j >= jmax) jmax=j;
 #ifdef unix            else if (j <= jmin)jmin=j;
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
 #endif            /*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++;
   /*2 eme*/              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   for (k1=1; k1<= m ; k1 ++) {            }
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);            sum=sum+j;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);          }
              jk= j/stepm;
     for (i=1; i<= nlstate+1 ; i ++) {          jl= j -jk*stepm;
       k=2*i;          ju= j -(jk+1)*stepm;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       for (j=1; j<= nlstate+1 ; j ++) {            if(jl==0){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              dh[mi][i]=jk;
   else fprintf(ficgp," \%%*lf (\%%*lf)");              bh[mi][i]=0;
 }              }else{ /* We want a negative bias in order to only have interpolation ie
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");                    * at the price of an extra matrix product in likelihood */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);              dh[mi][i]=jk+1;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);              bh[mi][i]=ju;
       for (j=1; j<= nlstate+1 ; j ++) {            }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          }else{
         else fprintf(ficgp," \%%*lf (\%%*lf)");            if(jl <= -ju){
 }                dh[mi][i]=jk;
       fprintf(ficgp,"\" t\"\" w l 0,");              bh[mi][i]=jl;       /* bias is positive if real duration
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);                                   * is higher than the multiple of stepm and negative otherwise.
       for (j=1; j<= nlstate+1 ; j ++) {                                   */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            }
   else fprintf(ficgp," \%%*lf (\%%*lf)");            else{
 }                dh[mi][i]=jk+1;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");              bh[mi][i]=ju;
       else fprintf(ficgp,"\" t\"\" w l 0,");            }
     }            if(dh[mi][i]==0){
   }              dh[mi][i]=1; /* At least one step */
                bh[mi][i]=ju; /* At least one step */
   /*3eme*/              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
             }
   for (k1=1; k1<= m ; k1 ++) {          } /* end if mle */
     for (cpt=1; cpt<= nlstate ; cpt ++) {        }
       k=2+nlstate*(2*cpt-2);      } /* end wave */
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    }
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    jmean=sum/k;
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);   }
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");  /*********** Tricode ****************************/
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  void tricode(int *Tvar, int **nbcode, int imx)
   {
 */    
       for (i=1; i< nlstate ; i ++) {    int Ndum[20],ij=1, k, j, i, maxncov=19;
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);    int cptcode=0;
     cptcoveff=0; 
       }   
     }    for (k=0; k<maxncov; k++) Ndum[k]=0;
   }    for (k=1; k<=7; k++) ncodemax[k]=0;
    
   /* CV preval stat */    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     for (k1=1; k1<= m ; k1 ++) {      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     for (cpt=1; cpt<nlstate ; cpt ++) {                                 modality*/ 
       k=3;        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        Ndum[ij]++; /*store the modality */
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
       for (i=1; i< nlstate ; i ++)                                         Tvar[j]. If V=sex and male is 0 and 
         fprintf(ficgp,"+$%d",k+i+1);                                         female is 1, then  cptcode=1.*/
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      }
        
       l=3+(nlstate+ndeath)*cpt;      for (i=0; i<=cptcode; i++) {
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
       for (i=1; i< nlstate ; i ++) {      }
         l=3+(nlstate+ndeath)*cpt;  
         fprintf(ficgp,"+$%d",l+i+1);      ij=1; 
       }      for (i=1; i<=ncodemax[j]; i++) {
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          for (k=0; k<= maxncov; k++) {
     }          if (Ndum[k] != 0) {
   }              nbcode[Tvar[j]][ij]=k; 
              /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   /* proba elementaires */            
    for(i=1,jk=1; i <=nlstate; i++){            ij++;
     for(k=1; k <=(nlstate+ndeath); k++){          }
       if (k != i) {          if (ij > ncodemax[j]) break; 
         for(j=1; j <=ncovmodel; j++){        }  
              } 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    }  
           jk++;  
           fprintf(ficgp,"\n");   for (k=0; k< maxncov; k++) Ndum[k]=0;
         }  
       }   for (i=1; i<=ncovmodel-2; i++) { 
     }     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
    }     ij=Tvar[i];
      Ndum[ij]++;
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/   }
      for(jk=1; jk <=m; jk++) {  
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);   ij=1;
        if (ng==2)   for (i=1; i<= maxncov; i++) {
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");     if((Ndum[i]!=0) && (i<=ncovcol)){
        else       Tvaraff[ij]=i; /*For printing */
          fprintf(ficgp,"\nset title \"Probability\"\n");       ij++;
        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;   cptcoveff=ij-1; /*Number of simple covariates*/
          for(k=1; k<=(nlstate+ndeath); k++) {  }
            if (k != k2){  
              if(ng==2)  /*********** Health Expectancies ****************/
                fprintf(ficgp," %f*exp(p%d+p%d*x",stepm/YEARM,i,i+1);  
              else  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  
              ij=1;  {
              for(j=3; j <=ncovmodel; j++) {    /* Health expectancies */
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    double age, agelim, hf;
                  ij++;    double ***p3mat,***varhe;
                }    double **dnewm,**doldm;
                else    double *xp;
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    double **gp, **gm;
              }    double ***gradg, ***trgradg;
              fprintf(ficgp,")/(1");    int theta;
                
              for(k1=1; k1 <=nlstate; k1++){      varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    xp=vector(1,npar);
                ij=1;    dnewm=matrix(1,nlstate*nlstate,1,npar);
                for(j=3; j <=ncovmodel; j++){    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
                  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]]]);    fprintf(ficreseij,"# Health expectancies\n");
                    ij++;    fprintf(ficreseij,"# Age");
                  }    for(i=1; i<=nlstate;i++)
                  else      for(j=1; j<=nlstate;j++)
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
                }    fprintf(ficreseij,"\n");
                fprintf(ficgp,")");  
              }    if(estepm < stepm){
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);      printf ("Problem %d lower than %d\n",estepm, stepm);
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    }
              i=i+ncovmodel;    else  hstepm=estepm;   
            }    /* We compute the life expectancy from trapezoids spaced every estepm months
          }     * This is mainly to measure the difference between two models: for example
        }     * if stepm=24 months pijx are given only every 2 years and by summing them
      }     * we are calculating an estimate of the Life Expectancy assuming a linear 
    }     * progression in between and thus overestimating or underestimating according
    fclose(ficgp);     * to the curvature of the survival function. If, for the same date, we 
 }  /* end gnuplot */     * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
 /*************** Moving average **************/     * curvature will be obtained if estepm is as small as stepm. */
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){  
     /* For example we decided to compute the life expectancy with the smallest unit */
   int i, cpt, cptcod;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)       nhstepm is the number of hstepm from age to agelim 
       for (i=1; i<=nlstate;i++)       nstepm is the number of stepm from age to agelin. 
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)       Look at hpijx to understand the reason of that which relies in memory size
           mobaverage[(int)agedeb][i][cptcod]=0.;       and note for a fixed period like estepm months */
        /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){       survival function given by stepm (the optimization length). Unfortunately it
       for (i=1; i<=nlstate;i++){       means that if the survival funtion is printed only each two years of age and if
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           for (cpt=0;cpt<=4;cpt++){       results. So we changed our mind and took the option of the best precision.
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    */
           }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  
         }    agelim=AGESUP;
       }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     }      /* nhstepm age range expressed in number of stepm */
          nstepm=(int) rint((agelim-age)*YEARM/stepm); 
 }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 /************** Forecasting ******************/      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 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){      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
        gp=matrix(0,nhstepm,1,nlstate*nlstate);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   int *popage;  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   double *popeffectif,*popcount;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   double ***p3mat;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   char fileresf[FILENAMELENGTH];   
   
  agelim=AGESUP;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  
       /* Computing  Variances of health expectancies */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  
         for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ 
   strcpy(fileresf,"f");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   strcat(fileresf,fileres);        }
   if((ficresf=fopen(fileresf,"w"))==NULL) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     printf("Problem with forecast resultfile: %s\n", fileresf);    
   }        cptj=0;
   printf("Computing forecasting: result on file '%s' \n", fileresf);        for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            cptj=cptj+1;
             for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   if (mobilav==1) {              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            }
     movingaverage(agedeb, fage, ageminpar, mobaverage);          }
   }        }
        
   stepsize=(int) (stepm+YEARM-1)/YEARM;       
   if (stepm<=12) stepsize=1;        for(i=1; i<=npar; i++) 
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
   agelim=AGESUP;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          
   hstepm=1;        cptj=0;
   hstepm=hstepm/stepm;        for(j=1; j<= nlstate; j++){
   yp1=modf(dateintmean,&yp);          for(i=1;i<=nlstate;i++){
   anprojmean=yp;            cptj=cptj+1;
   yp2=modf((yp1*12),&yp);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   mprojmean=yp;  
   yp1=modf((yp2*30.5),&yp);              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   jprojmean=yp;            }
   if(jprojmean==0) jprojmean=1;          }
   if(mprojmean==0) jprojmean=1;        }
          for(j=1; j<= nlstate*nlstate; j++)
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);          for(h=0; h<=nhstepm-1; h++){
              gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   for(cptcov=1;cptcov<=i2;cptcov++){          }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       } 
       k=k+1;     
       fprintf(ficresf,"\n#******");  /* End theta */
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
       }  
       fprintf(ficresf,"******\n");       for(h=0; h<=nhstepm-1; h++)
       fprintf(ficresf,"# StartingAge FinalAge");        for(j=1; j<=nlstate*nlstate;j++)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);          for(theta=1; theta <=npar; theta++)
                  trgradg[h][j][theta]=gradg[h][theta][j];
             
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {  
         fprintf(ficresf,"\n");       for(i=1;i<=nlstate*nlstate;i++)
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);          for(j=1;j<=nlstate*nlstate;j++)
           varhe[i][j][(int)age] =0.;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);       printf("%d|",(int)age);fflush(stdout);
           nhstepm = nhstepm/hstepm;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                 for(h=0;h<=nhstepm-1;h++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(k=0;k<=nhstepm-1;k++){
           oldm=oldms;savm=savms;          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
                  for(i=1;i<=nlstate*nlstate;i++)
           for (h=0; h<=nhstepm; h++){            for(j=1;j<=nlstate*nlstate;j++)
             if (h==(int) (calagedate+YEARM*cpt)) {              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);        }
             }      }
             for(j=1; j<=nlstate+ndeath;j++) {      /* Computing expectancies */
               kk1=0.;kk2=0;      for(i=1; i<=nlstate;i++)
               for(i=1; i<=nlstate;i++) {                      for(j=1; j<=nlstate;j++)
                 if (mobilav==1)          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
                 else {            
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  /* 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]);*/
                 }  
                          }
               }  
               if (h==(int)(calagedate+12*cpt)){      fprintf(ficreseij,"%3.0f",age );
                 fprintf(ficresf," %.3f", kk1);      cptj=0;
                              for(i=1; i<=nlstate;i++)
               }        for(j=1; j<=nlstate;j++){
             }          cptj++;
           }          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
         }      fprintf(ficreseij,"\n");
       }     
     }      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
              free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fclose(ficresf);    }
 }    printf("\n");
 /************** Forecasting ******************/    fprintf(ficlog,"\n");
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){  
      free_vector(xp,1,npar);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   int *popage;    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   double *popeffectif,*popcount;  }
   double ***p3mat,***tabpop,***tabpopprev;  
   char filerespop[FILENAMELENGTH];  /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  {
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* Variance of health expectancies */
   agelim=AGESUP;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    /* double **newm;*/
      double **dnewm,**doldm;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    double **dnewmp,**doldmp;
      int i, j, nhstepm, hstepm, h, nstepm ;
      int k, cptcode;
   strcpy(filerespop,"pop");    double *xp;
   strcat(filerespop,fileres);    double **gp, **gm;  /* for var eij */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    double ***gradg, ***trgradg; /*for var eij */
     printf("Problem with forecast resultfile: %s\n", filerespop);    double **gradgp, **trgradgp; /* for var p point j */
   }    double *gpp, *gmp; /* for var p point j */
   printf("Computing forecasting: result on file '%s' \n", filerespop);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    double age,agelim, hf;
     double ***mobaverage;
   if (mobilav==1) {    int theta;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    char digit[4];
     movingaverage(agedeb, fage, ageminpar, mobaverage);    char digitp[25];
   }  
     char fileresprobmorprev[FILENAMELENGTH];
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   if (stepm<=12) stepsize=1;    if(popbased==1){
        if(mobilav!=0)
   agelim=AGESUP;        strcpy(digitp,"-populbased-mobilav-");
        else strcpy(digitp,"-populbased-nomobil-");
   hstepm=1;    }
   hstepm=hstepm/stepm;    else 
        strcpy(digitp,"-stablbased-");
   if (popforecast==1) {  
     if((ficpop=fopen(popfile,"r"))==NULL) {    if (mobilav!=0) {
       printf("Problem with population file : %s\n",popfile);exit(0);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     popage=ivector(0,AGESUP);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     popeffectif=vector(0,AGESUP);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     popcount=vector(0,AGESUP);      }
        }
     i=1;    
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    strcpy(fileresprobmorprev,"prmorprev"); 
        sprintf(digit,"%-d",ij);
     imx=i;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
   for(cptcov=1;cptcov<=i2;cptcov++){    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       k=k+1;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficrespop,"\n#******");    }
       for(j=1;j<=cptcoveff;j++) {    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       }    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
       fprintf(ficrespop,"******\n");    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
       fprintf(ficrespop,"# Age");    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      fprintf(ficresprobmorprev," p.%-d SE",j);
       if (popforecast==1)  fprintf(ficrespop," [Population]");      for(i=1; i<=nlstate;i++)
              fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
       for (cpt=0; cpt<=0;cpt++) {    }  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      fprintf(ficresprobmorprev,"\n");
            fprintf(ficgp,"\n# Routine varevsij");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    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");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
           nhstepm = nhstepm/hstepm;  /*   } */
              varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;    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");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(ficresvij,"# Age");
            for(i=1; i<=nlstate;i++)
           for (h=0; h<=nhstepm; h++){      for(j=1; j<=nlstate;j++)
             if (h==(int) (calagedate+YEARM*cpt)) {        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    fprintf(ficresvij,"\n");
             }  
             for(j=1; j<=nlstate+ndeath;j++) {    xp=vector(1,npar);
               kk1=0.;kk2=0;    dnewm=matrix(1,nlstate,1,npar);
               for(i=1; i<=nlstate;i++) {                  doldm=matrix(1,nlstate,1,nlstate);
                 if (mobilav==1)    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
                 }    gpp=vector(nlstate+1,nlstate+ndeath);
               }    gmp=vector(nlstate+1,nlstate+ndeath);
               if (h==(int)(calagedate+12*cpt)){    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    
                   /*fprintf(ficrespop," %.3f", kk1);    if(estepm < stepm){
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      printf ("Problem %d lower than %d\n",estepm, stepm);
               }    }
             }    else  hstepm=estepm;   
             for(i=1; i<=nlstate;i++){    /* For example we decided to compute the life expectancy with the smallest unit */
               kk1=0.;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                 for(j=1; j<=nlstate;j++){       nhstepm is the number of hstepm from age to agelim 
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];       nstepm is the number of stepm from age to agelin. 
                 }       Look at hpijx to understand the reason of that which relies in memory size
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];       and note for a fixed period like k years */
             }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)       means that if the survival funtion is printed every two years of age and if
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);       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.
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    */
         }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       }    agelim = AGESUP;
      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   /******/      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      gp=matrix(0,nhstepm,1,nlstate);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      gm=matrix(0,nhstepm,1,nlstate);
           nhstepm = nhstepm/hstepm;  
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(theta=1; theta <=npar; theta++){
           oldm=oldms;savm=savms;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            xp[i] = x[i] + (i==theta ?delti[theta]:0);
           for (h=0; h<=nhstepm; h++){        }
             if (h==(int) (calagedate+YEARM*cpt)) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             }  
             for(j=1; j<=nlstate+ndeath;j++) {        if (popbased==1) {
               kk1=0.;kk2=0;          if(mobilav ==0){
               for(i=1; i<=nlstate;i++) {                          for(i=1; i<=nlstate;i++)
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                  prlim[i][i]=probs[(int)age][i][ij];
               }          }else{ /* mobilav */ 
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);            for(i=1; i<=nlstate;i++)
             }              prlim[i][i]=mobaverage[(int)age][i][ij];
           }          }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
         }    
       }        for(j=1; j<= nlstate; j++){
    }          for(h=0; h<=nhstepm; h++){
   }            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
         }
   if (popforecast==1) {        /* This for computing probability of death (h=1 means
     free_ivector(popage,0,AGESUP);           computed over hstepm matrices product = hstepm*stepm months) 
     free_vector(popeffectif,0,AGESUP);           as a weighted average of prlim.
     free_vector(popcount,0,AGESUP);        */
   }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
   fclose(ficrespop);        }    
 }        /* end probability of death */
   
 /***********************************************/        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
 /**************** Main Program *****************/          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);
 int main(int argc, char *argv[])   
 {        if (popbased==1) {
           if(mobilav ==0){
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;            for(i=1; i<=nlstate;i++)
   double agedeb, agefin,hf;              prlim[i][i]=probs[(int)age][i][ij];
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
   double fret;              prlim[i][i]=mobaverage[(int)age][i][ij];
   double **xi,tmp,delta;          }
         }
   double dum; /* Dummy variable */  
   double ***p3mat;        for(j=1; j<= nlstate; j++){
   int *indx;          for(h=0; h<=nhstepm; h++){
   char line[MAXLINE], linepar[MAXLINE];            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   char title[MAXLINE];              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          }
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];        }
          /* This for computing probability of death (h=1 means
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
   char filerest[FILENAMELENGTH];        */
   char fileregp[FILENAMELENGTH];        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   char popfile[FILENAMELENGTH];          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   int firstobs=1, lastobs=10;        }    
   int sdeb, sfin; /* Status at beginning and end */        /* end probability of death */
   int c,  h , cpt,l;  
   int ju,jl, mi;        for(j=1; j<= nlstate; j++) /* vareij */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          for(h=0; h<=nhstepm; h++){
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   int mobilav=0,popforecast=0;          }
   int hstepm, nhstepm;  
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   double bage, fage, age, agelim, agebase;        }
   double ftolpl=FTOL;  
   double **prlim;      } /* End theta */
   double *severity;  
   double ***param; /* Matrix of parameters */      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   double  *p;  
   double **matcov; /* Matrix of covariance */      for(h=0; h<=nhstepm; h++) /* veij */
   double ***delti3; /* Scale */        for(j=1; j<=nlstate;j++)
   double *delti; /* Scale */          for(theta=1; theta <=npar; theta++)
   double ***eij, ***vareij;            trgradg[h][j][theta]=gradg[h][theta][j];
   double **varpl; /* Variances of prevalence limits by age */  
   double *epj, vepp;      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   double kk1, kk2;        for(theta=1; theta <=npar; theta++)
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;          trgradgp[j][theta]=gradgp[theta][j];
      
   
   char version[80]="Imach version 0.8e, May 2002, INED-EUROREVES ";      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   char *alph[]={"a","a","b","c","d","e"}, str[4];      for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   char z[1]="c", occ;  
 #include <sys/time.h>      for(h=0;h<=nhstepm;h++){
 #include <time.h>        for(k=0;k<=nhstepm;k++){
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   /* long total_usecs;          for(i=1;i<=nlstate;i++)
   struct timeval start_time, end_time;            for(j=1;j<=nlstate;j++)
                vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        }
   getcwd(pathcd, size);      }
     
   printf("\n%s",version);      /* pptj */
   if(argc <=1){      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
     printf("\nEnter the parameter file name: ");      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
     scanf("%s",pathtot);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   else{          varppt[j][i]=doldmp[j][i];
     strcpy(pathtot,argv[1]);      /* end ppptj */
   }      /*  x centered again */
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   /*cygwin_split_path(pathtot,path,optionfile);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/   
   /* cutv(path,optionfile,pathtot,'\\');*/      if (popbased==1) {
         if(mobilav ==0){
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);          for(i=1; i<=nlstate;i++)
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);            prlim[i][i]=probs[(int)age][i][ij];
   chdir(path);        }else{ /* mobilav */ 
   replace(pathc,path);          for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
 /*-------- arguments in the command line --------*/        }
       }
   strcpy(fileres,"r");               
   strcat(fileres, optionfilefiname);      /* This for computing probability of death (h=1 means
   strcat(fileres,".txt");    /* Other files have txt extension */         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
   /*---------arguments file --------*/      */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     printf("Problem with optionfile %s\n",optionfile);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     goto end;      }    
   }      /* end probability of death */
   
   strcpy(filereso,"o");      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   strcat(filereso,fileres);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   if((ficparo=fopen(filereso,"w"))==NULL) {        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        for(i=1; i<=nlstate;i++){
   }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
   /* Reads comments: lines beginning with '#' */      } 
   while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficresprobmorprev,"\n");
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      fprintf(ficresvij,"%.0f ",age );
     puts(line);      for(i=1; i<=nlstate;i++)
     fputs(line,ficparo);        for(j=1; j<=nlstate;j++){
   }          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   ungetc(c,ficpar);        }
       fprintf(ficresvij,"\n");
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);      free_matrix(gp,0,nhstepm,1,nlstate);
   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);      free_matrix(gm,0,nhstepm,1,nlstate);
   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);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
 while((c=getc(ficpar))=='#' && c!= EOF){      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     ungetc(c,ficpar);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fgets(line, MAXLINE, ficpar);    } /* End age */
     puts(line);    free_vector(gpp,nlstate+1,nlstate+ndeath);
     fputs(line,ficparo);    free_vector(gmp,nlstate+1,nlstate+ndeath);
   }    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   ungetc(c,ficpar);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
        /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   covar=matrix(0,NCOVMAX,1,n);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   cptcovn=0;  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   ncovmodel=2+cptcovn;    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
      fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
   /* Read guess parameters */    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   /* Reads comments: lines beginning with '#' */    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);
   while((c=getc(ficpar))=='#' && c!= EOF){    /*  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);
     ungetc(c,ficpar);  */
     fgets(line, MAXLINE, ficpar);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     puts(line);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     fputs(line,ficparo);  
   }    free_vector(xp,1,npar);
   ungetc(c,ficpar);    free_matrix(doldm,1,nlstate,1,nlstate);
      free_matrix(dnewm,1,nlstate,1,npar);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     for(i=1; i <=nlstate; i++)    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     for(j=1; j <=nlstate+ndeath-1; j++){    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fprintf(ficparo,"%1d%1d",i1,j1);    fclose(ficresprobmorprev);
       printf("%1d%1d",i,j);    fflush(ficgp);
       for(k=1; k<=ncovmodel;k++){    fflush(fichtm); 
         fscanf(ficpar," %lf",&param[i][j][k]);  }  /* end varevsij */
         printf(" %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);  /************ Variance of prevlim ******************/
       }  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
       fscanf(ficpar,"\n");  {
       printf("\n");    /* Variance of prevalence limit */
       fprintf(ficparo,"\n");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     }    double **newm;
      double **dnewm,**doldm;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    int i, j, nhstepm, hstepm;
     int k, cptcode;
   p=param[1][1];    double *xp;
      double *gp, *gm;
   /* Reads comments: lines beginning with '#' */    double **gradg, **trgradg;
   while((c=getc(ficpar))=='#' && c!= EOF){    double age,agelim;
     ungetc(c,ficpar);    int theta;
     fgets(line, MAXLINE, ficpar);     
     puts(line);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     fputs(line,ficparo);    fprintf(ficresvpl,"# Age");
   }    for(i=1; i<=nlstate;i++)
   ungetc(c,ficpar);        fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    xp=vector(1,npar);
   for(i=1; i <=nlstate; i++){    dnewm=matrix(1,nlstate,1,npar);
     for(j=1; j <=nlstate+ndeath-1; j++){    doldm=matrix(1,nlstate,1,nlstate);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    
       printf("%1d%1d",i,j);    hstepm=1*YEARM; /* Every year of age */
       fprintf(ficparo,"%1d%1d",i1,j1);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
       for(k=1; k<=ncovmodel;k++){    agelim = AGESUP;
         fscanf(ficpar,"%le",&delti3[i][j][k]);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         printf(" %le",delti3[i][j][k]);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         fprintf(ficparo," %le",delti3[i][j][k]);      if (stepm >= YEARM) hstepm=1;
       }      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       fscanf(ficpar,"\n");      gradg=matrix(1,npar,1,nlstate);
       printf("\n");      gp=vector(1,nlstate);
       fprintf(ficparo,"\n");      gm=vector(1,nlstate);
     }  
   }      for(theta=1; theta <=npar; theta++){
   delti=delti3[1][1];        for(i=1; i<=npar; i++){ /* Computes gradient */
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
   /* Reads comments: lines beginning with '#' */        }
   while((c=getc(ficpar))=='#' && c!= EOF){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     ungetc(c,ficpar);        for(i=1;i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);          gp[i] = prlim[i][i];
     puts(line);      
     fputs(line,ficparo);        for(i=1; i<=npar; i++) /* Computes gradient */
   }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   ungetc(c,ficpar);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
          for(i=1;i<=nlstate;i++)
   matcov=matrix(1,npar,1,npar);          gm[i] = prlim[i][i];
   for(i=1; i <=npar; i++){  
     fscanf(ficpar,"%s",&str);        for(i=1;i<=nlstate;i++)
     printf("%s",str);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     fprintf(ficparo,"%s",str);      } /* End theta */
     for(j=1; j <=i; j++){  
       fscanf(ficpar," %le",&matcov[i][j]);      trgradg =matrix(1,nlstate,1,npar);
       printf(" %.5le",matcov[i][j]);  
       fprintf(ficparo," %.5le",matcov[i][j]);      for(j=1; j<=nlstate;j++)
     }        for(theta=1; theta <=npar; theta++)
     fscanf(ficpar,"\n");          trgradg[j][theta]=gradg[theta][j];
     printf("\n");  
     fprintf(ficparo,"\n");      for(i=1;i<=nlstate;i++)
   }        varpl[i][(int)age] =0.;
   for(i=1; i <=npar; i++)      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     for(j=i+1;j<=npar;j++)      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       matcov[i][j]=matcov[j][i];      for(i=1;i<=nlstate;i++)
            varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   printf("\n");  
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
     /*-------- Rewriting paramater file ----------*/        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
      strcpy(rfileres,"r");    /* "Rparameterfile */      fprintf(ficresvpl,"\n");
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/      free_vector(gp,1,nlstate);
      strcat(rfileres,".");    /* */      free_vector(gm,1,nlstate);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */      free_matrix(gradg,1,npar,1,nlstate);
     if((ficres =fopen(rfileres,"w"))==NULL) {      free_matrix(trgradg,1,nlstate,1,npar);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    } /* End age */
     }  
     fprintf(ficres,"#%s\n",version);    free_vector(xp,1,npar);
        free_matrix(doldm,1,nlstate,1,npar);
     /*-------- data file ----------*/    free_matrix(dnewm,1,nlstate,1,nlstate);
     if((fic=fopen(datafile,"r"))==NULL)    {  
       printf("Problem with datafile: %s\n", datafile);goto end;  }
     }  
   /************ Variance of one-step probabilities  ******************/
     n= lastobs;  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
     severity = vector(1,maxwav);  {
     outcome=imatrix(1,maxwav+1,1,n);    int i, j=0,  i1, k1, l1, t, tj;
     num=ivector(1,n);    int k2, l2, j1,  z1;
     moisnais=vector(1,n);    int k=0,l, cptcode;
     annais=vector(1,n);    int first=1, first1;
     moisdc=vector(1,n);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     andc=vector(1,n);    double **dnewm,**doldm;
     agedc=vector(1,n);    double *xp;
     cod=ivector(1,n);    double *gp, *gm;
     weight=vector(1,n);    double **gradg, **trgradg;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    double **mu;
     mint=matrix(1,maxwav,1,n);    double age,agelim, cov[NCOVMAX];
     anint=matrix(1,maxwav,1,n);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     s=imatrix(1,maxwav+1,1,n);    int theta;
     adl=imatrix(1,maxwav+1,1,n);        char fileresprob[FILENAMELENGTH];
     tab=ivector(1,NCOVMAX);    char fileresprobcov[FILENAMELENGTH];
     ncodemax=ivector(1,8);    char fileresprobcor[FILENAMELENGTH];
   
     i=1;    double ***varpij;
     while (fgets(line, MAXLINE, fic) != NULL)    {  
       if ((i >= firstobs) && (i <=lastobs)) {    strcpy(fileresprob,"prob"); 
            strcat(fileresprob,fileres);
         for (j=maxwav;j>=1;j--){    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      printf("Problem with resultfile: %s\n", fileresprob);
           strcpy(line,stra);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
           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);    strcpy(fileresprobcov,"probcov"); 
         }    strcat(fileresprobcov,fileres);
            if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      printf("Problem with resultfile: %s\n", fileresprobcov);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    strcpy(fileresprobcor,"probcor"); 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      printf("Problem with resultfile: %s\n", fileresprobcor);
         for (j=ncovcol;j>=1;j--){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    }
         }    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
         num[i]=atol(stra);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
            printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           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;}*/    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);
         i=i+1;    
       }    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     }    fprintf(ficresprob,"# Age");
     /* printf("ii=%d", ij);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
        scanf("%d",i);*/    fprintf(ficresprobcov,"# Age");
   imx=i-1; /* Number of individuals */    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# Age");
   /* 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;    for(i=1; i<=nlstate;i++)
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      for(j=1; j<=(nlstate+ndeath);j++){
     }*/        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
    /*  for (i=1; i<=imx; i++){        fprintf(ficresprobcov," p%1d-%1d ",i,j);
      if (s[4][i]==9)  s[4][i]=-1;        fprintf(ficresprobcor," p%1d-%1d ",i,j);
      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]));}*/      }  
     /* fprintf(ficresprob,"\n");
      fprintf(ficresprobcov,"\n");
   /* Calculation of the number of parameter from char model*/    fprintf(ficresprobcor,"\n");
   Tvar=ivector(1,15);   */
   Tprod=ivector(1,15);   xp=vector(1,npar);
   Tvaraff=ivector(1,15);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   Tvard=imatrix(1,15,1,2);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   Tage=ivector(1,15);          mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
        varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   if (strlen(model) >1){    first=1;
     j=0, j1=0, k1=1, k2=1;    fprintf(ficgp,"\n# Routine varprob");
     j=nbocc(model,'+');    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     j1=nbocc(model,'*');    fprintf(fichtm,"\n");
     cptcovn=j+1;  
     cptcovprod=j1;    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
        fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     strcpy(modelsav,model);    file %s<br>\n",optionfilehtmcov);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
       printf("Error. Non available option model=%s ",model);  and drawn. It helps understanding how is the covariance between two incidences.\
       goto end;   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     }    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
      It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
     for(i=(j+1); i>=1;i--){  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
       cutv(stra,strb,modelsav,'+');  standard deviations wide on each axis. <br>\
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
       /*scanf("%d",i);*/  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
       if (strchr(strb,'*')) {  
         cutv(strd,strc,strb,'*');    cov[1]=1;
         if (strcmp(strc,"age")==0) {    tj=cptcoveff;
           cptcovprod--;    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
           cutv(strb,stre,strd,'V');    j1=0;
           Tvar[i]=atoi(stre);    for(t=1; t<=tj;t++){
           cptcovage++;      for(i1=1; i1<=ncodemax[t];i1++){ 
             Tage[cptcovage]=i;        j1++;
             /*printf("stre=%s ", stre);*/        if  (cptcovn>0) {
         }          fprintf(ficresprob, "\n#********** Variable "); 
         else if (strcmp(strd,"age")==0) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           cptcovprod--;          fprintf(ficresprob, "**********\n#\n");
           cutv(strb,stre,strc,'V');          fprintf(ficresprobcov, "\n#********** Variable "); 
           Tvar[i]=atoi(stre);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           cptcovage++;          fprintf(ficresprobcov, "**********\n#\n");
           Tage[cptcovage]=i;          
         }          fprintf(ficgp, "\n#********** Variable "); 
         else {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           cutv(strb,stre,strc,'V');          fprintf(ficgp, "**********\n#\n");
           Tvar[i]=ncovcol+k1;          
           cutv(strb,strc,strd,'V');          
           Tprod[k1]=i;          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           Tvard[k1][1]=atoi(strc);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           Tvard[k1][2]=atoi(stre);          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           Tvar[cptcovn+k2]=Tvard[k1][1];          
           Tvar[cptcovn+k2+1]=Tvard[k1][2];          fprintf(ficresprobcor, "\n#********** Variable ");    
           for (k=1; k<=lastobs;k++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];          fprintf(ficresprobcor, "**********\n#");    
           k1++;        }
           k2=k2+2;        
         }        for (age=bage; age<=fage; age ++){ 
       }          cov[2]=age;
       else {          for (k=1; k<=cptcovn;k++) {
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
        /*  scanf("%d",i);*/          }
       cutv(strd,strc,strb,'V');          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       Tvar[i]=atoi(strc);          for (k=1; k<=cptcovprod;k++)
       }            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       strcpy(modelsav,stra);            
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         scanf("%d",i);*/          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     }          gp=vector(1,(nlstate)*(nlstate+ndeath));
 }          gm=vector(1,(nlstate)*(nlstate+ndeath));
        
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);          for(theta=1; theta <=npar; theta++){
   printf("cptcovprod=%d ", cptcovprod);            for(i=1; i<=npar; i++)
   scanf("%d ",i);*/              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
     fclose(fic);            
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
     /*  if(mle==1){*/            
     if (weightopt != 1) { /* Maximisation without weights*/            k=0;
       for(i=1;i<=n;i++) weight[i]=1.0;            for(i=1; i<= (nlstate); i++){
     }              for(j=1; j<=(nlstate+ndeath);j++){
     /*-calculation of age at interview from date of interview and age at death -*/                k=k+1;
     agev=matrix(1,maxwav,1,imx);                gp[k]=pmmij[i][j];
               }
     for (i=1; i<=imx; i++) {            }
       for(m=2; (m<= maxwav); m++) {            
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){            for(i=1; i<=npar; i++)
          anint[m][i]=9999;              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
          s[m][i]=-1;      
        }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;            k=0;
       }            for(i=1; i<=(nlstate); i++){
     }              for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
     for (i=1; i<=imx; i++)  {                gm[k]=pmmij[i][j];
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);              }
       for(m=1; (m<= maxwav); m++){            }
         if(s[m][i] >0){       
           if (s[m][i] >= nlstate+1) {            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
             if(agedc[i]>0)              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
               if(moisdc[i]!=99 && andc[i]!=9999)          }
                 agev[m][i]=agedc[i];  
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
            else {            for(theta=1; theta <=npar; theta++)
               if (andc[i]!=9999){              trgradg[j][theta]=gradg[theta][j];
               printf("Warning negative age at death: %d line:%d\n",num[i],i);          
               agev[m][i]=-1;          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
               }          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
             }          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           }          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           else if(s[m][i] !=9){ /* Should no more exist */          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
             if(mint[m][i]==99 || anint[m][i]==9999)  
               agev[m][i]=1;          pmij(pmmij,cov,ncovmodel,x,nlstate);
             else if(agev[m][i] <agemin){          
               agemin=agev[m][i];          k=0;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/          for(i=1; i<=(nlstate); i++){
             }            for(j=1; j<=(nlstate+ndeath);j++){
             else if(agev[m][i] >agemax){              k=k+1;
               agemax=agev[m][i];              mu[k][(int) age]=pmmij[i][j];
              /* 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];*/          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             /*   agev[m][i] = age[i]+2*m;*/            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
           }              varpij[i][j][(int)age] = doldm[i][j];
           else { /* =9 */  
             agev[m][i]=1;          /*printf("\n%d ",(int)age);
             s[m][i]=-1;            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
           }            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         }            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         else /*= 0 Unknown */            }*/
           agev[m][i]=1;  
       }          fprintf(ficresprob,"\n%d ",(int)age);
              fprintf(ficresprobcov,"\n%d ",(int)age);
     }          fprintf(ficresprobcor,"\n%d ",(int)age);
     for (i=1; i<=imx; i++)  {  
       for(m=1; (m<= maxwav); m++){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
         if (s[m][i] > (nlstate+ndeath)) {            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           printf("Error: Wrong value in nlstate or ndeath\n");            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
           goto end;            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
         }            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
       }          }
     }          i=0;
           for (k=1; k<=(nlstate);k++){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);            for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
     free_vector(severity,1,maxwav);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     free_imatrix(outcome,1,maxwav+1,1,n);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     free_vector(moisnais,1,n);              for (j=1; j<=i;j++){
     free_vector(annais,1,n);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     /* free_matrix(mint,1,maxwav,1,n);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
        free_matrix(anint,1,maxwav,1,n);*/              }
     free_vector(moisdc,1,n);            }
     free_vector(andc,1,n);          }/* end of loop for state */
         } /* end of loop for age */
      
     wav=ivector(1,imx);        /* Confidence intervalle of pij  */
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        /*
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          fprintf(ficgp,"\nset noparametric;unset label");
              fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     /* Concatenates waves */          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       Tcode=ivector(1,100);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        */
       ncodemax[1]=1;  
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
              first1=1;
    codtab=imatrix(1,100,1,10);        for (k2=1; k2<=(nlstate);k2++){
    h=0;          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
    m=pow(2,cptcoveff);            if(l2==k2) continue;
              j=(k2-1)*(nlstate+ndeath)+l2;
    for(k=1;k<=cptcoveff; k++){            for (k1=1; k1<=(nlstate);k1++){
      for(i=1; i <=(m/pow(2,k));i++){              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
        for(j=1; j <= ncodemax[k]; j++){                if(l1==k1) continue;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){                i=(k1-1)*(nlstate+ndeath)+l1;
            h++;                if(i<=j) continue;
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;                for (age=bage; age<=fage; age ++){ 
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/                  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;
      }                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
    }                    mu1=mu[i][(int) age]/stepm*YEARM ;
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);                    mu2=mu[j][(int) age]/stepm*YEARM;
       codtab[1][2]=1;codtab[2][2]=2; */                    c12=cv12/sqrt(v1*v2);
    /* for(i=1; i <=m ;i++){                    /* Computing eigen value of matrix of covariance */
       for(k=1; k <=cptcovn; k++){                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       }                    /* Eigen vectors */
       printf("\n");                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
       }                    /*v21=sqrt(1.-v11*v11); *//* error */
       scanf("%d",i);*/                    v21=(lc1-v1)/cv12*v11;
                        v12=-v21;
    /* Calculates basic frequencies. Computes observed prevalence at single age                    v22=v11;
        and prints on file fileres'p'. */                    tnalp=v21/v11;
                     if(first1==1){
                          first1=0;
                          printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    }
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    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);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    /*printf(fignu*/
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                          if(first==1){
     /* For Powell, parameters are in a vector p[] starting at p[1]                      first=0;
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */                      fprintf(ficgp,"\nset parametric;unset label");
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */                      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);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     if(mle==1){                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
     }  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                                  subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
     /*--------- results files --------------*/                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     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(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);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
    jk=1;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");                      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",\
    for(i=1,jk=1; i <=nlstate; i++){                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
      for(k=1; k <=(nlstate+ndeath); k++){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
        if (k != i)                    }else{
          {                      first=0;
            printf("%d%d ",i,k);                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
            fprintf(ficres,"%1d%1d ",i,k);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
            for(j=1; j <=ncovmodel; j++){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
              printf("%f ",p[jk]);                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
              fprintf(ficres,"%f ",p[jk]);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
              jk++;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
            }                    }/* if first */
            printf("\n");                  } /* age mod 5 */
            fprintf(ficres,"\n");                } /* end loop age */
          }                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
      }                first=1;
    }              } /*l12 */
  if(mle==1){            } /* k12 */
     /* Computing hessian and covariance matrix */          } /*l1 */
     ftolhess=ftol; /* Usually correct */        }/* k1 */
     hesscov(matcov, p, npar, delti, ftolhess, func);      } /* loop covariates */
  }    }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     printf("# Scales (for hessian or gradient estimation)\n");    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
      for(i=1,jk=1; i <=nlstate; i++){    free_vector(xp,1,npar);
       for(j=1; j <=nlstate+ndeath; j++){    fclose(ficresprob);
         if (j!=i) {    fclose(ficresprobcov);
           fprintf(ficres,"%1d%1d",i,j);    fclose(ficresprobcor);
           printf("%1d%1d",i,j);    fflush(ficgp);
           for(k=1; k<=ncovmodel;k++){    fflush(fichtmcov);
             printf(" %.5e",delti[jk]);  }
             fprintf(ficres," %.5e",delti[jk]);  
             jk++;  
           }  /******************* Printing html file ***********/
           printf("\n");  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
           fprintf(ficres,"\n");                    int lastpass, int stepm, int weightopt, char model[],\
         }                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
       }                    int popforecast, int estepm ,\
      }                    double jprev1, double mprev1,double anprev1, \
                        double jprev2, double mprev2,double anprev2){
     k=1;    int jj1, k1, i1, cpt;
     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");  
     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(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
     for(i=1;i<=npar;i++){   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
       /*  if (k>nlstate) k=1;             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
       i1=(i-1)/(ncovmodel*nlstate)+1;     fprintf(fichtm,"\
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
       printf("%s%d%d",alph[k],i1,tab[i]);*/             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
       fprintf(ficres,"%3d",i);     fprintf(fichtm,"\
       printf("%3d",i);   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
       for(j=1; j<=i;j++){             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
         fprintf(ficres," %.5e",matcov[i][j]);     fprintf(fichtm,"\
         printf(" %.5e",matcov[i][j]);   - Life expectancies by age and initial health status (estepm=%2d months): \
       }     <a href=\"%s\">%s</a> <br>\n</li>",
       fprintf(ficres,"\n");             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
       printf("\n");  
       k++;  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     }  
       m=cptcoveff;
     while((c=getc(ficpar))=='#' && c!= EOF){   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       ungetc(c,ficpar);  
       fgets(line, MAXLINE, ficpar);   jj1=0;
       puts(line);   for(k1=1; k1<=m;k1++){
       fputs(line,ficparo);     for(i1=1; i1<=ncodemax[k1];i1++){
     }       jj1++;
     ungetc(c,ficpar);       if (cptcovn > 0) {
     estepm=0;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);         for (cpt=1; cpt<=cptcoveff;cpt++) 
     if (estepm==0 || estepm < stepm) estepm=stepm;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     if (fage <= 2) {         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       bage = ageminpar;       }
       fage = agemaxpar;       /* Pij */
     }       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);     
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");       /* Quasi-incidences */
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);   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); 
     while((c=getc(ficpar))=='#' && c!= EOF){         /* Stable prevalence in each health state */
     ungetc(c,ficpar);         for(cpt=1; cpt<nlstate;cpt++){
     fgets(line, MAXLINE, ficpar);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
     puts(line);  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
     fputs(line,ficparo);         }
   }       for(cpt=1; cpt<=nlstate;cpt++) {
   ungetc(c,ficpar);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
    <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);       }
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);     } /* end i1 */
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);   }/* End k1 */
         fprintf(fichtm,"</ul>");
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);   fprintf(fichtm,"\
     puts(line);  \n<br><li><h4> Result files (second order: variances)</h4>\n\
     fputs(line,ficparo);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   }  
   ungetc(c,ficpar);   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
             subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    dateprev1=anprev1+mprev1/12.+jprev1/365.;   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
    dateprev2=anprev2+mprev2/12.+jprev2/365.;           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);   fprintf(fichtm,"\
   fprintf(ficparo,"pop_based=%d\n",popbased);     - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   fprintf(ficres,"pop_based=%d\n",popbased);             subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
     fprintf(fichtm,"\
   while((c=getc(ficpar))=='#' && c!= EOF){   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
     ungetc(c,ficpar);           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
     fgets(line, MAXLINE, ficpar);   fprintf(fichtm,"\
     puts(line);   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
     fputs(line,ficparo);           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
   }   fprintf(fichtm,"\
   ungetc(c,ficpar);   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);  
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  /*  if(popforecast==1) fprintf(fichtm,"\n */
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
 while((c=getc(ficpar))=='#' && c!= EOF){  /*  else  */
     ungetc(c,ficpar);  /*    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); */
     fgets(line, MAXLINE, ficpar);   fflush(fichtm);
     puts(line);   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
     fputs(line,ficparo);  
   }   m=cptcoveff;
   ungetc(c,ficpar);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);   jj1=0;
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);   for(k1=1; k1<=m;k1++){
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);     for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
 /*------------ gnuplot -------------*/         for (cpt=1; cpt<=cptcoveff;cpt++) 
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
 /*------------ free_vector  -------------*/       }
  chdir(path);       for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
  free_ivector(wav,1,imx);  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);         }
  free_ivector(num,1,n);       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
  free_vector(agedc,1,n);  health expectancies in states (1) and (2): %s%d.png<br>\
  /*free_matrix(covar,1,NCOVMAX,1,n);*/  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
  fclose(ficparo);     } /* end i1 */
  fclose(ficres);   }/* End k1 */
    fprintf(fichtm,"</ul>");
 /*--------- index.htm --------*/   fflush(fichtm);
   }
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);  
   /******************* Gnuplot file **************/
    void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   /*--------------- Prevalence limit --------------*/  
      char dirfileres[132],optfileres[132];
   strcpy(filerespl,"pl");    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   strcat(filerespl,fileres);    int ng;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  /*     printf("Problem with file %s",optionfilegnuplot); */
   }  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  /*   } */
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");    /*#ifdef windows */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    fprintf(ficgp,"cd \"%s\" \n",pathc);
   fprintf(ficrespl,"\n");      /*#endif */
      m=pow(2,cptcoveff);
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    strcpy(dirfileres,optionfilefiname);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    strcpy(optfileres,"vpl");
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   /* 1eme*/
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    for (cpt=1; cpt<= nlstate ; cpt ++) {
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */     for (k1=1; k1<= m ; k1 ++) {
   k=0;       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
   agebase=ageminpar;       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
   agelim=agemaxpar;       fprintf(ficgp,"set xlabel \"Age\" \n\
   ftolpl=1.e-10;  set ylabel \"Probability\" \n\
   i1=cptcoveff;  set ter png small\n\
   if (cptcovn < 1){i1=1;}  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(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       for (i=1; i<= nlstate ; i ++) {
         k=k+1;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/         else fprintf(ficgp," \%%*lf (\%%*lf)");
         fprintf(ficrespl,"\n#******");       }
         for(j=1;j<=cptcoveff;j++)       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);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       for (i=1; i<= nlstate ; i ++) {
         fprintf(ficrespl,"******\n");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
                 else fprintf(ficgp," \%%*lf (\%%*lf)");
         for (age=agebase; age<=agelim; age++){       } 
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
           fprintf(ficrespl,"%.0f",age );       for (i=1; i<= nlstate ; i ++) {
           for(i=1; i<=nlstate;i++)         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           fprintf(ficrespl," %.5f", prlim[i][i]);         else fprintf(ficgp," \%%*lf (\%%*lf)");
           fprintf(ficrespl,"\n");       }  
         }       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
       }     }
     }    }
   fclose(ficrespl);    /*2 eme*/
     
   /*------------- h Pij x at various ages ------------*/    for (k1=1; k1<= m ; k1 ++) { 
        fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      for (i=1; i<= nlstate+1 ; i ++) {
   }        k=2*i;
   printf("Computing pij: result on file '%s' \n", filerespij);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
          for (j=1; j<= nlstate+1 ; j ++) {
   stepsize=(int) (stepm+YEARM-1)/YEARM;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   /*if (stepm<=24) stepsize=2;*/          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
   agelim=AGESUP;        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   hstepm=stepsize*YEARM; /* Every year of age */        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */        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 ++) {
   k=0;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   for(cptcov=1;cptcov<=i1;cptcov++){          else fprintf(ficgp," \%%*lf (\%%*lf)");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        }   
       k=k+1;        fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficrespij,"\n#****** ");        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for(j=1;j<=cptcoveff;j++)        for (j=1; j<= nlstate+1 ; j ++) {
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         fprintf(ficrespij,"******\n");          else fprintf(ficgp," \%%*lf (\%%*lf)");
                }   
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        else fprintf(ficgp,"\" t\"\" w l 0,");
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
           oldm=oldms;savm=savms;    
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      /*3eme*/
           fprintf(ficrespij,"# Age");    
           for(i=1; i<=nlstate;i++)    for (k1=1; k1<= m ; k1 ++) { 
             for(j=1; j<=nlstate+ndeath;j++)      for (cpt=1; cpt<= nlstate ; cpt ++) {
               fprintf(ficrespij," %1d-%1d",i,j);        k=2+nlstate*(2*cpt-2);
           fprintf(ficrespij,"\n");        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
            for (h=0; h<=nhstepm; h++){        fprintf(ficgp,"set ter png small\n\
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  set size 0.65,0.65\n\
             for(i=1; i<=nlstate;i++)  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
               for(j=1; j<=nlstate+ndeath;j++)        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
             fprintf(ficrespij,"\n");          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
              }          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficrespij,"\n");          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
         }          
     }        */
   }        for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);          
         } 
   fclose(ficrespij);      }
     }
     
   /*---------- Forecasting ------------------*/    /* CV preval stable (period) */
   if((stepm == 1) && (strcmp(model,".")==0)){    for (k1=1; k1<= m ; k1 ++) { 
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);      for (cpt=1; cpt<=nlstate ; cpt ++) {
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);        k=3;
   }        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
   else{        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
     erreur=108;  set ter png small\nset size 0.65,0.65\n\
     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);  unset log y\n\
   }  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
          
         for (i=1; i< nlstate ; i ++)
   /*---------- Health expectancies and variances ------------*/          fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   strcpy(filerest,"t");        
   strcat(filerest,fileres);        l=3+(nlstate+ndeath)*cpt;
   if((ficrest=fopen(filerest,"w"))==NULL) {        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;        for (i=1; i< nlstate ; i ++) {
   }          l=3+(nlstate+ndeath)*cpt;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
   strcpy(filerese,"e");      } 
   strcat(filerese,fileres);    }  
   if((ficreseij=fopen(filerese,"w"))==NULL) {    
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    /* proba elementaires */
   }    for(i=1,jk=1; i <=nlstate; i++){
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
  strcpy(fileresv,"v");          for(j=1; j <=ncovmodel; j++){
   strcat(fileresv,fileres);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {            jk++; 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);            fprintf(ficgp,"\n");
   }          }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        }
   calagedate=-1;      }
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);     }
   
   k=0;     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   for(cptcov=1;cptcov<=i1;cptcov++){       for(jk=1; jk <=m; jk++) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
       k=k+1;         if (ng==2)
       fprintf(ficrest,"\n#****** ");           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
       for(j=1;j<=cptcoveff;j++)         else
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);           fprintf(ficgp,"\nset title \"Probability\"\n");
       fprintf(ficrest,"******\n");         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
       fprintf(ficreseij,"\n#****** ");         for(k2=1; k2<=nlstate; k2++) {
       for(j=1;j<=cptcoveff;j++)           k3=i;
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);           for(k=1; k<=(nlstate+ndeath); k++) {
       fprintf(ficreseij,"******\n");             if (k != k2){
                if(ng==2)
       fprintf(ficresvij,"\n#****** ");                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
       for(j=1;j<=cptcoveff;j++)               else
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
       fprintf(ficresvij,"******\n");               ij=1;
                for(j=3; j <=ncovmodel; j++) {
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
       oldm=oldms;savm=savms;                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);                     ij++;
                   }
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                 else
       oldm=oldms;savm=savms;                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);               }
                   fprintf(ficgp,")/(1");
                
                 for(k1=1; k1 <=nlstate; k1++){   
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                 ij=1;
       fprintf(ficrest,"\n");                 for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
       epj=vector(1,nlstate+1);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       for(age=bage; age <=fage ;age++){                     ij++;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                   }
         if (popbased==1) {                   else
           for(i=1; i<=nlstate;i++)                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
             prlim[i][i]=probs[(int)age][i][k];                 }
         }                 fprintf(ficgp,")");
                       }
         fprintf(ficrest," %4.0f",age);               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
           for(i=1, epj[j]=0.;i <=nlstate;i++) {               i=i+ncovmodel;
             epj[j] += prlim[i][i]*eij[i][j][(int)age];             }
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/           } /* end k */
           }         } /* end k2 */
           epj[nlstate+1] +=epj[j];       } /* end jk */
         }     } /* end ng */
      fflush(ficgp); 
         for(i=1, vepp=0.;i <=nlstate;i++)  }  /* end gnuplot */
           for(j=1;j <=nlstate;j++)  
             vepp += vareij[i][j][(int)age];  
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));  /*************** Moving average **************/
         for(j=1;j <=nlstate;j++){  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));  
         }    int i, cpt, cptcod;
         fprintf(ficrest,"\n");    int modcovmax =1;
       }    int mobilavrange, mob;
     }    double age;
   }  
 free_matrix(mint,1,maxwav,1,n);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);                             a covariate has 2 modalities */
     free_vector(weight,1,n);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   fclose(ficreseij);  
   fclose(ficresvij);    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
   fclose(ficrest);      if(mobilav==1) mobilavrange=5; /* default */
   fclose(ficpar);      else mobilavrange=mobilav;
   free_vector(epj,1,nlstate+1);      for (age=bage; age<=fage; age++)
          for (i=1; i<=nlstate;i++)
   /*------- Variance limit prevalence------*/            for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   strcpy(fileresvpl,"vpl");      /* We keep the original values on the extreme ages bage, fage and for 
   strcat(fileresvpl,fileres);         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {         we use a 5 terms etc. until the borders are no more concerned. 
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      */ 
     exit(0);      for (mob=3;mob <=mobilavrange;mob=mob+2){
   }        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
   k=0;              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   for(cptcov=1;cptcov<=i1;cptcov++){                for (cpt=1;cpt<=(mob-1)/2;cpt++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
       k=k+1;                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
       fprintf(ficresvpl,"\n#****** ");                }
       for(j=1;j<=cptcoveff;j++)              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            }
       fprintf(ficresvpl,"******\n");          }
              }/* end age */
       varpl=matrix(1,nlstate,(int) bage, (int) fage);      }/* end mob */
       oldm=oldms;savm=savms;    }else return -1;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    return 0;
     }  }/* End movingaverage */
  }  
   
   fclose(ficresvpl);  /************** 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){
   /*---------- End : free ----------------*/    /* proj1, year, month, day of starting projection 
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);       agemin, agemax range of age
         dateprev1 dateprev2 range of dates during which prevalence is computed
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);       anproj2 year of en of projection (same day and month as proj1).
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    */
      int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
      int *popage;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    double agec; /* generic age */
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    double *popeffectif,*popcount;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    double ***p3mat;
      double ***mobaverage;
   free_matrix(matcov,1,npar,1,npar);    char fileresf[FILENAMELENGTH];
   free_vector(delti,1,npar);  
   free_matrix(agev,1,maxwav,1,imx);    agelim=AGESUP;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
   if(erreur >0)    strcpy(fileresf,"f"); 
     printf("End of Imach with error or warning %d\n",erreur);    strcat(fileresf,fileres);
   else   printf("End of Imach\n");    if((ficresf=fopen(fileresf,"w"))==NULL) {
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      printf("Problem with forecast resultfile: %s\n", fileresf);
        fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/    }
   /*printf("Total time was %d uSec.\n", total_usecs);*/    printf("Computing forecasting: result on file '%s' \n", fileresf);
   /*------ End -----------*/    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
  end:  
 #ifdef windows    if (mobilav!=0) {
   /* chdir(pathcd);*/      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 #endif      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
  /*system("wgnuplot graph.plt");*/        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
  /*system("../gp37mgw/wgnuplot graph.plt");*/        printf(" Error in movingaverage mobilav=%d\n",mobilav);
  /*system("cd ../gp37mgw");*/      }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    }
  strcpy(plotcmd,GNUPLOTPROGRAM);  
  strcat(plotcmd," ");    stepsize=(int) (stepm+YEARM-1)/YEARM;
  strcat(plotcmd,optionfilegnuplot);    if (stepm<=12) stepsize=1;
  system(plotcmd);    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
 #ifdef windows    }
   while (z[0] != 'q') {    else  hstepm=estepm;   
     /* chdir(path); */  
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    hstepm=hstepm/stepm; 
     scanf("%s",z);    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
     if (z[0] == 'c') system("./imach");                                 fractional in yp1 */
     else if (z[0] == 'e') system(optionfilehtm);    anprojmean=yp;
     else if (z[0] == 'g') system(plotcmd);    yp2=modf((yp1*12),&yp);
     else if (z[0] == 'q') exit(0);    mprojmean=yp;
   }    yp1=modf((yp2*30.5),&yp);
 #endif    jprojmean=yp;
 }    if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i]==1 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i]==0 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         if (wav[i]>1 & agecens[i]>15) {
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov){
     int i;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
         for(j=0; line[j] != '\n';j++){  /* Untabifies line */
           if(line[j] == '\t')
             line[j] = ' ';
         }
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (j=1; j<=lastpass; j++)
           if (s[j][i]>nlstate) {
             dcwave[i]=j;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];agecens[i]=1.; 
           if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
           cens[i]=1;
           
           if (ageexmed[i]<1) cens[i]=-1;
           if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
   
       p[1]=0.1; p[2]=0.1;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow-mort"); 
     strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
     /*  for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     */
     fprintf(ficrespow,"\n");
   
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM,delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov);
     } /* Endof if mle==-3 */
   
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficrespl,"#Stable prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
   
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /*---------- Health expectancies and variances ------------*/
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total LEs with variances: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficreseij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
           }
   
    
           fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficreseij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of stable prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocaltime at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
     strcpy(plotcmd,"\"");
     strcat(plotcmd,pathimach);
     strcat(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd,"\"");
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     if((outcmd=system(plotcmd)) != 0){
       printf(" Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.44  
changed lines
  Added in v.1.104


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