Diff for /imach/src/imach.c between versions 1.32 and 1.107

version 1.32, 2002/03/11 14:17:15 version 1.107, 2006/01/19 16:20:37
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.107  2006/01/19 16:20:37  brouard
      Test existence of gnuplot in imach path
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.106  2006/01/19 13:24:36  brouard
   first survey ("cross") where individuals from different ages are    Some cleaning and links added in html output
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.105  2006/01/05 20:23:19  lievre
   second wave of interviews ("longitudinal") which measure each change    *** empty log message ***
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.104  2005/09/30 16:11:43  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    (Module): If the status is missing at the last wave but we know
   simplest model is the multinomial logistic model where pij is the    that the person is alive, then we can code his/her status as -2
   probabibility to be observed in state j at the second wave    (instead of missing=-1 in earlier versions) and his/her
   conditional to be observed in state i at the first wave. Therefore    contributions to the likelihood is 1 - Prob of dying from last
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   'age' is age and 'sex' is a covariate. If you want to have a more    the healthy state at last known wave). Version is 0.98
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.103  2005/09/30 15:54:49  lievre
   you to do it.  More covariates you add, slower the    (Module): sump fixed, loop imx fixed, and simplifications.
   convergence.  
     Revision 1.102  2004/09/15 17:31:30  brouard
   The advantage of this computer programme, compared to a simple    Add the possibility to read data file including tab characters.
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.101  2004/09/15 10:38:38  brouard
   intermediate interview, the information is lost, but taken into    Fix on curr_time
   account using an interpolation or extrapolation.    
     Revision 1.100  2004/07/12 18:29:06  brouard
   hPijx is the probability to be observed in state i at age x+h    Add version for Mac OS X. Just define UNIX in Makefile
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Revision 1.99  2004/06/05 08:57:40  brouard
   states. This elementary transition (by month or quarter trimester,    *** empty log message ***
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.98  2004/05/16 15:05:56  brouard
   and the contribution of each individual to the likelihood is simply    New version 0.97 . First attempt to estimate force of mortality
   hPijx.    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 .
   Also this programme outputs the covariance matrix of the parameters but also    This is the basic analysis of mortality and should be done before any
   of the life expectancies. It also computes the prevalence limits.    other analysis, in order to test if the mortality estimated from the
      cross-longitudinal survey is different from the mortality estimated
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    from other sources like vital statistic data.
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    The same imach parameter file can be used but the option for mle should be -3.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Agnès, who wrote this part of the code, tried to keep most of the
   software can be distributed freely for non commercial use. Latest version    former routines in order to include the new code within the former code.
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    The output is very simple: only an estimate of the intercept and of
      the slope with 95% confident intervals.
 #include <math.h>  
 #include <stdio.h>    Current limitations:
 #include <stdlib.h>    A) Even if you enter covariates, i.e. with the
 #include <unistd.h>    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
     B) There is no computation of Life Expectancy nor Life Table.
 #define MAXLINE 256  
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    Revision 1.97  2004/02/20 13:25:42  lievre
 #define FILENAMELENGTH 80    Version 0.96d. Population forecasting command line is (temporarily)
 /*#define DEBUG*/    suppressed.
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.96  2003/07/15 15:38:55  brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     rewritten within the same printf. Workaround: many printfs.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.95  2003/07/08 07:54:34  brouard
     * imach.c (Repository):
 #define NINTERVMAX 8    (Repository): Using imachwizard code to output a more meaningful covariance
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    matrix (cov(a12,c31) instead of numbers.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.94  2003/06/27 13:00:02  brouard
 #define MAXN 20000    Just cleaning
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.93  2003/06/25 16:33:55  brouard
 #define AGEBASE 40    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
     (Module): Version 0.96b
 int erreur; /* Error number */  
 int nvar;    Revision 1.92  2003/06/25 16:30:45  brouard
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    (Module): On windows (cygwin) function asctime_r doesn't
 int npar=NPARMAX;    exist so I changed back to asctime which exists.
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.91  2003/06/25 15:30:29  brouard
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    * imach.c (Repository): Duplicated warning errors corrected.
 int popbased=0;    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
 int *wav; /* Number of waves for this individuual 0 is possible */    is stamped in powell.  We created a new html file for the graphs
 int maxwav; /* Maxim number of waves */    concerning matrix of covariance. It has extension -cov.htm.
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.90  2003/06/24 12:34:15  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Module): Some bugs corrected for windows. Also, when
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    mle=-1 a template is output in file "or"mypar.txt with the design
 double jmean; /* Mean space between 2 waves */    of the covariance matrix to be input.
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.89  2003/06/24 12:30:52  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    (Module): Some bugs corrected for windows. Also, when
 FILE *ficgp,*ficresprob,*ficpop;    mle=-1 a template is output in file "or"mypar.txt with the design
 FILE *ficreseij;    of the covariance matrix to be input.
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.88  2003/06/23 17:54:56  brouard
   char fileresv[FILENAMELENGTH];    * 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.
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.86  2003/06/17 20:04:08  brouard
 #define FTOL 1.0e-10    (Module): Change position of html and gnuplot routines and added
     routine fileappend.
 #define NRANSI  
 #define ITMAX 200    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
 #define TOL 2.0e-4    current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
 #define CGOLD 0.3819660    was wrong (infinity). We still send an "Error" but patch by
 #define ZEPS 1.0e-10    assuming that the date of death was just one stepm after the
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    interview.
     (Repository): Because some people have very long ID (first column)
 #define GOLD 1.618034    we changed int to long in num[] and we added a new lvector for
 #define GLIMIT 100.0    memory allocation. But we also truncated to 8 characters (left
 #define TINY 1.0e-20    truncation)
     (Repository): No more line truncation errors.
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.84  2003/06/13 21:44:43  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    * imach.c (Repository): Replace "freqsummary" at a correct
      place. It differs from routine "prevalence" which may be called
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    many times. Probs is memory consuming and must be used with
 #define rint(a) floor(a+0.5)    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.83  2003/06/10 13:39:11  lievre
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    *** empty log message ***
   
 int imx;    Revision 1.82  2003/06/05 15:57:20  brouard
 int stepm;    Add log in  imach.c and  fullversion number is now printed.
 /* Stepm, step in month: minimum step interpolation*/  
   */
 int m,nb;  /*
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;     Interpolated Markov Chain
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Short summary of the programme:
 double dateintmean=0;    
     This program computes Healthy Life Expectancies from
 double *weight;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 int **s; /* Status */    first survey ("cross") where individuals from different ages are
 double *agedc, **covar, idx;    interviewed on their health status or degree of disability (in the
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    case of a health survey which is our main interest) -2- at least a
     second wave of interviews ("longitudinal") which measure each change
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    (if any) in individual health status.  Health expectancies are
 double ftolhess; /* Tolerance for computing hessian */    computed from the time spent in each health state according to a
     model. More health states you consider, more time is necessary to reach the
 /**************** split *************************/    Maximum Likelihood of the parameters involved in the model.  The
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    simplest model is the multinomial logistic model where pij is the
 {    probability to be observed in state j at the second wave
    char *s;                             /* pointer */    conditional to be observed in state i at the first wave. Therefore
    int  l1, l2;                         /* length counters */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     'age' is age and 'sex' is a covariate. If you want to have a more
    l1 = strlen( path );                 /* length of path */    complex model than "constant and age", you should modify the program
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    where the markup *Covariates have to be included here again* invites
 #ifdef windows    you to do it.  More covariates you add, slower the
    s = strrchr( path, '\\' );           /* find last / */    convergence.
 #else  
    s = strrchr( path, '/' );            /* find last / */    The advantage of this computer programme, compared to a simple
 #endif    multinomial logistic model, is clear when the delay between waves is not
    if ( s == NULL ) {                   /* no directory, so use current */    identical for each individual. Also, if a individual missed an
 #if     defined(__bsd__)                /* get current working directory */    intermediate interview, the information is lost, but taken into
       extern char       *getwd( );    account using an interpolation or extrapolation.  
   
       if ( getwd( dirc ) == NULL ) {    hPijx is the probability to be observed in state i at age x+h
 #else    conditional to the observed state i at age x. The delay 'h' can be
       extern char       *getcwd( );    split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    semester or year) is modelled as a multinomial logistic.  The hPx
 #endif    matrix is simply the matrix product of nh*stepm elementary matrices
          return( GLOCK_ERROR_GETCWD );    and the contribution of each individual to the likelihood is simply
       }    hPijx.
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Also this programme outputs the covariance matrix of the parameters but also
       s++;                              /* after this, the filename */    of the life expectancies. It also computes the stable prevalence. 
       l2 = strlen( s );                 /* length of filename */    
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
       strcpy( name, s );                /* save file name */             Institut national d'études démographiques, Paris.
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    This software have been partly granted by Euro-REVES, a concerted action
       dirc[l1-l2] = 0;                  /* add zero */    from the European Union.
    }    It is copyrighted identically to a GNU software product, ie programme and
    l1 = strlen( dirc );                 /* length of directory */    software can be distributed freely for non commercial use. Latest version
 #ifdef windows    can be accessed at http://euroreves.ined.fr/imach .
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #endif    
    s = strrchr( name, '.' );            /* find last / */    **********************************************************************/
    s++;  /*
    strcpy(ext,s);                       /* save extension */    main
    l1= strlen( name);    read parameterfile
    l2= strlen( s)+1;    read datafile
    strncpy( finame, name, l1-l2);    concatwav
    finame[l1-l2]= 0;    freqsummary
    return( 0 );                         /* we're done */    if (mle >= 1)
 }      mlikeli
     print results files
     if mle==1 
 /******************************************/       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 void replace(char *s, char*t)        begin-prev-date,...
 {    open gnuplot file
   int i;    open html file
   int lg=20;    stable prevalence
   i=0;     for age prevalim()
   lg=strlen(t);    h Pij x
   for(i=0; i<= lg; i++) {    variance of p varprob
     (s[i] = t[i]);    forecasting if prevfcast==1 prevforecast call prevalence()
     if (t[i]== '\\') s[i]='/';    health expectancies
   }    Variance-covariance of DFLE
 }    prevalence()
      movingaverage()
 int nbocc(char *s, char occ)    varevsij() 
 {    if popbased==1 varevsij(,popbased)
   int i,j=0;    total life expectancies
   int lg=20;    Variance of stable prevalence
   i=0;   end
   lg=strlen(s);  */
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;  
   }  
   return j;   
 }  #include <math.h>
   #include <stdio.h>
 void cutv(char *u,char *v, char*t, char occ)  #include <stdlib.h>
 {  #include <string.h>
   int i,lg,j,p=0;  #include <unistd.h>
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {  #include <sys/types.h>
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  #include <sys/stat.h>
   }  #include <errno.h>
   extern int errno;
   lg=strlen(t);  
   for(j=0; j<p; j++) {  /* #include <sys/time.h> */
     (u[j] = t[j]);  #include <time.h>
   }  #include "timeval.h"
      u[p]='\0';  
   /* #include <libintl.h> */
    for(j=0; j<= lg; j++) {  /* #define _(String) gettext (String) */
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }  #define MAXLINE 256
 }  #define GNUPLOTPROGRAM "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 /********************** nrerror ********************/  #define FILENAMELENGTH 132
   /*#define DEBUG*/
 void nrerror(char error_text[])  /*#define windows*/
 {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   fprintf(stderr,"ERREUR ...\n");  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 }  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 /*********************** vector *******************/  
 double *vector(int nl, int nh)  #define NINTERVMAX 8
 {  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   double *v;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #define NCOVMAX 8 /* Maximum number of covariates */
   if (!v) nrerror("allocation failure in vector");  #define MAXN 20000
   return v-nl+NR_END;  #define YEARM 12. /* Number of months per year */
 }  #define AGESUP 130
   #define AGEBASE 40
 /************************ free vector ******************/  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
 void free_vector(double*v, int nl, int nh)  #ifdef UNIX
 {  #define DIRSEPARATOR '/'
   free((FREE_ARG)(v+nl-NR_END));  #define CHARSEPARATOR "/"
 }  #define ODIRSEPARATOR '\\'
   #else
 /************************ivector *******************************/  #define DIRSEPARATOR '\\'
 int *ivector(long nl,long nh)  #define CHARSEPARATOR "\\"
 {  #define ODIRSEPARATOR '/'
   int *v;  #endif
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");  /* $Id$ */
   return v-nl+NR_END;  /* $State$ */
 }  
   char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";
 /******************free ivector **************************/  char fullversion[]="$Revision$ $Date$"; 
 void free_ivector(int *v, long nl, long nh)  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 {  int nvar;
   free((FREE_ARG)(v+nl-NR_END));  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 }  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
 /******************* imatrix *******************************/  int ndeath=1; /* Number of dead states */
 int **imatrix(long nrl, long nrh, long ncl, long nch)  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  int popbased=0;
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  int *wav; /* Number of waves for this individuual 0 is possible */
   int **m;  int maxwav; /* Maxim number of waves */
    int jmin, jmax; /* min, max spacing between 2 waves */
   /* allocate pointers to rows */  int gipmx, gsw; /* Global variables on the number of contributions 
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));                     to the likelihood and the sum of weights (done by funcone)*/
   if (!m) nrerror("allocation failure 1 in matrix()");  int mle, weightopt;
   m += NR_END;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   m -= nrl;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
    int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
               * wave mi and wave mi+1 is not an exact multiple of stepm. */
   /* allocate rows and set pointers to them */  double jmean; /* Mean space between 2 waves */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  double **oldm, **newm, **savm; /* Working pointers to matrices */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   m[nrl] += NR_END;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   m[nrl] -= ncl;  FILE *ficlog, *ficrespow;
    int globpr; /* Global variable for printing or not */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  double fretone; /* Only one call to likelihood */
    long ipmx; /* Number of contributions */
   /* return pointer to array of pointers to rows */  double sw; /* Sum of weights */
   return m;  char filerespow[FILENAMELENGTH];
 }  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   FILE *ficresilk;
 /****************** free_imatrix *************************/  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 void free_imatrix(m,nrl,nrh,ncl,nch)  FILE *ficresprobmorprev;
       int **m;  FILE *fichtm, *fichtmcov; /* Html File */
       long nch,ncl,nrh,nrl;  FILE *ficreseij;
      /* free an int matrix allocated by imatrix() */  char filerese[FILENAMELENGTH];
 {  FILE  *ficresvij;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  char fileresv[FILENAMELENGTH];
   free((FREE_ARG) (m+nrl-NR_END));  FILE  *ficresvpl;
 }  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
 /******************* matrix *******************************/  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 double **matrix(long nrl, long nrh, long ncl, long nch)  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 {  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  char command[FILENAMELENGTH];
   double **m;  int  outcmd=0;
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  char filelog[FILENAMELENGTH]; /* Log file */
   m -= nrl;  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  char popfile[FILENAMELENGTH];
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   m[nrl] -= ncl;  
   struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  struct timezone tzp;
   return m;  extern int gettimeofday();
 }  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   long time_value;
 /*************************free matrix ************************/  extern long time();
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  char strcurr[80], strfor[80];
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define NR_END 1
   free((FREE_ARG)(m+nrl-NR_END));  #define FREE_ARG char*
 }  #define FTOL 1.0e-10
   
 /******************* ma3x *******************************/  #define NRANSI 
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  #define ITMAX 200 
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  #define TOL 2.0e-4 
   double ***m;  
   #define CGOLD 0.3819660 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define ZEPS 1.0e-10 
   if (!m) nrerror("allocation failure 1 in matrix()");  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   m += NR_END;  
   m -= nrl;  #define GOLD 1.618034 
   #define GLIMIT 100.0 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define TINY 1.0e-20 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  static double maxarg1,maxarg2;
   m[nrl] -= ncl;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #define rint(a) floor(a+0.5)
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  static double sqrarg;
   m[nrl][ncl] -= nll;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   for (j=ncl+1; j<=nch; j++)  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
     m[nrl][j]=m[nrl][j-1]+nlay;  int agegomp= AGEGOMP;
    
   for (i=nrl+1; i<=nrh; i++) {  int imx; 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  int stepm=1;
     for (j=ncl+1; j<=nch; j++)  /* Stepm, step in month: minimum step interpolation*/
       m[i][j]=m[i][j-1]+nlay;  
   }  int estepm;
   return m;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 }  
   int m,nb;
 /*************************free ma3x ************************/  long *num;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  double **pmmij, ***probs;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  double *ageexmed,*agecens;
   free((FREE_ARG)(m+nrl-NR_END));  double dateintmean=0;
 }  
   double *weight;
 /***************** f1dim *************************/  int **s; /* Status */
 extern int ncom;  double *agedc, **covar, idx;
 extern double *pcom,*xicom;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 extern double (*nrfunc)(double []);  double *lsurv, *lpop, *tpop;
    
 double f1dim(double x)  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 {  double ftolhess; /* Tolerance for computing hessian */
   int j;  
   double f;  /**************** split *************************/
   double *xt;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
    {
   xt=vector(1,ncom);    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   f=(*nrfunc)(xt);    */ 
   free_vector(xt,1,ncom);    char  *ss;                            /* pointer */
   return f;    int   l1, l2;                         /* length counters */
 }  
     l1 = strlen(path );                   /* length of path */
 /*****************brent *************************/    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 {    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   int iter;      strcpy( name, path );               /* we got the fullname name because no directory */
   double a,b,d,etemp;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   double fu,fv,fw,fx;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   double ftemp;      /* get current working directory */
   double p,q,r,tol1,tol2,u,v,w,x,xm;      /*    extern  char* getcwd ( char *buf , int len);*/
   double e=0.0;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
          return( GLOCK_ERROR_GETCWD );
   a=(ax < cx ? ax : cx);      }
   b=(ax > cx ? ax : cx);      /* got dirc from getcwd*/
   x=w=v=bx;      printf(" DIRC = %s \n",dirc);
   fw=fv=fx=(*f)(x);    } else {                              /* strip direcotry from path */
   for (iter=1;iter<=ITMAX;iter++) {      ss++;                               /* after this, the filename */
     xm=0.5*(a+b);      l2 = strlen( ss );                  /* length of filename */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/      strcpy( name, ss );         /* save file name */
     printf(".");fflush(stdout);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 #ifdef DEBUG      dirc[l1-l2] = 0;                    /* add zero */
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);      printf(" DIRC2 = %s \n",dirc);
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    }
 #endif    /* We add a separator at the end of dirc if not exists */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    l1 = strlen( dirc );                  /* length of directory */
       *xmin=x;    if( dirc[l1-1] != DIRSEPARATOR ){
       return fx;      dirc[l1] =  DIRSEPARATOR;
     }      dirc[l1+1] = 0; 
     ftemp=fu;      printf(" DIRC3 = %s \n",dirc);
     if (fabs(e) > tol1) {    }
       r=(x-w)*(fx-fv);    ss = strrchr( name, '.' );            /* find last / */
       q=(x-v)*(fx-fw);    if (ss >0){
       p=(x-v)*q-(x-w)*r;      ss++;
       q=2.0*(q-r);      strcpy(ext,ss);                     /* save extension */
       if (q > 0.0) p = -p;      l1= strlen( name);
       q=fabs(q);      l2= strlen(ss)+1;
       etemp=e;      strncpy( finame, name, l1-l2);
       e=d;      finame[l1-l2]= 0;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    }
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  
       else {    return( 0 );                          /* we're done */
         d=p/q;  }
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  /******************************************/
       }  
     } else {  void replace_back_to_slash(char *s, char*t)
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  {
     }    int i;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    int lg=0;
     fu=(*f)(u);    i=0;
     if (fu <= fx) {    lg=strlen(t);
       if (u >= x) a=x; else b=x;    for(i=0; i<= lg; i++) {
       SHFT(v,w,x,u)      (s[i] = t[i]);
         SHFT(fv,fw,fx,fu)      if (t[i]== '\\') s[i]='/';
         } else {    }
           if (u < x) a=u; else b=u;  }
           if (fu <= fw || w == x) {  
             v=w;  int nbocc(char *s, char occ)
             w=u;  {
             fv=fw;    int i,j=0;
             fw=fu;    int lg=20;
           } else if (fu <= fv || v == x || v == w) {    i=0;
             v=u;    lg=strlen(s);
             fv=fu;    for(i=0; i<= lg; i++) {
           }    if  (s[i] == occ ) j++;
         }    }
   }    return j;
   nrerror("Too many iterations in brent");  }
   *xmin=x;  
   return fx;  void cutv(char *u,char *v, char*t, char occ)
 }  {
     /* cuts string t into u and v where u ends before first occurence of char 'occ' 
 /****************** mnbrak ***********************/       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
        gives u="abcedf" and v="ghi2j" */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    int i,lg,j,p=0;
             double (*func)(double))    i=0;
 {    for(j=0; j<=strlen(t)-1; j++) {
   double ulim,u,r,q, dum;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   double fu;    }
    
   *fa=(*func)(*ax);    lg=strlen(t);
   *fb=(*func)(*bx);    for(j=0; j<p; j++) {
   if (*fb > *fa) {      (u[j] = t[j]);
     SHFT(dum,*ax,*bx,dum)    }
       SHFT(dum,*fb,*fa,dum)       u[p]='\0';
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);     for(j=0; j<= lg; j++) {
   *fc=(*func)(*cx);      if (j>=(p+1))(v[j-p-1] = t[j]);
   while (*fb > *fc) {    }
     r=(*bx-*ax)*(*fb-*fc);  }
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  /********************** nrerror ********************/
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  
     ulim=(*bx)+GLIMIT*(*cx-*bx);  void nrerror(char error_text[])
     if ((*bx-u)*(u-*cx) > 0.0) {  {
       fu=(*func)(u);    fprintf(stderr,"ERREUR ...\n");
     } else if ((*cx-u)*(u-ulim) > 0.0) {    fprintf(stderr,"%s\n",error_text);
       fu=(*func)(u);    exit(EXIT_FAILURE);
       if (fu < *fc) {  }
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  /*********************** vector *******************/
           SHFT(*fb,*fc,fu,(*func)(u))  double *vector(int nl, int nh)
           }  {
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    double *v;
       u=ulim;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       fu=(*func)(u);    if (!v) nrerror("allocation failure in vector");
     } else {    return v-nl+NR_END;
       u=(*cx)+GOLD*(*cx-*bx);  }
       fu=(*func)(u);  
     }  /************************ free vector ******************/
     SHFT(*ax,*bx,*cx,u)  void free_vector(double*v, int nl, int nh)
       SHFT(*fa,*fb,*fc,fu)  {
       }    free((FREE_ARG)(v+nl-NR_END));
 }  }
   
 /*************** linmin ************************/  /************************ivector *******************************/
   int *ivector(long nl,long nh)
 int ncom;  {
 double *pcom,*xicom;    int *v;
 double (*nrfunc)(double []);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
      if (!v) nrerror("allocation failure in ivector");
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    return v-nl+NR_END;
 {  }
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);  /******************free ivector **************************/
   double f1dim(double x);  void free_ivector(int *v, long nl, long nh)
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  {
               double *fc, double (*func)(double));    free((FREE_ARG)(v+nl-NR_END));
   int j;  }
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  /************************lvector *******************************/
    long *lvector(long nl,long nh)
   ncom=n;  {
   pcom=vector(1,n);    long *v;
   xicom=vector(1,n);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   nrfunc=func;    if (!v) nrerror("allocation failure in ivector");
   for (j=1;j<=n;j++) {    return v-nl+NR_END;
     pcom[j]=p[j];  }
     xicom[j]=xi[j];  
   }  /******************free lvector **************************/
   ax=0.0;  void free_lvector(long *v, long nl, long nh)
   xx=1.0;  {
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    free((FREE_ARG)(v+nl-NR_END));
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  }
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  /******************* imatrix *******************************/
 #endif  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   for (j=1;j<=n;j++) {       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     xi[j] *= xmin;  { 
     p[j] += xi[j];    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   }    int **m; 
   free_vector(xicom,1,n);    
   free_vector(pcom,1,n);    /* allocate pointers to rows */ 
 }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
 /*************** powell ************************/    m += NR_END; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    m -= nrl; 
             double (*func)(double []))    
 {    
   void linmin(double p[], double xi[], int n, double *fret,    /* allocate rows and set pointers to them */ 
               double (*func)(double []));    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   int i,ibig,j;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   double del,t,*pt,*ptt,*xit;    m[nrl] += NR_END; 
   double fp,fptt;    m[nrl] -= ncl; 
   double *xits;    
   pt=vector(1,n);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   ptt=vector(1,n);    
   xit=vector(1,n);    /* return pointer to array of pointers to rows */ 
   xits=vector(1,n);    return m; 
   *fret=(*func)(p);  } 
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  /****************** free_imatrix *************************/
     fp=(*fret);  void free_imatrix(m,nrl,nrh,ncl,nch)
     ibig=0;        int **m;
     del=0.0;        long nch,ncl,nrh,nrl; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);       /* free an int matrix allocated by imatrix() */ 
     for (i=1;i<=n;i++)  { 
       printf(" %d %.12f",i, p[i]);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     printf("\n");    free((FREE_ARG) (m+nrl-NR_END)); 
     for (i=1;i<=n;i++) {  } 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  /******************* matrix *******************************/
 #ifdef DEBUG  double **matrix(long nrl, long nrh, long ncl, long nch)
       printf("fret=%lf \n",*fret);  {
 #endif    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       printf("%d",i);fflush(stdout);    double **m;
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         del=fabs(fptt-(*fret));    if (!m) nrerror("allocation failure 1 in matrix()");
         ibig=i;    m += NR_END;
       }    m -= nrl;
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       for (j=1;j<=n;j++) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    m[nrl] += NR_END;
         printf(" x(%d)=%.12e",j,xit[j]);    m[nrl] -= ncl;
       }  
       for(j=1;j<=n;j++)    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         printf(" p=%.12e",p[j]);    return m;
       printf("\n");    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
 #endif     */
     }  }
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  
 #ifdef DEBUG  /*************************free matrix ************************/
       int k[2],l;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       k[0]=1;  {
       k[1]=-1;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       printf("Max: %.12e",(*func)(p));    free((FREE_ARG)(m+nrl-NR_END));
       for (j=1;j<=n;j++)  }
         printf(" %.12e",p[j]);  
       printf("\n");  /******************* ma3x *******************************/
       for(l=0;l<=1;l++) {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
         for (j=1;j<=n;j++) {  {
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    double ***m;
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       }    if (!m) nrerror("allocation failure 1 in matrix()");
 #endif    m += NR_END;
     m -= nrl;
   
       free_vector(xit,1,n);    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       free_vector(xits,1,n);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       free_vector(ptt,1,n);    m[nrl] += NR_END;
       free_vector(pt,1,n);    m[nrl] -= ncl;
       return;  
     }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  
     for (j=1;j<=n;j++) {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       ptt[j]=2.0*p[j]-pt[j];    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       xit[j]=p[j]-pt[j];    m[nrl][ncl] += NR_END;
       pt[j]=p[j];    m[nrl][ncl] -= nll;
     }    for (j=ncl+1; j<=nch; j++) 
     fptt=(*func)(ptt);      m[nrl][j]=m[nrl][j-1]+nlay;
     if (fptt < fp) {    
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    for (i=nrl+1; i<=nrh; i++) {
       if (t < 0.0) {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         linmin(p,xit,n,fret,func);      for (j=ncl+1; j<=nch; j++) 
         for (j=1;j<=n;j++) {        m[i][j]=m[i][j-1]+nlay;
           xi[j][ibig]=xi[j][n];    }
           xi[j][n]=xit[j];    return m; 
         }    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 #ifdef DEBUG             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    */
         for(j=1;j<=n;j++)  }
           printf(" %.12e",xit[j]);  
         printf("\n");  /*************************free ma3x ************************/
 #endif  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       }  {
     }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 }    free((FREE_ARG)(m+nrl-NR_END));
   }
 /**** Prevalence limit ****************/  
   /*************** function subdirf ***********/
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  char *subdirf(char fileres[])
 {  {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    /* Caution optionfilefiname is hidden */
      matrix by transitions matrix until convergence is reached */    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
   int i, ii,j,k;    strcat(tmpout,fileres);
   double min, max, maxmin, maxmax,sumnew=0.;    return tmpout;
   double **matprod2();  }
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;  /*************** function subdirf2 ***********/
   double agefin, delaymax=50 ; /* Max number of years to converge */  char *subdirf2(char fileres[], char *preop)
   {
   for (ii=1;ii<=nlstate+ndeath;ii++)    
     for (j=1;j<=nlstate+ndeath;j++){    /* Caution optionfilefiname is hidden */
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    strcpy(tmpout,optionfilefiname);
     }    strcat(tmpout,"/");
     strcat(tmpout,preop);
    cov[1]=1.;    strcat(tmpout,fileres);
      return tmpout;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  }
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  
     newm=savm;  /*************** function subdirf3 ***********/
     /* Covariates have to be included here again */  char *subdirf3(char fileres[], char *preop, char *preop2)
      cov[2]=agefin;  {
      
       for (k=1; k<=cptcovn;k++) {    /* Caution optionfilefiname is hidden */
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    strcpy(tmpout,optionfilefiname);
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    strcat(tmpout,"/");
       }    strcat(tmpout,preop);
       for (k=1; k<=cptcovage;k++)    strcat(tmpout,preop2);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    strcat(tmpout,fileres);
       for (k=1; k<=cptcovprod;k++)    return tmpout;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  }
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  /***************** f1dim *************************/
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  extern int ncom; 
   extern double *pcom,*xicom;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  extern double (*nrfunc)(double []); 
    
     savm=oldm;  double f1dim(double x) 
     oldm=newm;  { 
     maxmax=0.;    int j; 
     for(j=1;j<=nlstate;j++){    double f;
       min=1.;    double *xt; 
       max=0.;   
       for(i=1; i<=nlstate; i++) {    xt=vector(1,ncom); 
         sumnew=0;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    f=(*nrfunc)(xt); 
         prlim[i][j]= newm[i][j]/(1-sumnew);    free_vector(xt,1,ncom); 
         max=FMAX(max,prlim[i][j]);    return f; 
         min=FMIN(min,prlim[i][j]);  } 
       }  
       maxmin=max-min;  /*****************brent *************************/
       maxmax=FMAX(maxmax,maxmin);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     }  { 
     if(maxmax < ftolpl){    int iter; 
       return prlim;    double a,b,d,etemp;
     }    double fu,fv,fw,fx;
   }    double ftemp;
 }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     double e=0.0; 
 /*************** transition probabilities ***************/   
     a=(ax < cx ? ax : cx); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    b=(ax > cx ? ax : cx); 
 {    x=w=v=bx; 
   double s1, s2;    fw=fv=fx=(*f)(x); 
   /*double t34;*/    for (iter=1;iter<=ITMAX;iter++) { 
   int i,j,j1, nc, ii, jj;      xm=0.5*(a+b); 
       tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     for(i=1; i<= nlstate; i++){      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     for(j=1; j<i;j++){      printf(".");fflush(stdout);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      fprintf(ficlog,".");fflush(ficlog);
         /*s2 += param[i][j][nc]*cov[nc];*/  #ifdef DEBUG
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       ps[i][j]=s2;  #endif
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     }        *xmin=x; 
     for(j=i+1; j<=nlstate+ndeath;j++){        return fx; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      } 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      ftemp=fu;
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      if (fabs(e) > tol1) { 
       }        r=(x-w)*(fx-fv); 
       ps[i][j]=s2;        q=(x-v)*(fx-fw); 
     }        p=(x-v)*q-(x-w)*r; 
   }        q=2.0*(q-r); 
     /*ps[3][2]=1;*/        if (q > 0.0) p = -p; 
         q=fabs(q); 
   for(i=1; i<= nlstate; i++){        etemp=e; 
      s1=0;        e=d; 
     for(j=1; j<i; j++)        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       s1+=exp(ps[i][j]);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     for(j=i+1; j<=nlstate+ndeath; j++)        else { 
       s1+=exp(ps[i][j]);          d=p/q; 
     ps[i][i]=1./(s1+1.);          u=x+d; 
     for(j=1; j<i; j++)          if (u-a < tol2 || b-u < tol2) 
       ps[i][j]= exp(ps[i][j])*ps[i][i];            d=SIGN(tol1,xm-x); 
     for(j=i+1; j<=nlstate+ndeath; j++)        } 
       ps[i][j]= exp(ps[i][j])*ps[i][i];      } else { 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   } /* end i */      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      fu=(*f)(u); 
     for(jj=1; jj<= nlstate+ndeath; jj++){      if (fu <= fx) { 
       ps[ii][jj]=0;        if (u >= x) a=x; else b=x; 
       ps[ii][ii]=1;        SHFT(v,w,x,u) 
     }          SHFT(fv,fw,fx,fu) 
   }          } else { 
             if (u < x) a=u; else b=u; 
             if (fu <= fw || w == x) { 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){              v=w; 
     for(jj=1; jj<= nlstate+ndeath; jj++){              w=u; 
      printf("%lf ",ps[ii][jj]);              fv=fw; 
    }              fw=fu; 
     printf("\n ");            } else if (fu <= fv || v == x || v == w) { 
     }              v=u; 
     printf("\n ");printf("%lf ",cov[2]);*/              fv=fu; 
 /*            } 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          } 
   goto end;*/    } 
     return ps;    nrerror("Too many iterations in brent"); 
 }    *xmin=x; 
     return fx; 
 /**************** Product of 2 matrices ******************/  } 
   
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  /****************** mnbrak ***********************/
 {  
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */              double (*func)(double)) 
   /* in, b, out are matrice of pointers which should have been initialized  { 
      before: only the contents of out is modified. The function returns    double ulim,u,r,q, dum;
      a pointer to pointers identical to out */    double fu; 
   long i, j, k;   
   for(i=nrl; i<= nrh; i++)    *fa=(*func)(*ax); 
     for(k=ncolol; k<=ncoloh; k++)    *fb=(*func)(*bx); 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    if (*fb > *fa) { 
         out[i][k] +=in[i][j]*b[j][k];      SHFT(dum,*ax,*bx,dum) 
         SHFT(dum,*fb,*fa,dum) 
   return out;        } 
 }    *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
     while (*fb > *fc) { 
 /************* Higher Matrix Product ***************/      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 {        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      ulim=(*bx)+GLIMIT*(*cx-*bx); 
      duration (i.e. until      if ((*bx-u)*(u-*cx) > 0.0) { 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        fu=(*func)(u); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      } else if ((*cx-u)*(u-ulim) > 0.0) { 
      (typically every 2 years instead of every month which is too big).        fu=(*func)(u); 
      Model is determined by parameters x and covariates have to be        if (fu < *fc) { 
      included manually here.          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             SHFT(*fb,*fc,fu,(*func)(u)) 
      */            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   int i, j, d, h, k;        u=ulim; 
   double **out, cov[NCOVMAX];        fu=(*func)(u); 
   double **newm;      } else { 
         u=(*cx)+GOLD*(*cx-*bx); 
   /* Hstepm could be zero and should return the unit matrix */        fu=(*func)(u); 
   for (i=1;i<=nlstate+ndeath;i++)      } 
     for (j=1;j<=nlstate+ndeath;j++){      SHFT(*ax,*bx,*cx,u) 
       oldm[i][j]=(i==j ? 1.0 : 0.0);        SHFT(*fa,*fb,*fc,fu) 
       po[i][j][0]=(i==j ? 1.0 : 0.0);        } 
     }  } 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(h=1; h <=nhstepm; h++){  /*************** linmin ************************/
     for(d=1; d <=hstepm; d++){  
       newm=savm;  int ncom; 
       /* Covariates have to be included here again */  double *pcom,*xicom;
       cov[1]=1.;  double (*nrfunc)(double []); 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;   
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       for (k=1; k<=cptcovage;k++)  { 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    double brent(double ax, double bx, double cx, 
       for (k=1; k<=cptcovprod;k++)                 double (*f)(double), double tol, double *xmin); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    int j; 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    double xx,xmin,bx,ax; 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    double fx,fb,fa;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));   
       savm=oldm;    ncom=n; 
       oldm=newm;    pcom=vector(1,n); 
     }    xicom=vector(1,n); 
     for(i=1; i<=nlstate+ndeath; i++)    nrfunc=func; 
       for(j=1;j<=nlstate+ndeath;j++) {    for (j=1;j<=n;j++) { 
         po[i][j][h]=newm[i][j];      pcom[j]=p[j]; 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      xicom[j]=xi[j]; 
          */    } 
       }    ax=0.0; 
   } /* end h */    xx=1.0; 
   return po;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
 }    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   #ifdef DEBUG
     printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 /*************** log-likelihood *************/    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 double func( double *x)  #endif
 {    for (j=1;j<=n;j++) { 
   int i, ii, j, k, mi, d, kk;      xi[j] *= xmin; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      p[j] += xi[j]; 
   double **out;    } 
   double sw; /* Sum of weights */    free_vector(xicom,1,n); 
   double lli; /* Individual log likelihood */    free_vector(pcom,1,n); 
   long ipmx;  } 
   /*extern weight */  
   /* We are differentiating ll according to initial status */  char *asc_diff_time(long time_sec, char ascdiff[])
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  {
   /*for(i=1;i<imx;i++)    long sec_left, days, hours, minutes;
     printf(" %d\n",s[4][i]);    days = (time_sec) / (60*60*24);
   */    sec_left = (time_sec) % (60*60*24);
   cov[1]=1.;    hours = (sec_left) / (60*60) ;
     sec_left = (sec_left) %(60*60);
   for(k=1; k<=nlstate; k++) ll[k]=0.;    minutes = (sec_left) /60;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    sec_left = (sec_left) % (60);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     for(mi=1; mi<= wav[i]-1; mi++){    return ascdiff;
       for (ii=1;ii<=nlstate+ndeath;ii++)  }
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
       for(d=0; d<dh[mi][i]; d++){  /*************** powell ************************/
         newm=savm;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;              double (*func)(double [])) 
         for (kk=1; kk<=cptcovage;kk++) {  { 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    void linmin(double p[], double xi[], int n, double *fret, 
         }                double (*func)(double [])); 
            int i,ibig,j; 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    double del,t,*pt,*ptt,*xit;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    double fp,fptt;
         savm=oldm;    double *xits;
         oldm=newm;    int niterf, itmp;
          
            pt=vector(1,n); 
       } /* end mult */    ptt=vector(1,n); 
          xit=vector(1,n); 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    xits=vector(1,n); 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    *fret=(*func)(p); 
       ipmx +=1;    for (j=1;j<=n;j++) pt[j]=p[j]; 
       sw += weight[i];    for (*iter=1;;++(*iter)) { 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      fp=(*fret); 
     } /* end of wave */      ibig=0; 
   } /* end of individual */      del=0.0; 
       last_time=curr_time;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      (void) gettimeofday(&curr_time,&tzp);
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      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);
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      /*    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);
   return -l;      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
 }      */
      for (i=1;i<=n;i++) {
         printf(" %d %.12f",i, p[i]);
 /*********** Maximum Likelihood Estimation ***************/        fprintf(ficlog," %d %.12lf",i, p[i]);
         fprintf(ficrespow," %.12lf", p[i]);
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      }
 {      printf("\n");
   int i,j, iter;      fprintf(ficlog,"\n");
   double **xi,*delti;      fprintf(ficrespow,"\n");fflush(ficrespow);
   double fret;      if(*iter <=3){
   xi=matrix(1,npar,1,npar);        tm = *localtime(&curr_time.tv_sec);
   for (i=1;i<=npar;i++)        strcpy(strcurr,asctime(&tm));
     for (j=1;j<=npar;j++)  /*       asctime_r(&tm,strcurr); */
       xi[i][j]=(i==j ? 1.0 : 0.0);        forecast_time=curr_time; 
   printf("Powell\n");        itmp = strlen(strcurr);
   powell(p,xi,npar,ftol,&iter,&fret,func);        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           strcurr[itmp-1]='\0';
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         for(niterf=10;niterf<=30;niterf+=10){
 }          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
           tmf = *localtime(&forecast_time.tv_sec);
 /**** Computes Hessian and covariance matrix ***/  /*      asctime_r(&tmf,strfor); */
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          strcpy(strfor,asctime(&tmf));
 {          itmp = strlen(strfor);
   double  **a,**y,*x,pd;          if(strfor[itmp-1]=='\n')
   double **hess;          strfor[itmp-1]='\0';
   int i, j,jk;          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);
   int *indx;          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);
         }
   double hessii(double p[], double delta, int theta, double delti[]);      }
   double hessij(double p[], double delti[], int i, int j);      for (i=1;i<=n;i++) { 
   void lubksb(double **a, int npar, int *indx, double b[]) ;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   void ludcmp(double **a, int npar, int *indx, double *d) ;        fptt=(*fret); 
   #ifdef DEBUG
   hess=matrix(1,npar,1,npar);        printf("fret=%lf \n",*fret);
         fprintf(ficlog,"fret=%lf \n",*fret);
   printf("\nCalculation of the hessian matrix. Wait...\n");  #endif
   for (i=1;i<=npar;i++){        printf("%d",i);fflush(stdout);
     printf("%d",i);fflush(stdout);        fprintf(ficlog,"%d",i);fflush(ficlog);
     hess[i][i]=hessii(p,ftolhess,i,delti);        linmin(p,xit,n,fret,func); 
     /*printf(" %f ",p[i]);*/        if (fabs(fptt-(*fret)) > del) { 
     /*printf(" %lf ",hess[i][i]);*/          del=fabs(fptt-(*fret)); 
   }          ibig=i; 
          } 
   for (i=1;i<=npar;i++) {  #ifdef DEBUG
     for (j=1;j<=npar;j++)  {        printf("%d %.12e",i,(*fret));
       if (j>i) {        fprintf(ficlog,"%d %.12e",i,(*fret));
         printf(".%d%d",i,j);fflush(stdout);        for (j=1;j<=n;j++) {
         hess[i][j]=hessij(p,delti,i,j);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         hess[j][i]=hess[i][j];              printf(" x(%d)=%.12e",j,xit[j]);
         /*printf(" %lf ",hess[i][j]);*/          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       }        }
     }        for(j=1;j<=n;j++) {
   }          printf(" p=%.12e",p[j]);
   printf("\n");          fprintf(ficlog," p=%.12e",p[j]);
         }
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        printf("\n");
          fprintf(ficlog,"\n");
   a=matrix(1,npar,1,npar);  #endif
   y=matrix(1,npar,1,npar);      } 
   x=vector(1,npar);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   indx=ivector(1,npar);  #ifdef DEBUG
   for (i=1;i<=npar;i++)        int k[2],l;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        k[0]=1;
   ludcmp(a,npar,indx,&pd);        k[1]=-1;
         printf("Max: %.12e",(*func)(p));
   for (j=1;j<=npar;j++) {        fprintf(ficlog,"Max: %.12e",(*func)(p));
     for (i=1;i<=npar;i++) x[i]=0;        for (j=1;j<=n;j++) {
     x[j]=1;          printf(" %.12e",p[j]);
     lubksb(a,npar,indx,x);          fprintf(ficlog," %.12e",p[j]);
     for (i=1;i<=npar;i++){        }
       matcov[i][j]=x[i];        printf("\n");
     }        fprintf(ficlog,"\n");
   }        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
   printf("\n#Hessian matrix#\n");            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   for (i=1;i<=npar;i++) {            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     for (j=1;j<=npar;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("%.3e ",hess[i][j]);          }
     }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     printf("\n");          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   }        }
   #endif
   /* Recompute Inverse */  
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        free_vector(xit,1,n); 
   ludcmp(a,npar,indx,&pd);        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
   /*  printf("\n#Hessian matrix recomputed#\n");        free_vector(pt,1,n); 
         return; 
   for (j=1;j<=npar;j++) {      } 
     for (i=1;i<=npar;i++) x[i]=0;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     x[j]=1;      for (j=1;j<=n;j++) { 
     lubksb(a,npar,indx,x);        ptt[j]=2.0*p[j]-pt[j]; 
     for (i=1;i<=npar;i++){        xit[j]=p[j]-pt[j]; 
       y[i][j]=x[i];        pt[j]=p[j]; 
       printf("%.3e ",y[i][j]);      } 
     }      fptt=(*func)(ptt); 
     printf("\n");      if (fptt < fp) { 
   }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   */        if (t < 0.0) { 
           linmin(p,xit,n,fret,func); 
   free_matrix(a,1,npar,1,npar);          for (j=1;j<=n;j++) { 
   free_matrix(y,1,npar,1,npar);            xi[j][ibig]=xi[j][n]; 
   free_vector(x,1,npar);            xi[j][n]=xit[j]; 
   free_ivector(indx,1,npar);          }
   free_matrix(hess,1,npar,1,npar);  #ifdef DEBUG
           printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 }          for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
 /*************** hessian matrix ****************/            fprintf(ficlog," %.12e",xit[j]);
 double hessii( double x[], double delta, int theta, double delti[])          }
 {          printf("\n");
   int i;          fprintf(ficlog,"\n");
   int l=1, lmax=20;  #endif
   double k1,k2;        }
   double p2[NPARMAX+1];      } 
   double res;    } 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  } 
   double fx;  
   int k=0,kmax=10;  /**** Prevalence limit (stable prevalence)  ****************/
   double l1;  
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   fx=func(x);  {
   for (i=1;i<=npar;i++) p2[i]=x[i];    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   for(l=0 ; l <=lmax; l++){       matrix by transitions matrix until convergence is reached */
     l1=pow(10,l);  
     delts=delt;    int i, ii,j,k;
     for(k=1 ; k <kmax; k=k+1){    double min, max, maxmin, maxmax,sumnew=0.;
       delt = delta*(l1*k);    double **matprod2();
       p2[theta]=x[theta] +delt;    double **out, cov[NCOVMAX], **pmij();
       k1=func(p2)-fx;    double **newm;
       p2[theta]=x[theta]-delt;    double agefin, delaymax=50 ; /* Max number of years to converge */
       k2=func(p2)-fx;  
       /*res= (k1-2.0*fx+k2)/delt/delt; */    for (ii=1;ii<=nlstate+ndeath;ii++)
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      for (j=1;j<=nlstate+ndeath;j++){
              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 #ifdef DEBUG      }
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  
 #endif     cov[1]=1.;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */   
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         k=kmax;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       }      newm=savm;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      /* Covariates have to be included here again */
         k=kmax; l=lmax*10.;       cov[2]=agefin;
       }    
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        for (k=1; k<=cptcovn;k++) {
         delts=delt;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       }          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
     }        }
   }        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   delti[theta]=delts;        for (k=1; k<=cptcovprod;k++)
   return res;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
    
 }        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
 double hessij( double x[], double delti[], int thetai,int thetaj)        /*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);
   int i;  
   int l=1, l1, lmax=20;      savm=oldm;
   double k1,k2,k3,k4,res,fx;      oldm=newm;
   double p2[NPARMAX+1];      maxmax=0.;
   int k;      for(j=1;j<=nlstate;j++){
         min=1.;
   fx=func(x);        max=0.;
   for (k=1; k<=2; k++) {        for(i=1; i<=nlstate; i++) {
     for (i=1;i<=npar;i++) p2[i]=x[i];          sumnew=0;
     p2[thetai]=x[thetai]+delti[thetai]/k;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          prlim[i][j]= newm[i][j]/(1-sumnew);
     k1=func(p2)-fx;          max=FMAX(max,prlim[i][j]);
            min=FMIN(min,prlim[i][j]);
     p2[thetai]=x[thetai]+delti[thetai]/k;        }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        maxmin=max-min;
     k2=func(p2)-fx;        maxmax=FMAX(maxmax,maxmin);
        }
     p2[thetai]=x[thetai]-delti[thetai]/k;      if(maxmax < ftolpl){
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        return prlim;
     k3=func(p2)-fx;      }
      }
     p2[thetai]=x[thetai]-delti[thetai]/k;  }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k4=func(p2)-fx;  /*************** transition probabilities ***************/ 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  
 #ifdef DEBUG  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  {
 #endif    double s1, s2;
   }    /*double t34;*/
   return res;    int i,j,j1, nc, ii, jj;
 }  
       for(i=1; i<= nlstate; i++){
 /************** Inverse of matrix **************/        for(j=1; j<i;j++){
 void ludcmp(double **a, int n, int *indx, double *d)          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 {            /*s2 += param[i][j][nc]*cov[nc];*/
   int i,imax,j,k;            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   double big,dum,sum,temp;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
   double *vv;          }
            ps[i][j]=s2;
   vv=vector(1,n);  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
   *d=1.0;        }
   for (i=1;i<=n;i++) {        for(j=i+1; j<=nlstate+ndeath;j++){
     big=0.0;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     for (j=1;j<=n;j++)            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       if ((temp=fabs(a[i][j])) > big) big=temp;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          }
     vv[i]=1.0/big;          ps[i][j]=s2;
   }        }
   for (j=1;j<=n;j++) {      }
     for (i=1;i<j;i++) {      /*ps[3][2]=1;*/
       sum=a[i][j];      
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      for(i=1; i<= nlstate; i++){
       a[i][j]=sum;        s1=0;
     }        for(j=1; j<i; j++)
     big=0.0;          s1+=exp(ps[i][j]);
     for (i=j;i<=n;i++) {        for(j=i+1; j<=nlstate+ndeath; j++)
       sum=a[i][j];          s1+=exp(ps[i][j]);
       for (k=1;k<j;k++)        ps[i][i]=1./(s1+1.);
         sum -= a[i][k]*a[k][j];        for(j=1; j<i; j++)
       a[i][j]=sum;          ps[i][j]= exp(ps[i][j])*ps[i][i];
       if ( (dum=vv[i]*fabs(sum)) >= big) {        for(j=i+1; j<=nlstate+ndeath; j++)
         big=dum;          ps[i][j]= exp(ps[i][j])*ps[i][i];
         imax=i;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       }      } /* end i */
     }      
     if (j != imax) {      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for (k=1;k<=n;k++) {        for(jj=1; jj<= nlstate+ndeath; jj++){
         dum=a[imax][k];          ps[ii][jj]=0;
         a[imax][k]=a[j][k];          ps[ii][ii]=1;
         a[j][k]=dum;        }
       }      }
       *d = -(*d);      
       vv[imax]=vv[j];  
     }  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
     indx[j]=imax;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
     if (a[j][j] == 0.0) a[j][j]=TINY;  /*         printf("ddd %lf ",ps[ii][jj]); */
     if (j != n) {  /*       } */
       dum=1.0/(a[j][j]);  /*       printf("\n "); */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  /*        } */
     }  /*        printf("\n ");printf("%lf ",cov[2]); */
   }         /*
   free_vector(vv,1,n);  /* Doesn't work */        for(i=1; i<= npar; i++) printf("%f ",x[i]);
 ;        goto end;*/
 }      return ps;
   }
 void lubksb(double **a, int n, int *indx, double b[])  
 {  /**************** Product of 2 matrices ******************/
   int i,ii=0,ip,j;  
   double sum;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
    {
   for (i=1;i<=n;i++) {    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     ip=indx[i];       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     sum=b[ip];    /* in, b, out are matrice of pointers which should have been initialized 
     b[ip]=b[i];       before: only the contents of out is modified. The function returns
     if (ii)       a pointer to pointers identical to out */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    long i, j, k;
     else if (sum) ii=i;    for(i=nrl; i<= nrh; i++)
     b[i]=sum;      for(k=ncolol; k<=ncoloh; k++)
   }        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   for (i=n;i>=1;i--) {          out[i][k] +=in[i][j]*b[j][k];
     sum=b[i];  
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    return out;
     b[i]=sum/a[i][i];  }
   }  
 }  
   /************* Higher Matrix Product ***************/
 /************ Frequencies ********************/  
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
 {  /* Some frequencies */  {
      /* Computes the transition matrix starting at age 'age' over 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;       'nhstepm*hstepm*stepm' months (i.e. until
   double ***freq; /* Frequencies */       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   double *pp;       nhstepm*hstepm matrices. 
   double pos, k2, dateintsum=0,k2cpt=0;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   FILE *ficresp;       (typically every 2 years instead of every month which is too big 
   char fileresp[FILENAMELENGTH];       for the memory).
         Model is determined by parameters x and covariates have to be 
   pp=vector(1,nlstate);       included manually here. 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   strcpy(fileresp,"p");       */
   strcat(fileresp,fileres);  
   if((ficresp=fopen(fileresp,"w"))==NULL) {    int i, j, d, h, k;
     printf("Problem with prevalence resultfile: %s\n", fileresp);    double **out, cov[NCOVMAX];
     exit(0);    double **newm;
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    /* Hstepm could be zero and should return the unit matrix */
   j1=0;    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
   j=cptcoveff;        oldm[i][j]=(i==j ? 1.0 : 0.0);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
   for(k1=1; k1<=j;k1++){    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
    for(i1=1; i1<=ncodemax[k1];i1++){    for(h=1; h <=nhstepm; h++){
        j1++;      for(d=1; d <=hstepm; d++){
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        newm=savm;
          scanf("%d", i);*/        /* Covariates have to be included here again */
         for (i=-1; i<=nlstate+ndeath; i++)          cov[1]=1.;
          for (jk=-1; jk<=nlstate+ndeath; jk++)          cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
            for(m=agemin; m <= agemax+3; m++)        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
              freq[i][jk][m]=0;        for (k=1; k<=cptcovage;k++)
           cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         dateintsum=0;        for (k=1; k<=cptcovprod;k++)
         k2cpt=0;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
        for (i=1; i<=imx; i++) {  
          bool=1;  
          if  (cptcovn>0) {        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
            for (z1=1; z1<=cptcoveff; z1++)        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                bool=0;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
          }        savm=oldm;
          if (bool==1) {        oldm=newm;
            for(m=firstpass; m<=lastpass; m++){      }
              k2=anint[m][i]+(mint[m][i]/12.);      for(i=1; i<=nlstate+ndeath; i++)
              if ((k2>=dateprev1) && (k2<=dateprev2)) {        for(j=1;j<=nlstate+ndeath;j++) {
                if(agev[m][i]==0) agev[m][i]=agemax+1;          po[i][j][h]=newm[i][j];
                if(agev[m][i]==1) agev[m][i]=agemax+2;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
                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];        }
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    } /* end h */
                  dateintsum=dateintsum+k2;    return po;
                  k2cpt++;  }
                }  
   
              }  /*************** log-likelihood *************/
            }  double func( double *x)
          }  {
        }    int i, ii, j, k, mi, d, kk;
            double l, ll[NLSTATEMAX], cov[NCOVMAX];
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    double **out;
     double sw; /* Sum of weights */
         if  (cptcovn>0) {    double lli; /* Individual log likelihood */
          fprintf(ficresp, "\n#********** Variable ");    int s1, s2;
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double bbh, survp;
        fprintf(ficresp, "**********\n#");    long ipmx;
         }    /*extern weight */
        for(i=1; i<=nlstate;i++)    /* We are differentiating ll according to initial status */
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
        fprintf(ficresp, "\n");    /*for(i=1;i<imx;i++) 
              printf(" %d\n",s[4][i]);
   for(i=(int)agemin; i <= (int)agemax+3; i++){    */
     if(i==(int)agemax+3)    cov[1]=1.;
       printf("Total");  
     else    for(k=1; k<=nlstate; k++) ll[k]=0.;
       printf("Age %d", i);  
     for(jk=1; jk <=nlstate ; jk++){    if(mle==1){
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         pp[jk] += freq[jk][m][i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
     for(jk=1; jk <=nlstate ; jk++){          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(m=-1, pos=0; m <=0 ; m++)            for (j=1;j<=nlstate+ndeath;j++){
         pos += freq[jk][m][i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       if(pp[jk]>=1.e-10)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            }
       else          for(d=0; d<dh[mi][i]; d++){
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
      for(jk=1; jk <=nlstate ; jk++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            }
         pp[jk] += freq[jk][m][i];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
     for(jk=1,pos=0; jk <=nlstate ; jk++)            oldm=newm;
       pos += pp[jk];          } /* end mult */
     for(jk=1; jk <=nlstate ; jk++){        
       if(pos>=1.e-5)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          /* But now since version 0.9 we anticipate for bias at large stepm.
       else           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);           * (in months) between two waves is not a multiple of stepm, we rounded to 
       if( i <= (int) agemax){           * the nearest (and in case of equal distance, to the lowest) interval but now
         if(pos>=1.e-5){           * we keep into memory the bias bh[mi][i] and also the previous matrix product
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
           probs[i][jk][j1]= pp[jk]/pos;           * probability in order to take into account the bias as a fraction of the way
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
         }           * -stepm/2 to stepm/2 .
       else           * For stepm=1 the results are the same as for previous versions of Imach.
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);           * For stepm > 1 the results are less biased than in previous versions. 
       }           */
     }          s1=s[mw[mi][i]][i];
     for(jk=-1; jk <=nlstate+ndeath; jk++)          s2=s[mw[mi+1][i]][i];
       for(m=-1; m <=nlstate+ndeath; m++)          bbh=(double)bh[mi][i]/(double)stepm; 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          /* bias bh is positive if real duration
     if(i <= (int) agemax)           * is higher than the multiple of stepm and negative otherwise.
       fprintf(ficresp,"\n");           */
     printf("\n");          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     }          if( s2 > nlstate){ 
     }            /* 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 
   dateintmean=dateintsum/k2cpt;               die between last step unit time and current  step unit time, 
                 which is also equal to probability to die before dh 
   fclose(ficresp);               minus probability to die before dh-stepm . 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);               In version up to 0.92 likelihood was computed
   free_vector(pp,1,nlstate);          as if date of death was unknown. Death was treated as any other
           health state: the date of the interview describes the actual state
   /* End of Freq */          and not the date of a change in health state. The former idea was
 }          to consider that at each interview the state was recorded
           (healthy, disable or death) and IMaCh was corrected; but when we
 /************ Prevalence ********************/          introduced the exact date of death then we should have modified
 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)          the contribution of an exact death to the likelihood. This new
 {  /* Some frequencies */          contribution is smaller and very dependent of the step unit
            stepm. It is no more the probability to die between last interview
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          and month of death but the probability to survive from last
   double ***freq; /* Frequencies */          interview up to one month before death multiplied by the
   double *pp;          probability to die within a month. Thanks to Chris
   double pos, k2;          Jackson for correcting this bug.  Former versions increased
           mortality artificially. The bad side is that we add another loop
   pp=vector(1,nlstate);          which slows down the processing. The difference can be up to 10%
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          lower mortality.
              */
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            lli=log(out[s1][s2] - savm[s1][s2]);
   j1=0;  
    
   j=cptcoveff;          } else if  (s2==-2) {
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            for (j=1,survp=0. ; j<=nlstate; j++) 
                survp += out[s1][j];
  for(k1=1; k1<=j;k1++){            lli= survp;
     for(i1=1; i1<=ncodemax[k1];i1++){          }
       j1++;          
            else if  (s2==-4) {
       for (i=-1; i<=nlstate+ndeath; i++)              for (j=3,survp=0. ; j<=nlstate; j++) 
         for (jk=-1; jk<=nlstate+ndeath; jk++)                survp += out[s1][j];
           for(m=agemin; m <= agemax+3; m++)            lli= survp;
             freq[i][jk][m]=0;          }
                
       for (i=1; i<=imx; i++) {          else if  (s2==-5) {
         bool=1;            for (j=1,survp=0. ; j<=2; j++) 
         if  (cptcovn>0) {              survp += out[s1][j];
           for (z1=1; z1<=cptcoveff; z1++)            lli= survp;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          }
               bool=0;  
         }  
         if (bool==1) {          else{
           for(m=firstpass; m<=lastpass; m++){            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             k2=anint[m][i]+(mint[m][i]/12.);            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          } 
               if(agev[m][i]==0) agev[m][i]=agemax+1;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
               if(agev[m][i]==1) agev[m][i]=agemax+2;          /*if(lli ==000.0)*/
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          /*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); */
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */          ipmx +=1;
             }          sw += weight[i];
           }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         }        } /* end of wave */
       }      } /* end of individual */
         for(i=(int)agemin; i <= (int)agemax+3; i++){    }  else if(mle==2){
           for(jk=1; jk <=nlstate ; jk++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
               pp[jk] += freq[jk][m][i];        for(mi=1; mi<= wav[i]-1; mi++){
           }          for (ii=1;ii<=nlstate+ndeath;ii++)
           for(jk=1; jk <=nlstate ; jk++){            for (j=1;j<=nlstate+ndeath;j++){
             for(m=-1, pos=0; m <=0 ; m++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             pos += freq[jk][m][i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            }
                  for(d=0; d<=dh[mi][i]; d++){
          for(jk=1; jk <=nlstate ; jk++){            newm=savm;
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              pp[jk] += freq[jk][m][i];            for (kk=1; kk<=cptcovage;kk++) {
          }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                      }
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
          for(jk=1; jk <=nlstate ; jk++){                      savm=oldm;
            if( i <= (int) agemax){            oldm=newm;
              if(pos>=1.e-5){          } /* end mult */
                probs[i][jk][j1]= pp[jk]/pos;        
              }          s1=s[mw[mi][i]][i];
            }          s2=s[mw[mi+1][i]][i];
          }          bbh=(double)bh[mi][i]/(double)stepm; 
                    lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         }          ipmx +=1;
     }          sw += weight[i];
   }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
        } /* end of individual */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    }  else if(mle==3){  /* exponential inter-extrapolation */
   free_vector(pp,1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 }  /* End of Freq */        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
 /************* Waves Concatenation ***************/            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 {            }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          for(d=0; d<dh[mi][i]; d++){
      Death is a valid wave (if date is known).            newm=savm;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            for (kk=1; kk<=cptcovage;kk++) {
      and mw[mi+1][i]. dh depends on stepm.              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      */            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int i, mi, m;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;            savm=oldm;
      double sum=0., jmean=0.;*/            oldm=newm;
           } /* end mult */
   int j, k=0,jk, ju, jl;        
   double sum=0.;          s1=s[mw[mi][i]][i];
   jmin=1e+5;          s2=s[mw[mi+1][i]][i];
   jmax=-1;          bbh=(double)bh[mi][i]/(double)stepm; 
   jmean=0.;          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   for(i=1; i<=imx; i++){          ipmx +=1;
     mi=0;          sw += weight[i];
     m=firstpass;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     while(s[m][i] <= nlstate){        } /* end of wave */
       if(s[m][i]>=1)      } /* end of individual */
         mw[++mi][i]=m;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       if(m >=lastpass)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         break;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       else        for(mi=1; mi<= wav[i]-1; mi++){
         m++;          for (ii=1;ii<=nlstate+ndeath;ii++)
     }/* end while */            for (j=1;j<=nlstate+ndeath;j++){
     if (s[m][i] > nlstate){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       mi++;     /* Death is another wave */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       /* if(mi==0)  never been interviewed correctly before death */            }
          /* Only death is a correct wave */          for(d=0; d<dh[mi][i]; d++){
       mw[mi][i]=m;            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     wav[i]=mi;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     if(mi==0)            }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          
   }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for(i=1; i<=imx; i++){            savm=oldm;
     for(mi=1; mi<wav[i];mi++){            oldm=newm;
       if (stepm <=0)          } /* end mult */
         dh[mi][i]=1;        
       else{          s1=s[mw[mi][i]][i];
         if (s[mw[mi+1][i]][i] > nlstate) {          s2=s[mw[mi+1][i]][i];
           if (agedc[i] < 2*AGESUP) {          if( s2 > nlstate){ 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);            lli=log(out[s1][s2] - savm[s1][s2]);
           if(j==0) j=1;  /* Survives at least one month after exam */          }else{
           k=k+1;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           if (j >= jmax) jmax=j;          }
           if (j <= jmin) jmin=j;          ipmx +=1;
           sum=sum+j;          sw += weight[i];
           /*if (j<0) printf("j=%d num=%d \n",j,i); */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           }  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         }        } /* end of wave */
         else{      } /* end of individual */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
           k=k+1;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           if (j >= jmax) jmax=j;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           else if (j <= jmin)jmin=j;        for(mi=1; mi<= wav[i]-1; mi++){
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          for (ii=1;ii<=nlstate+ndeath;ii++)
           sum=sum+j;            for (j=1;j<=nlstate+ndeath;j++){
         }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         jk= j/stepm;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         jl= j -jk*stepm;            }
         ju= j -(jk+1)*stepm;          for(d=0; d<dh[mi][i]; d++){
         if(jl <= -ju)            newm=savm;
           dh[mi][i]=jk;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         else            for (kk=1; kk<=cptcovage;kk++) {
           dh[mi][i]=jk+1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         if(dh[mi][i]==0)            }
           dh[mi][i]=1; /* At least one step */          
       }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
   jmean=sum/k;            oldm=newm;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          } /* end mult */
  }        
 /*********** Tricode ****************************/          s1=s[mw[mi][i]][i];
 void tricode(int *Tvar, int **nbcode, int imx)          s2=s[mw[mi+1][i]][i];
 {          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   int Ndum[20],ij=1, k, j, i;          ipmx +=1;
   int cptcode=0;          sw += weight[i];
   cptcoveff=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
            /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
   for (k=0; k<19; k++) Ndum[k]=0;        } /* end of wave */
   for (k=1; k<=7; k++) ncodemax[k]=0;      } /* end of individual */
     } /* End of if */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     for (i=1; i<=imx; i++) {    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       ij=(int)(covar[Tvar[j]][i]);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       Ndum[ij]++;    return -l;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  }
       if (ij > cptcode) cptcode=ij;  
     }  /*************** log-likelihood *************/
   double funcone( double *x)
     for (i=0; i<=cptcode; i++) {  {
       if(Ndum[i]!=0) ncodemax[j]++;    /* Same as likeli but slower because of a lot of printf and if */
     }    int i, ii, j, k, mi, d, kk;
     ij=1;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
     double lli; /* Individual log likelihood */
     for (i=1; i<=ncodemax[j]; i++) {    double llt;
       for (k=0; k<=19; k++) {    int s1, s2;
         if (Ndum[k] != 0) {    double bbh, survp;
           nbcode[Tvar[j]][ij]=k;    /*extern weight */
           ij++;    /* We are differentiating ll according to initial status */
         }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         if (ij > ncodemax[j]) break;    /*for(i=1;i<imx;i++) 
       }        printf(" %d\n",s[4][i]);
     }    */
   }      cov[1]=1.;
   
  for (k=0; k<19; k++) Ndum[k]=0;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
  for (i=1; i<=ncovmodel-2; i++) {    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       ij=Tvar[i];      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       Ndum[ij]++;      for(mi=1; mi<= wav[i]-1; mi++){
     }        for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
  ij=1;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  for (i=1; i<=10; i++) {            savm[ii][j]=(ii==j ? 1.0 : 0.0);
    if((Ndum[i]!=0) && (i<=ncov)){          }
      Tvaraff[ij]=i;        for(d=0; d<dh[mi][i]; d++){
      ij++;          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];
     cptcoveff=ij-1;          }
 }          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 /*********** Health Expectancies ****************/          savm=oldm;
           oldm=newm;
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        } /* end mult */
 {        
   /* Health expectancies */        s1=s[mw[mi][i]][i];
   int i, j, nhstepm, hstepm, h, nstepm, k;        s2=s[mw[mi+1][i]][i];
   double age, agelim,hf;        bbh=(double)bh[mi][i]/(double)stepm; 
   double ***p3mat;        /* bias is positive if real duration
           * is higher than the multiple of stepm and negative otherwise.
   fprintf(ficreseij,"# Health expectancies\n");         */
   fprintf(ficreseij,"# Age");        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   for(i=1; i<=nlstate;i++)          lli=log(out[s1][s2] - savm[s1][s2]);
     for(j=1; j<=nlstate;j++)        } else if (mle==1){
       fprintf(ficreseij," %1d-%1d",i,j);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   fprintf(ficreseij,"\n");        } 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 */
   k=1;             /* For example stepm=6 months */        } else if(mle==3){  /* exponential inter-extrapolation */
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */          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 */
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          lli=log(out[s1][s2]); /* Original formula */
      nhstepm is the number of hstepm from age to agelim        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
      nstepm is the number of stepm from age to agelin.          lli=log(out[s1][s2]); /* Original formula */
      Look at hpijx to understand the reason of that which relies in memory size        } /* End of if */
      and note for a fixed period like k years */        ipmx +=1;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        sw += weight[i];
      survival function given by stepm (the optimization length). Unfortunately it        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      means that if the survival funtion is printed only each two years of age and if  /*       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]); */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        if(globpr){
      results. So we changed our mind and took the option of the best precision.          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
   */   %10.6f %10.6f %10.6f ", \
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                   2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   agelim=AGESUP;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            llt +=ll[k]*gipmx/gsw;
     /* nhstepm age range expressed in number of stepm */            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);          }
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */          fprintf(ficresilk," %10.6f\n", -llt);
     if (stepm >= YEARM) hstepm=1;        }
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      } /* end of wave */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    } /* end of individual */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    if(globpr==0){ /* First time we count the contributions and weights */
     for(i=1; i<=nlstate;i++)      gipmx=ipmx;
       for(j=1; j<=nlstate;j++)      gsw=sw;
         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;    return -l;
           /* 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]);*/  }
         }  
     fprintf(ficreseij,"%3.0f",age );  
     for(i=1; i<=nlstate;i++)  /*************** function likelione ***********/
       for(j=1; j<=nlstate;j++){  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);  {
       }    /* This routine should help understanding what is done with 
     fprintf(ficreseij,"\n");       the selection of individuals/waves and
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       to check the exact contribution to the likelihood.
   }       Plotting could be done.
 }     */
     int k;
 /************ 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)    if(*globpri !=0){ /* Just counts and sums, no printings */
 {      strcpy(fileresilk,"ilk"); 
   /* Variance of health expectancies */      strcat(fileresilk,fileres);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   double **newm;        printf("Problem with resultfile: %s\n", fileresilk);
   double **dnewm,**doldm;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   int i, j, nhstepm, hstepm, h;      }
   int k, cptcode;      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");
   double *xp;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   double **gp, **gm;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   double ***gradg, ***trgradg;      for(k=1; k<=nlstate; k++) 
   double ***p3mat;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   double age,agelim;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   int theta;    }
   
    fprintf(ficresvij,"# Covariances of life expectancies\n");    *fretone=(*funcone)(p);
   fprintf(ficresvij,"# Age");    if(*globpri !=0){
   for(i=1; i<=nlstate;i++)      fclose(ficresilk);
     for(j=1; j<=nlstate;j++)      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      fflush(fichtm); 
   fprintf(ficresvij,"\n");    } 
     return;
   xp=vector(1,npar);  }
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);  
    /*********** Maximum Likelihood Estimation ***************/
   hstepm=1*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   agelim = AGESUP;  {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    int i,j, iter;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double **xi;
     if (stepm >= YEARM) hstepm=1;    double fret;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    double fretone; /* Only one call to likelihood */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*  char filerespow[FILENAMELENGTH];*/
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    xi=matrix(1,npar,1,npar);
     gp=matrix(0,nhstepm,1,nlstate);    for (i=1;i<=npar;i++)
     gm=matrix(0,nhstepm,1,nlstate);      for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
     for(theta=1; theta <=npar; theta++){    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       for(i=1; i<=npar; i++){ /* Computes gradient */    strcpy(filerespow,"pow"); 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    strcat(filerespow,fileres);
       }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        printf("Problem with resultfile: %s\n", filerespow);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
       if (popbased==1) {    fprintf(ficrespow,"# Powell\n# iter -2*LL");
         for(i=1; i<=nlstate;i++)    for (i=1;i<=nlstate;i++)
           prlim[i][i]=probs[(int)age][i][ij];      for(j=1;j<=nlstate+ndeath;j++)
       }        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
      fprintf(ficrespow,"\n");
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){    powell(p,xi,npar,ftol,&iter,&fret,func);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    fclose(ficrespow);
         }    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       }    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
        fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  /**** Computes Hessian and covariance matrix ***/
    void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       if (popbased==1) {  {
         for(i=1; i<=nlstate;i++)    double  **a,**y,*x,pd;
           prlim[i][i]=probs[(int)age][i][ij];    double **hess;
       }    int i, j,jk;
     int *indx;
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    void lubksb(double **a, int npar, int *indx, double b[]) ;
         }    void ludcmp(double **a, int npar, int *indx, double *d) ;
       }    double gompertz(double p[]);
     hess=matrix(1,npar,1,npar);
       for(j=1; j<= nlstate; j++)  
         for(h=0; h<=nhstepm; h++){    printf("\nCalculation of the hessian matrix. Wait...\n");
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         }    for (i=1;i<=npar;i++){
     } /* End theta */      printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);     
        hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     for(h=0; h<=nhstepm; h++)      
       for(j=1; j<=nlstate;j++)      /*  printf(" %f ",p[i]);
         for(theta=1; theta <=npar; theta++)          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
           trgradg[h][j][theta]=gradg[h][theta][j];    }
     
     for(i=1;i<=nlstate;i++)    for (i=1;i<=npar;i++) {
       for(j=1;j<=nlstate;j++)      for (j=1;j<=npar;j++)  {
         vareij[i][j][(int)age] =0.;        if (j>i) { 
     for(h=0;h<=nhstepm;h++){          printf(".%d%d",i,j);fflush(stdout);
       for(k=0;k<=nhstepm;k++){          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          hess[i][j]=hessij(p,delti,i,j,func,npar);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          
         for(i=1;i<=nlstate;i++)          hess[j][i]=hess[i][j];    
           for(j=1;j<=nlstate;j++)          /*printf(" %lf ",hess[i][j]);*/
             vareij[i][j][(int)age] += doldm[i][j];        }
       }      }
     }    }
     h=1;    printf("\n");
     if (stepm >= YEARM) h=stepm/YEARM;    fprintf(ficlog,"\n");
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       for(j=1; j<=nlstate;j++){    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    
       }    a=matrix(1,npar,1,npar);
     fprintf(ficresvij,"\n");    y=matrix(1,npar,1,npar);
     free_matrix(gp,0,nhstepm,1,nlstate);    x=vector(1,npar);
     free_matrix(gm,0,nhstepm,1,nlstate);    indx=ivector(1,npar);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    for (i=1;i<=npar;i++)
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    ludcmp(a,npar,indx,&pd);
   } /* End age */  
      for (j=1;j<=npar;j++) {
   free_vector(xp,1,npar);      for (i=1;i<=npar;i++) x[i]=0;
   free_matrix(doldm,1,nlstate,1,npar);      x[j]=1;
   free_matrix(dnewm,1,nlstate,1,nlstate);      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
 }        matcov[i][j]=x[i];
       }
 /************ 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)  
 {    printf("\n#Hessian matrix#\n");
   /* Variance of prevalence limit */    fprintf(ficlog,"\n#Hessian matrix#\n");
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    for (i=1;i<=npar;i++) { 
   double **newm;      for (j=1;j<=npar;j++) { 
   double **dnewm,**doldm;        printf("%.3e ",hess[i][j]);
   int i, j, nhstepm, hstepm;        fprintf(ficlog,"%.3e ",hess[i][j]);
   int k, cptcode;      }
   double *xp;      printf("\n");
   double *gp, *gm;      fprintf(ficlog,"\n");
   double **gradg, **trgradg;    }
   double age,agelim;  
   int theta;    /* Recompute Inverse */
        for (i=1;i<=npar;i++)
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   fprintf(ficresvpl,"# Age");    ludcmp(a,npar,indx,&pd);
   for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %1d-%1d",i,i);    /*  printf("\n#Hessian matrix recomputed#\n");
   fprintf(ficresvpl,"\n");  
     for (j=1;j<=npar;j++) {
   xp=vector(1,npar);      for (i=1;i<=npar;i++) x[i]=0;
   dnewm=matrix(1,nlstate,1,npar);      x[j]=1;
   doldm=matrix(1,nlstate,1,nlstate);      lubksb(a,npar,indx,x);
        for (i=1;i<=npar;i++){ 
   hstepm=1*YEARM; /* Every year of age */        y[i][j]=x[i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        printf("%.3e ",y[i][j]);
   agelim = AGESUP;        fprintf(ficlog,"%.3e ",y[i][j]);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      printf("\n");
     if (stepm >= YEARM) hstepm=1;      fprintf(ficlog,"\n");
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    }
     gradg=matrix(1,npar,1,nlstate);    */
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);    free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
     for(theta=1; theta <=npar; theta++){    free_vector(x,1,npar);
       for(i=1; i<=npar; i++){ /* Computes gradient */    free_ivector(indx,1,npar);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    free_matrix(hess,1,npar,1,npar);
       }  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)  }
         gp[i] = prlim[i][i];  
      /*************** hessian matrix ****************/
       for(i=1; i<=npar; i++) /* Computes gradient */  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int i;
       for(i=1;i<=nlstate;i++)    int l=1, lmax=20;
         gm[i] = prlim[i][i];    double k1,k2;
     double p2[NPARMAX+1];
       for(i=1;i<=nlstate;i++)    double res;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     } /* End theta */    double fx;
     int k=0,kmax=10;
     trgradg =matrix(1,nlstate,1,npar);    double l1;
   
     for(j=1; j<=nlstate;j++)    fx=func(x);
       for(theta=1; theta <=npar; theta++)    for (i=1;i<=npar;i++) p2[i]=x[i];
         trgradg[j][theta]=gradg[theta][j];    for(l=0 ; l <=lmax; l++){
       l1=pow(10,l);
     for(i=1;i<=nlstate;i++)      delts=delt;
       varpl[i][(int)age] =0.;      for(k=1 ; k <kmax; k=k+1){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        delt = delta*(l1*k);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        p2[theta]=x[theta] +delt;
     for(i=1;i<=nlstate;i++)        k1=func(p2)-fx;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
     fprintf(ficresvpl,"%.0f ",age );        /*res= (k1-2.0*fx+k2)/delt/delt; */
     for(i=1; i<=nlstate;i++)        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        
     fprintf(ficresvpl,"\n");  #ifdef DEBUG
     free_vector(gp,1,nlstate);        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);
     free_vector(gm,1,nlstate);        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);
     free_matrix(gradg,1,npar,1,nlstate);  #endif
     free_matrix(trgradg,1,nlstate,1,npar);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   } /* End age */        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k=kmax;
   free_vector(xp,1,npar);        }
   free_matrix(doldm,1,nlstate,1,npar);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   free_matrix(dnewm,1,nlstate,1,nlstate);          k=kmax; l=lmax*10.;
         }
 }        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
 /************ Variance of one-step probabilities  ******************/        }
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)      }
 {    }
   int i, j;    delti[theta]=delts;
   int k=0, cptcode;    return res; 
   double **dnewm,**doldm;    
   double *xp;  }
   double *gp, *gm;  
   double **gradg, **trgradg;  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   double age,agelim, cov[NCOVMAX];  {
   int theta;    int i;
   char fileresprob[FILENAMELENGTH];    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
   strcpy(fileresprob,"prob");    double p2[NPARMAX+1];
   strcat(fileresprob,fileres);    int k;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprob);    fx=func(x);
   }    for (k=1; k<=2; k++) {
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);      for (i=1;i<=npar;i++) p2[i]=x[i];
        p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   xp=vector(1,npar);      k1=func(p2)-fx;
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      p2[thetai]=x[thetai]+delti[thetai]/k;
        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   cov[1]=1;      k2=func(p2)-fx;
   for (age=bage; age<=fage; age ++){    
     cov[2]=age;      p2[thetai]=x[thetai]-delti[thetai]/k;
     gradg=matrix(1,npar,1,9);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     trgradg=matrix(1,9,1,npar);      k3=func(p2)-fx;
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      p2[thetai]=x[thetai]-delti[thetai]/k;
          p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     for(theta=1; theta <=npar; theta++){      k4=func(p2)-fx;
       for(i=1; i<=npar; i++)      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  #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);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
      #endif
       k=0;    }
       for(i=1; i<= (nlstate+ndeath); i++){    return res;
         for(j=1; j<=(nlstate+ndeath);j++){  }
            k=k+1;  
           gp[k]=pmmij[i][j];  /************** Inverse of matrix **************/
         }  void ludcmp(double **a, int n, int *indx, double *d) 
       }  { 
     int i,imax,j,k; 
       for(i=1; i<=npar; i++)    double big,dum,sum,temp; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double *vv; 
       
     vv=vector(1,n); 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    *d=1.0; 
       k=0;    for (i=1;i<=n;i++) { 
       for(i=1; i<=(nlstate+ndeath); i++){      big=0.0; 
         for(j=1; j<=(nlstate+ndeath);j++){      for (j=1;j<=n;j++) 
           k=k+1;        if ((temp=fabs(a[i][j])) > big) big=temp; 
           gm[k]=pmmij[i][j];      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         }      vv[i]=1.0/big; 
       }    } 
          for (j=1;j<=n;j++) { 
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)      for (i=1;i<j;i++) { 
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          sum=a[i][j]; 
     }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)      } 
       for(theta=1; theta <=npar; theta++)      big=0.0; 
       trgradg[j][theta]=gradg[theta][j];      for (i=j;i<=n;i++) { 
          sum=a[i][j]; 
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        for (k=1;k<j;k++) 
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
      pmij(pmmij,cov,ncovmodel,x,nlstate);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
      k=0;          imax=i; 
      for(i=1; i<=(nlstate+ndeath); i++){        } 
        for(j=1; j<=(nlstate+ndeath);j++){      } 
          k=k+1;      if (j != imax) { 
          gm[k]=pmmij[i][j];        for (k=1;k<=n;k++) { 
         }          dum=a[imax][k]; 
      }          a[imax][k]=a[j][k]; 
                a[j][k]=dum; 
      /*printf("\n%d ",(int)age);        } 
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        *d = -(*d); 
                vv[imax]=vv[j]; 
       } 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      indx[j]=imax; 
      }*/      if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
   fprintf(ficresprob,"\n%d ",(int)age);        dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      } 
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    } 
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    free_vector(vv,1,n);  /* Doesn't work */
   }  ;
   } 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  void lubksb(double **a, int n, int *indx, double b[]) 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  { 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    int i,ii=0,ip,j; 
 }    double sum; 
  free_vector(xp,1,npar);   
 fclose(ficresprob);    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
 }      sum=b[ip]; 
       b[ip]=b[i]; 
 /******************* Printing html file ***********/      if (ii) 
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   int jj1, k1, i1, cpt;      else if (sum) ii=i; 
   FILE *fichtm;      b[i]=sum; 
   /*char optionfilehtm[FILENAMELENGTH];*/    } 
     for (i=n;i>=1;i--) { 
   strcpy(optionfilehtm,optionfile);      sum=b[i]; 
   strcat(optionfilehtm,".htm");      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      b[i]=sum/a[i][i]; 
     printf("Problem with %s \n",optionfilehtm), exit(0);    } 
   }  } 
   
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71c </font> <hr size=\"2\" color=\"#EC5E5E\">  /************ Frequencies ********************/
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>  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, char strstart[])
   {  /* Some frequencies */
 Total number of observations=%d <br>    
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
 <hr  size=\"2\" color=\"#EC5E5E\">    int first;
 <li>Outputs files<br><br>\n    double ***freq; /* Frequencies */
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    double *pp, **prop;
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    double pos,posprop, k2, dateintsum=0,k2cpt=0;
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    FILE *ficresp;
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    char fileresp[FILENAMELENGTH];
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    pp=vector(1,nlstate);
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    prop=matrix(1,nlstate,iagemin,iagemax+3);
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    strcpy(fileresp,"p");
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>    strcat(fileresp,fileres);
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>    if((ficresp=fopen(fileresp,"w"))==NULL) {
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>      printf("Problem with prevalence resultfile: %s\n", fileresp);
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
        exit(0);
 fprintf(fichtm," <li>Graphs</li><p>");    }
     freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
  m=cptcoveff;    j1=0;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    
     j=cptcoveff;
  jj1=0;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){    first=1;
        jj1++;  
        if (cptcovn > 0) {    for(k1=1; k1<=j;k1++){
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      for(i1=1; i1<=ncodemax[k1];i1++){
          for (cpt=1; cpt<=cptcoveff;cpt++)        j1++;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          scanf("%d", i);*/
        }        for (i=-5; i<=nlstate+ndeath; i++)  
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          for (jk=-5; jk<=nlstate+ndeath; jk++)  
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                for(m=iagemin; m <= iagemax+3; m++)
        for(cpt=1; cpt<nlstate;cpt++){              freq[i][jk][m]=0;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>  
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      for (i=1; i<=nlstate; i++)  
        }        for(m=iagemin; m <= iagemax+3; m++)
     for(cpt=1; cpt<=nlstate;cpt++) {          prop[i][m]=0;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        
 interval) in state (%d): v%s%d%d.gif <br>        dateintsum=0;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          k2cpt=0;
      }        for (i=1; i<=imx; i++) {
      for(cpt=1; cpt<=nlstate;cpt++) {          bool=1;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>          if  (cptcovn>0) {
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            for (z1=1; z1<=cptcoveff; z1++) 
      }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
      fprintf(fichtm,"\n<br>- Total life expectancy by age and                bool=0;
 health expectancies in states (1) and (2): e%s%d.gif<br>          }
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          if (bool==1){
 fprintf(fichtm,"\n</body>");            for(m=firstpass; m<=lastpass; m++){
    }              k2=anint[m][i]+(mint[m][i]/12.);
    }              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
 fclose(fichtm);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
 /******************* Gnuplot file **************/                if (m<lastpass) {
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                   freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;                }
                 
   strcpy(optionfilegnuplot,optionfilefiname);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   strcat(optionfilegnuplot,".plt");                  dateintsum=dateintsum+k2;
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {                  k2cpt++;
     printf("Problem with file %s",optionfilegnuplot);                }
   }                /*}*/
             }
 #ifdef windows          }
     fprintf(ficgp,"cd \"%s\" \n",pathc);        }
 #endif         
 m=pow(2,cptcoveff);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
    fprintf(ficresp, "#Local time at start: %s", strstart);
  /* 1eme*/        if  (cptcovn>0) {
   for (cpt=1; cpt<= nlstate ; cpt ++) {          fprintf(ficresp, "\n#********** Variable "); 
    for (k1=1; k1<= m ; k1 ++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresp, "**********\n#");
 #ifdef windows        }
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);        for(i=1; i<=nlstate;i++) 
 #endif          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 #ifdef unix        fprintf(ficresp, "\n");
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);        
 #endif        for(i=iagemin; i <= iagemax+3; i++){
           if(i==iagemax+3){
 for (i=1; i<= nlstate ; i ++) {            fprintf(ficlog,"Total");
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          }else{
   else fprintf(ficgp," \%%*lf (\%%*lf)");            if(first==1){
 }              first=0;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);              printf("See log file for details...\n");
     for (i=1; i<= nlstate ; i ++) {            }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            fprintf(ficlog,"Age %d", i);
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }          for(jk=1; jk <=nlstate ; jk++){
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
      for (i=1; i<= nlstate ; i ++) {              pp[jk] += freq[jk][m][i]; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(jk=1; jk <=nlstate ; jk++){
 }              for(m=-1, pos=0; m <=0 ; m++)
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));              pos += freq[jk][m][i];
 #ifdef unix            if(pp[jk]>=1.e-10){
 fprintf(ficgp,"\nset ter gif small size 400,300");              if(first==1){
 #endif              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              }
    }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   }            }else{
   /*2 eme*/              if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   for (k1=1; k1<= m ; k1 ++) {              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);            }
              }
     for (i=1; i<= nlstate+1 ; i ++) {  
       k=2*i;          for(jk=1; jk <=nlstate ; jk++){
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       for (j=1; j<= nlstate+1 ; j ++) {              pp[jk] += freq[jk][m][i];
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          }       
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
 }              pos += pp[jk];
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            posprop += prop[jk][i];
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          }
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          for(jk=1; jk <=nlstate ; jk++){
       for (j=1; j<= nlstate+1 ; j ++) {            if(pos>=1.e-5){
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              if(first==1)
         else fprintf(ficgp," \%%*lf (\%%*lf)");                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 }                fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       fprintf(ficgp,"\" t\"\" w l 0,");            }else{
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);              if(first==1)
       for (j=1; j<= nlstate+1 ; j ++) {                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   else fprintf(ficgp," \%%*lf (\%%*lf)");            }
 }              if( i <= iagemax){
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");              if(pos>=1.e-5){
       else fprintf(ficgp,"\" t\"\" w l 0,");                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     }                /*probs[i][jk][j1]= pp[jk]/pos;*/
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   }              }
                else
   /*3eme*/                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
   for (k1=1; k1<= m ; k1 ++) {          }
     for (cpt=1; cpt<= nlstate ; cpt ++) {          
       k=2+nlstate*(cpt-1);          for(jk=-1; jk <=nlstate+ndeath; jk++)
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);            for(m=-1; m <=nlstate+ndeath; m++)
       for (i=1; i< nlstate ; i ++) {              if(freq[jk][m][i] !=0 ) {
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);              if(first==1)
       }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     }              }
     }          if(i <= iagemax)
              fprintf(ficresp,"\n");
   /* CV preval stat */          if(first==1)
     for (k1=1; k1<= m ; k1 ++) {            printf("Others in log...\n");
     for (cpt=1; cpt<nlstate ; cpt ++) {          fprintf(ficlog,"\n");
       k=3;        }
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);      }
     }
       for (i=1; i< nlstate ; i ++)    dateintmean=dateintsum/k2cpt; 
         fprintf(ficgp,"+$%d",k+i+1);   
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    fclose(ficresp);
          free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
       l=3+(nlstate+ndeath)*cpt;    free_vector(pp,1,nlstate);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       for (i=1; i< nlstate ; i ++) {    /* End of Freq */
         l=3+(nlstate+ndeath)*cpt;  }
         fprintf(ficgp,"+$%d",l+i+1);  
       }  /************ Prevalence ********************/
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  {  
     }    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   }         in each health status at the date of interview (if between dateprev1 and dateprev2).
         We still use firstpass and lastpass as another selection.
   /* proba elementaires */    */
    for(i=1,jk=1; i <=nlstate; i++){   
     for(k=1; k <=(nlstate+ndeath); k++){    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
       if (k != i) {    double ***freq; /* Frequencies */
         for(j=1; j <=ncovmodel; j++){    double *pp, **prop;
            double pos,posprop; 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    double  y2; /* in fractional years */
           jk++;    int iagemin, iagemax;
           fprintf(ficgp,"\n");  
         }    iagemin= (int) agemin;
       }    iagemax= (int) agemax;
     }    /*pp=vector(1,nlstate);*/
     }    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     for(jk=1; jk <=m; jk++) {    j1=0;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);    
    i=1;    j=cptcoveff;
    for(k2=1; k2<=nlstate; k2++) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      k3=i;    
      for(k=1; k<=(nlstate+ndeath); k++) {    for(k1=1; k1<=j;k1++){
        if (k != k2){      for(i1=1; i1<=ncodemax[k1];i1++){
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        j1++;
 ij=1;        
         for(j=3; j <=ncovmodel; j++) {        for (i=1; i<=nlstate; i++)  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          for(m=iagemin; m <= iagemax+3; m++)
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            prop[i][m]=0.0;
             ij++;       
           }        for (i=1; i<=imx; i++) { /* Each individual */
           else          bool=1;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          if  (cptcovn>0) {
         }            for (z1=1; z1<=cptcoveff; z1++) 
           fprintf(ficgp,")/(1");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                        bool=0;
         for(k1=1; k1 <=nlstate; k1++){            } 
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);          if (bool==1) { 
 ij=1;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
           for(j=3; j <=ncovmodel; j++){              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
             ij++;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
           else                if (s[m][i]>0 && s[m][i]<=nlstate) { 
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
           }                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
           fprintf(ficgp,")");                  prop[s[m][i]][iagemax+3] += weight[i]; 
         }                } 
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);              }
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");            } /* end selection of waves */
         i=i+ncovmodel;          }
        }        }
      }        for(i=iagemin; i <= iagemax+3; i++){  
    }          
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
    }            posprop += prop[jk][i]; 
              } 
   fclose(ficgp);  
 }  /* end gnuplot */          for(jk=1; jk <=nlstate ; jk++){     
             if( i <=  iagemax){ 
               if(posprop>=1.e-5){ 
 /*************** Moving average **************/                probs[i][jk][j1]= prop[jk][i]/posprop;
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){              } 
             } 
   int i, cpt, cptcod;          }/* end jk */ 
     for (agedeb=agemin; agedeb<=fage; agedeb++)        }/* end i */ 
       for (i=1; i<=nlstate;i++)      } /* end i1 */
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    } /* end k1 */
           mobaverage[(int)agedeb][i][cptcod]=0.;    
        /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){    /*free_vector(pp,1,nlstate);*/
       for (i=1; i<=nlstate;i++){    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  }  /* End of prevalence */
           for (cpt=0;cpt<=4;cpt++){  
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  /************* Waves Concatenation ***************/
           }  
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  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)
         }  {
       }    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     }       Death is a valid wave (if date is known).
           mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
 }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
        */
 /************** Forecasting ******************/  
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){    int i, mi, m;
      /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;       double sum=0., jmean=0.;*/
   int *popage;    int first;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    int j, k=0,jk, ju, jl;
   double *popeffectif,*popcount;    double sum=0.;
   double ***p3mat;    first=0;
   char fileresf[FILENAMELENGTH];    jmin=1e+5;
     jmax=-1;
  agelim=AGESUP;    jmean=0.;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    for(i=1; i<=imx; i++){
       mi=0;
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      m=firstpass;
        while(s[m][i] <= nlstate){
          if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   strcpy(fileresf,"f");          mw[++mi][i]=m;
   strcat(fileresf,fileres);        if(m >=lastpass)
   if((ficresf=fopen(fileresf,"w"))==NULL) {          break;
     printf("Problem with forecast resultfile: %s\n", fileresf);        else
   }          m++;
   printf("Computing forecasting: result on file '%s' \n", fileresf);      }/* end while */
       if (s[m][i] > nlstate){
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        mi++;     /* Death is another wave */
         /* if(mi==0)  never been interviewed correctly before death */
   if (mobilav==1) {           /* Only death is a correct wave */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        mw[mi][i]=m;
     movingaverage(agedeb, fage, agemin, mobaverage);      }
   }  
       wav[i]=mi;
   stepsize=(int) (stepm+YEARM-1)/YEARM;      if(mi==0){
   if (stepm<=12) stepsize=1;        nbwarn++;
          if(first==0){
   agelim=AGESUP;          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
            first=1;
   hstepm=1;        }
   hstepm=hstepm/stepm;        if(first==1){
   yp1=modf(dateintmean,&yp);          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
   anprojmean=yp;        }
   yp2=modf((yp1*12),&yp);      } /* end mi==0 */
   mprojmean=yp;    } /* End individuals */
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;    for(i=1; i<=imx; i++){
   if(jprojmean==0) jprojmean=1;      for(mi=1; mi<wav[i];mi++){
   if(mprojmean==0) jprojmean=1;        if (stepm <=0)
            dh[mi][i]=1;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        else{
            if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   for(cptcov=1;cptcov<=i2;cptcov++){            if (agedc[i] < 2*AGESUP) {
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       k=k+1;              if(j==0) j=1;  /* Survives at least one month after exam */
       fprintf(ficresf,"\n#******");              else if(j<0){
       for(j=1;j<=cptcoveff;j++) {                nberr++;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       }                j=1; /* Temporary Dangerous patch */
       fprintf(ficresf,"******\n");                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. You MUST fix the contradiction between dates.\n",stepm);
       fprintf(ficresf,"# StartingAge FinalAge");                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]);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);                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. You MUST fix the contradiction between dates.\n",stepm);
                    }
                    k=k+1;
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {              if (j >= jmax) jmax=j;
         fprintf(ficresf,"\n");              if (j <= jmin) jmin=j;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);                sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            }
           nhstepm = nhstepm/hstepm;          }
                    else{
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
           oldm=oldms;savm=savms;  /*        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]); */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
                    k=k+1;
           for (h=0; h<=nhstepm; h++){            if (j >= jmax) jmax=j;
             if (h==(int) (calagedate+YEARM*cpt)) {            else if (j <= jmin)jmin=j;
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             }            /*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]);*/
             for(j=1; j<=nlstate+ndeath;j++) {            if(j<0){
               kk1=0.;kk2=0;              nberr++;
               for(i=1; i<=nlstate;i++) {                            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]);
                 if (mobilav==1)              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]);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            }
                 else {            sum=sum+j;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          }
                 }          jk= j/stepm;
                          jl= j -jk*stepm;
               }          ju= j -(jk+1)*stepm;
               if (h==(int)(calagedate+12*cpt)){          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
                 fprintf(ficresf," %.3f", kk1);            if(jl==0){
                                      dh[mi][i]=jk;
               }              bh[mi][i]=0;
             }            }else{ /* We want a negative bias in order to only have interpolation ie
           }                    * at the price of an extra matrix product in likelihood */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              dh[mi][i]=jk+1;
         }              bh[mi][i]=ju;
       }            }
     }          }else{
   }            if(jl <= -ju){
                      dh[mi][i]=jk;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
   fclose(ficresf);                                   */
 }            }
 /************** Forecasting ******************/            else{
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){              dh[mi][i]=jk+1;
                bh[mi][i]=ju;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            }
   int *popage;            if(dh[mi][i]==0){
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;              dh[mi][i]=1; /* At least one step */
   double *popeffectif,*popcount;              bh[mi][i]=ju; /* At least one step */
   double ***p3mat,***tabpop,***tabpopprev;              /*  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);*/
   char filerespop[FILENAMELENGTH];            }
           } /* end if mle */
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      } /* end wave */
   agelim=AGESUP;    }
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    jmean=sum/k;
      printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     }
    
   strcpy(filerespop,"pop");  /*********** Tricode ****************************/
   strcat(filerespop,fileres);  void tricode(int *Tvar, int **nbcode, int imx)
   if((ficrespop=fopen(filerespop,"w"))==NULL) {  {
     printf("Problem with forecast resultfile: %s\n", filerespop);    
   }    int Ndum[20],ij=1, k, j, i, maxncov=19;
   printf("Computing forecasting: result on file '%s' \n", filerespop);    int cptcode=0;
     cptcoveff=0; 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;   
     for (k=0; k<maxncov; k++) Ndum[k]=0;
   if (mobilav==1) {    for (k=1; k<=7; k++) ncodemax[k]=0;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     movingaverage(agedeb, fage, agemin, mobaverage);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
   stepsize=(int) (stepm+YEARM-1)/YEARM;        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   if (stepm<=12) stepsize=1;        Ndum[ij]++; /*store the modality */
          /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   agelim=AGESUP;        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                                           Tvar[j]. If V=sex and male is 0 and 
   hstepm=1;                                         female is 1, then  cptcode=1.*/
   hstepm=hstepm/stepm;      }
    
   if (popforecast==1) {      for (i=0; i<=cptcode; i++) {
     if((ficpop=fopen(popfile,"r"))==NULL) {        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 */
       printf("Problem with population file : %s\n",popfile);exit(0);      }
     }  
     popage=ivector(0,AGESUP);      ij=1; 
     popeffectif=vector(0,AGESUP);      for (i=1; i<=ncodemax[j]; i++) {
     popcount=vector(0,AGESUP);        for (k=0; k<= maxncov; k++) {
              if (Ndum[k] != 0) {
     i=1;              nbcode[Tvar[j]][ij]=k; 
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;            /* 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; */
                
     imx=i;            ij++;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          }
   }          if (ij > ncodemax[j]) break; 
         }  
   for(cptcov=1;cptcov<=i2;cptcov++){      } 
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    }  
       k=k+1;  
       fprintf(ficrespop,"\n#******");   for (k=0; k< maxncov; k++) Ndum[k]=0;
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   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.*/
       fprintf(ficrespop,"******\n");     ij=Tvar[i];
       fprintf(ficrespop,"# Age");     Ndum[ij]++;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);   }
       if (popforecast==1)  fprintf(ficrespop," [Population]");  
         ij=1;
       for (cpt=0; cpt<=0;cpt++) {   for (i=1; i<= maxncov; i++) {
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);       if((Ndum[i]!=0) && (i<=ncovcol)){
               Tvaraff[ij]=i; /*For printing */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){       ij++;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);     }
           nhstepm = nhstepm/hstepm;   }
             
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   cptcoveff=ij-1; /*Number of simple covariates*/
           oldm=oldms;savm=savms;  }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
          /*********** Health Expectancies ****************/
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {  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,char strstart[] )
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  
             }  {
             for(j=1; j<=nlstate+ndeath;j++) {    /* Health expectancies */
               kk1=0.;kk2=0;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
               for(i=1; i<=nlstate;i++) {                  double age, agelim, hf;
                 if (mobilav==1)    double ***p3mat,***varhe;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    double **dnewm,**doldm;
                 else {    double *xp;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    double **gp, **gm;
                 }    double ***gradg, ***trgradg;
               }    int theta;
               if (h==(int)(calagedate+12*cpt)){  
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
                   /*fprintf(ficrespop," %.3f", kk1);    xp=vector(1,npar);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    dnewm=matrix(1,nlstate*nlstate,1,npar);
               }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
             }    
             for(i=1; i<=nlstate;i++){    fprintf(ficreseij,"# Local time at start: %s", strstart);
               kk1=0.;    fprintf(ficreseij,"# Health expectancies\n");
                 for(j=1; j<=nlstate;j++){    fprintf(ficreseij,"# Age");
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    for(i=1; i<=nlstate;i++)
                 }      for(j=1; j<=nlstate;j++)
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];        fprintf(ficreseij," %1d-%1d (SE)",i,j);
             }    fprintf(ficreseij,"\n");
   
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    if(estepm < stepm){
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      printf ("Problem %d lower than %d\n",estepm, stepm);
           }    }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    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
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {     * to the curvature of the survival function. If, for the same date, we 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);       * estimate the model with stepm=1 month, we can keep estepm to 24 months
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){     * to compare the new estimate of Life expectancy with the same linear 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);     * hypothesis. A more precise result, taking into account a more precise
           nhstepm = nhstepm/hstepm;     * curvature will be obtained if estepm is as small as stepm. */
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* For example we decided to compute the life expectancy with the smallest unit */
           oldm=oldms;savm=savms;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         nhstepm is the number of hstepm from age to agelim 
           for (h=0; h<=nhstepm; h++){       nstepm is the number of stepm from age to agelin. 
             if (h==(int) (calagedate+YEARM*cpt)) {       Look at hpijx to understand the reason of that which relies in memory size
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);       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(j=1; j<=nlstate+ndeath;j++) {       survival function given by stepm (the optimization length). Unfortunately it
               kk1=0.;kk2=0;       means that if the survival funtion is printed only each two years of age and if
               for(i=1; i<=nlstate;i++) {                     you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];           results. So we changed our mind and took the option of the best precision.
               }    */
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
             }  
           }    agelim=AGESUP;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    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 */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   if (popforecast==1) {      gp=matrix(0,nhstepm,1,nlstate*nlstate);
     free_ivector(popage,0,AGESUP);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
     free_vector(popeffectif,0,AGESUP);  
     free_vector(popcount,0,AGESUP);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   
   fclose(ficrespop);  
 }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
 /***********************************************/      /* Computing  Variances of health expectancies */
 /**************** Main Program *****************/  
 /***********************************************/       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
 int main(int argc, char *argv[])          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 {        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    
   double agedeb, agefin,hf;        cptj=0;
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;        for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
   double fret;            cptj=cptj+1;
   double **xi,tmp,delta;            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
               gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   double dum; /* Dummy variable */            }
   double ***p3mat;          }
   int *indx;        }
   char line[MAXLINE], linepar[MAXLINE];       
   char title[MAXLINE];       
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];        for(i=1; i<=npar; i++) 
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];        
         cptj=0;
   char filerest[FILENAMELENGTH];        for(j=1; j<= nlstate; j++){
   char fileregp[FILENAMELENGTH];          for(i=1;i<=nlstate;i++){
   char popfile[FILENAMELENGTH];            cptj=cptj+1;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   int firstobs=1, lastobs=10;  
   int sdeb, sfin; /* Status at beginning and end */              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   int c,  h , cpt,l;            }
   int ju,jl, mi;          }
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;        }
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        for(j=1; j<= nlstate*nlstate; j++)
   int mobilav=0,popforecast=0;          for(h=0; h<=nhstepm-1; h++){
   int hstepm, nhstepm;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;          }
        } 
   double bage, fage, age, agelim, agebase;     
   double ftolpl=FTOL;  /* End theta */
   double **prlim;  
   double *severity;       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   double ***param; /* Matrix of parameters */  
   double  *p;       for(h=0; h<=nhstepm-1; h++)
   double **matcov; /* Matrix of covariance */        for(j=1; j<=nlstate*nlstate;j++)
   double ***delti3; /* Scale */          for(theta=1; theta <=npar; theta++)
   double *delti; /* Scale */            trgradg[h][j][theta]=gradg[h][theta][j];
   double ***eij, ***vareij;       
   double **varpl; /* Variances of prevalence limits by age */  
   double *epj, vepp;       for(i=1;i<=nlstate*nlstate;i++)
   double kk1, kk2;        for(j=1;j<=nlstate*nlstate;j++)
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;          varhe[i][j][(int)age] =0.;
    
        printf("%d|",(int)age);fflush(stdout);
   char version[80]="Imach version 0.71c, March 2002, INED-EUROREVES ";       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   char *alph[]={"a","a","b","c","d","e"}, str[4];       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   char z[1]="c", occ;          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
 #include <sys/time.h>          for(i=1;i<=nlstate*nlstate;i++)
 #include <time.h>            for(j=1;j<=nlstate*nlstate;j++)
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
          }
   /* long total_usecs;      }
   struct timeval start_time, end_time;      /* Computing expectancies */
        for(i=1; i<=nlstate;i++)
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        for(j=1; j<=nlstate;j++)
           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;
   printf("\n%s",version);            
   if(argc <=1){  /* 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]);*/
     printf("\nEnter the parameter file name: ");  
     scanf("%s",pathtot);          }
   }  
   else{      fprintf(ficreseij,"%3.0f",age );
     strcpy(pathtot,argv[1]);      cptj=0;
   }      for(i=1; i<=nlstate;i++)
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        for(j=1; j<=nlstate;j++){
   /*cygwin_split_path(pathtot,path,optionfile);          cptj++;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   /* cutv(path,optionfile,pathtot,'\\');*/        }
       fprintf(ficreseij,"\n");
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);     
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   chdir(path);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   replace(pathc,path);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
 /*-------- arguments in the command line --------*/      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }
   strcpy(fileres,"r");    printf("\n");
   strcat(fileres, optionfilefiname);    fprintf(ficlog,"\n");
   strcat(fileres,".txt");    /* Other files have txt extension */  
     free_vector(xp,1,npar);
   /*---------arguments file --------*/    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     printf("Problem with optionfile %s\n",optionfile);  }
     goto end;  
   }  /************ 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, char strstart[])
   strcpy(filereso,"o");  {
   strcat(filereso,fileres);    /* Variance of health expectancies */
   if((ficparo=fopen(filereso,"w"))==NULL) {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    /* double **newm;*/
   }    double **dnewm,**doldm;
     double **dnewmp,**doldmp;
   /* Reads comments: lines beginning with '#' */    int i, j, nhstepm, hstepm, h, nstepm ;
   while((c=getc(ficpar))=='#' && c!= EOF){    int k, cptcode;
     ungetc(c,ficpar);    double *xp;
     fgets(line, MAXLINE, ficpar);    double **gp, **gm;  /* for var eij */
     puts(line);    double ***gradg, ***trgradg; /*for var eij */
     fputs(line,ficparo);    double **gradgp, **trgradgp; /* for var p point j */
   }    double *gpp, *gmp; /* for var p point j */
   ungetc(c,ficpar);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    double age,agelim, hf;
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    double ***mobaverage;
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    int theta;
 while((c=getc(ficpar))=='#' && c!= EOF){    char digit[4];
     ungetc(c,ficpar);    char digitp[25];
     fgets(line, MAXLINE, ficpar);  
     puts(line);    char fileresprobmorprev[FILENAMELENGTH];
     fputs(line,ficparo);  
   }    if(popbased==1){
   ungetc(c,ficpar);      if(mobilav!=0)
          strcpy(digitp,"-populbased-mobilav-");
          else strcpy(digitp,"-populbased-nomobil-");
   covar=matrix(0,NCOVMAX,1,n);    }
   cptcovn=0;    else 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      strcpy(digitp,"-stablbased-");
   
   ncovmodel=2+cptcovn;    if (mobilav!=0) {
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   /* Read guess parameters */        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   /* Reads comments: lines beginning with '#' */        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   while((c=getc(ficpar))=='#' && c!= EOF){      }
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);  
     puts(line);    strcpy(fileresprobmorprev,"prmorprev"); 
     fputs(line,ficparo);    sprintf(digit,"%-d",ij);
   }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   ungetc(c,ficpar);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
      strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    strcat(fileresprobmorprev,fileres);
     for(i=1; i <=nlstate; i++)    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     for(j=1; j <=nlstate+ndeath-1; j++){      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fscanf(ficpar,"%1d%1d",&i1,&j1);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficparo,"%1d%1d",i1,j1);    }
       printf("%1d%1d",i,j);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       for(k=1; k<=ncovmodel;k++){   
         fscanf(ficpar," %lf",&param[i][j][k]);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         printf(" %lf",param[i][j][k]);    fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
         fprintf(ficparo," %lf",param[i][j][k]);    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(ficresprobmorprev,"# Age cov=%-d",ij);
       fscanf(ficpar,"\n");    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       printf("\n");      fprintf(ficresprobmorprev," p.%-d SE",j);
       fprintf(ficparo,"\n");      for(i=1; i<=nlstate;i++)
     }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
      }  
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
   p=param[1][1];    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
      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");
   /* Reads comments: lines beginning with '#' */    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   while((c=getc(ficpar))=='#' && c!= EOF){  /*   } */
     ungetc(c,ficpar);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     fgets(line, MAXLINE, ficpar);   fprintf(ficresvij, "#Local time at start: %s", strstart);
     puts(line);    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");
     fputs(line,ficparo);    fprintf(ficresvij,"# Age");
   }    for(i=1; i<=nlstate;i++)
   ungetc(c,ficpar);      for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    fprintf(ficresvij,"\n");
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  
   for(i=1; i <=nlstate; i++){    xp=vector(1,npar);
     for(j=1; j <=nlstate+ndeath-1; j++){    dnewm=matrix(1,nlstate,1,npar);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    doldm=matrix(1,nlstate,1,nlstate);
       printf("%1d%1d",i,j);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
       fprintf(ficparo,"%1d%1d",i1,j1);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar,"%le",&delti3[i][j][k]);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
         printf(" %le",delti3[i][j][k]);    gpp=vector(nlstate+1,nlstate+ndeath);
         fprintf(ficparo," %le",delti3[i][j][k]);    gmp=vector(nlstate+1,nlstate+ndeath);
       }    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       fscanf(ficpar,"\n");    
       printf("\n");    if(estepm < stepm){
       fprintf(ficparo,"\n");      printf ("Problem %d lower than %d\n",estepm, stepm);
     }    }
   }    else  hstepm=estepm;   
   delti=delti3[1][1];    /* For example we decided to compute the life expectancy with the smallest unit */
      /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   /* Reads comments: lines beginning with '#' */       nhstepm is the number of hstepm from age to agelim 
   while((c=getc(ficpar))=='#' && c!= EOF){       nstepm is the number of stepm from age to agelin. 
     ungetc(c,ficpar);       Look at hpijx to understand the reason of that which relies in memory size
     fgets(line, MAXLINE, ficpar);       and note for a fixed period like k years */
     puts(line);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     fputs(line,ficparo);       survival function given by stepm (the optimization length). Unfortunately it
   }       means that if the survival funtion is printed every two years of age and if
   ungetc(c,ficpar);       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.
   matcov=matrix(1,npar,1,npar);    */
   for(i=1; i <=npar; i++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     fscanf(ficpar,"%s",&str);    agelim = AGESUP;
     printf("%s",str);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     fprintf(ficparo,"%s",str);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     for(j=1; j <=i; j++){      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       fscanf(ficpar," %le",&matcov[i][j]);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       printf(" %.5le",matcov[i][j]);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       fprintf(ficparo," %.5le",matcov[i][j]);      gp=matrix(0,nhstepm,1,nlstate);
     }      gm=matrix(0,nhstepm,1,nlstate);
     fscanf(ficpar,"\n");  
     printf("\n");  
     fprintf(ficparo,"\n");      for(theta=1; theta <=npar; theta++){
   }        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   for(i=1; i <=npar; i++)          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     for(j=i+1;j<=npar;j++)        }
       matcov[i][j]=matcov[j][i];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
            prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   printf("\n");  
         if (popbased==1) {
           if(mobilav ==0){
     /*-------- Rewriting paramater file ----------*/            for(i=1; i<=nlstate;i++)
      strcpy(rfileres,"r");    /* "Rparameterfile */              prlim[i][i]=probs[(int)age][i][ij];
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/          }else{ /* mobilav */ 
      strcat(rfileres,".");    /* */            for(i=1; i<=nlstate;i++)
      strcat(rfileres,optionfilext);    /* Other files have txt extension */              prlim[i][i]=mobaverage[(int)age][i][ij];
     if((ficres =fopen(rfileres,"w"))==NULL) {          }
       printf("Problem writing new parameter file: %s\n", fileres);goto end;        }
     }    
     fprintf(ficres,"#%s\n",version);        for(j=1; j<= nlstate; j++){
              for(h=0; h<=nhstepm; h++){
     /*-------- data file ----------*/            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     if((fic=fopen(datafile,"r"))==NULL)    {              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
       printf("Problem with datafile: %s\n", datafile);goto end;          }
     }        }
         /* This for computing probability of death (h=1 means
     n= lastobs;           computed over hstepm matrices product = hstepm*stepm months) 
     severity = vector(1,maxwav);           as a weighted average of prlim.
     outcome=imatrix(1,maxwav+1,1,n);        */
     num=ivector(1,n);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     moisnais=vector(1,n);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     annais=vector(1,n);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     moisdc=vector(1,n);        }    
     andc=vector(1,n);        /* end probability of death */
     agedc=vector(1,n);  
     cod=ivector(1,n);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     weight=vector(1,n);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     mint=matrix(1,maxwav,1,n);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     anint=matrix(1,maxwav,1,n);   
     s=imatrix(1,maxwav+1,1,n);        if (popbased==1) {
     adl=imatrix(1,maxwav+1,1,n);              if(mobilav ==0){
     tab=ivector(1,NCOVMAX);            for(i=1; i<=nlstate;i++)
     ncodemax=ivector(1,8);              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
     i=1;            for(i=1; i<=nlstate;i++)
     while (fgets(line, MAXLINE, fic) != NULL)    {              prlim[i][i]=mobaverage[(int)age][i][ij];
       if ((i >= firstobs) && (i <=lastobs)) {          }
                }
         for (j=maxwav;j>=1;j--){  
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        for(j=1; j<= nlstate; j++){
           strcpy(line,stra);          for(h=0; h<=nhstepm; h++){
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
         }          }
                }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        /* This for computing probability of death (h=1 means
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
         for (j=ncov;j>=1;j--){        }    
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        /* end probability of death */
         }  
         num[i]=atol(stra);        for(j=1; j<= nlstate; j++) /* vareij */
                  for(h=0; h<=nhstepm; h++){
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           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;}*/          }
   
         i=i+1;        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       }          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     }        }
     /* printf("ii=%d", ij);  
        scanf("%d",i);*/      } /* End theta */
   imx=i-1; /* Number of individuals */  
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   /* for (i=1; i<=imx; i++){  
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      for(h=0; h<=nhstepm; h++) /* veij */
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;        for(j=1; j<=nlstate;j++)
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          for(theta=1; theta <=npar; theta++)
     }            trgradg[h][j][theta]=gradg[h][theta][j];
   
     for (i=1; i<=imx; i++)      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/        for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
   /* Calculation of the number of parameter from char model*/    
   Tvar=ivector(1,15);  
   Tprod=ivector(1,15);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   Tvaraff=ivector(1,15);      for(i=1;i<=nlstate;i++)
   Tvard=imatrix(1,15,1,2);        for(j=1;j<=nlstate;j++)
   Tage=ivector(1,15);                vareij[i][j][(int)age] =0.;
      
   if (strlen(model) >1){      for(h=0;h<=nhstepm;h++){
     j=0, j1=0, k1=1, k2=1;        for(k=0;k<=nhstepm;k++){
     j=nbocc(model,'+');          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     j1=nbocc(model,'*');          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
     cptcovn=j+1;          for(i=1;i<=nlstate;i++)
     cptcovprod=j1;            for(j=1;j<=nlstate;j++)
                  vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
            }
     strcpy(modelsav,model);      }
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    
       printf("Error. Non available option model=%s ",model);      /* pptj */
       goto end;      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
     }      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
          for(j=nlstate+1;j<=nlstate+ndeath;j++)
     for(i=(j+1); i>=1;i--){        for(i=nlstate+1;i<=nlstate+ndeath;i++)
       cutv(stra,strb,modelsav,'+');          varppt[j][i]=doldmp[j][i];
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      /* end ppptj */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      /*  x centered again */
       /*scanf("%d",i);*/      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       if (strchr(strb,'*')) {      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
         cutv(strd,strc,strb,'*');   
         if (strcmp(strc,"age")==0) {      if (popbased==1) {
           cptcovprod--;        if(mobilav ==0){
           cutv(strb,stre,strd,'V');          for(i=1; i<=nlstate;i++)
           Tvar[i]=atoi(stre);            prlim[i][i]=probs[(int)age][i][ij];
           cptcovage++;        }else{ /* mobilav */ 
             Tage[cptcovage]=i;          for(i=1; i<=nlstate;i++)
             /*printf("stre=%s ", stre);*/            prlim[i][i]=mobaverage[(int)age][i][ij];
         }        }
         else if (strcmp(strd,"age")==0) {      }
           cptcovprod--;               
           cutv(strb,stre,strc,'V');      /* This for computing probability of death (h=1 means
           Tvar[i]=atoi(stre);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           cptcovage++;         as a weighted average of prlim.
           Tage[cptcovage]=i;      */
         }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         else {        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           cutv(strb,stre,strc,'V');          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           Tvar[i]=ncov+k1;      }    
           cutv(strb,strc,strd,'V');      /* end probability of death */
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
           Tvard[k1][2]=atoi(stre);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           Tvar[cptcovn+k2]=Tvard[k1][1];        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        for(i=1; i<=nlstate;i++){
           for (k=1; k<=lastobs;k++)          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        }
           k1++;      } 
           k2=k2+2;      fprintf(ficresprobmorprev,"\n");
         }  
       }      fprintf(ficresvij,"%.0f ",age );
       else {      for(i=1; i<=nlstate;i++)
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        for(j=1; j<=nlstate;j++){
        /*  scanf("%d",i);*/          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       cutv(strd,strc,strb,'V');        }
       Tvar[i]=atoi(strc);      fprintf(ficresvij,"\n");
       }      free_matrix(gp,0,nhstepm,1,nlstate);
       strcpy(modelsav,stra);        free_matrix(gm,0,nhstepm,1,nlstate);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
         scanf("%d",i);*/      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 }    } /* End age */
      free_vector(gpp,nlstate+1,nlstate+ndeath);
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    free_vector(gmp,nlstate+1,nlstate+ndeath);
   printf("cptcovprod=%d ", cptcovprod);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   scanf("%d ",i);*/    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fclose(fic);    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 */
     /*  if(mle==1){*/    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     if (weightopt != 1) { /* Maximisation without weights*/  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
       for(i=1;i<=n;i++) weight[i]=1.0;  /*   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); */
     /*-calculation of age at interview from date of interview and age at death -*/    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     agev=matrix(1,maxwav,1,imx);    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));
    for (i=1; i<=imx; i++)    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
      for(m=2; (m<= maxwav); m++)    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);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    /*  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);
          anint[m][i]=9999;  */
          s[m][i]=-1;  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
        }    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
      
     for (i=1; i<=imx; i++)  {    free_vector(xp,1,npar);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    free_matrix(doldm,1,nlstate,1,nlstate);
       for(m=1; (m<= maxwav); m++){    free_matrix(dnewm,1,nlstate,1,npar);
         if(s[m][i] >0){    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           if (s[m][i] == nlstate+1) {    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
             if(agedc[i]>0)    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
               if(moisdc[i]!=99 && andc[i]!=9999)    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
               agev[m][i]=agedc[i];    fclose(ficresprobmorprev);
             else {    fflush(ficgp);
               if (andc[i]!=9999){    fflush(fichtm); 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  }  /* end varevsij */
               agev[m][i]=-1;  
               }  /************ 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, char strstart[])
           }  {
           else if(s[m][i] !=9){ /* Should no more exist */    /* Variance of prevalence limit */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
             if(mint[m][i]==99 || anint[m][i]==9999)    double **newm;
               agev[m][i]=1;    double **dnewm,**doldm;
             else if(agev[m][i] <agemin){    int i, j, nhstepm, hstepm;
               agemin=agev[m][i];    int k, cptcode;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    double *xp;
             }    double *gp, *gm;
             else if(agev[m][i] >agemax){    double **gradg, **trgradg;
               agemax=agev[m][i];    double age,agelim;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    int theta;
             }    fprintf(ficresvpl, "#Local time at start: %s", strstart); 
             /*agev[m][i]=anint[m][i]-annais[i];*/    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
             /*   agev[m][i] = age[i]+2*m;*/    fprintf(ficresvpl,"# Age");
           }    for(i=1; i<=nlstate;i++)
           else { /* =9 */        fprintf(ficresvpl," %1d-%1d",i,i);
             agev[m][i]=1;    fprintf(ficresvpl,"\n");
             s[m][i]=-1;  
           }    xp=vector(1,npar);
         }    dnewm=matrix(1,nlstate,1,npar);
         else /*= 0 Unknown */    doldm=matrix(1,nlstate,1,nlstate);
           agev[m][i]=1;    
       }    hstepm=1*YEARM; /* Every year of age */
        hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     }    agelim = AGESUP;
     for (i=1; i<=imx; i++)  {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       for(m=1; (m<= maxwav); m++){      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         if (s[m][i] > (nlstate+ndeath)) {      if (stepm >= YEARM) hstepm=1;
           printf("Error: Wrong value in nlstate or ndeath\n");        nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           goto end;      gradg=matrix(1,npar,1,nlstate);
         }      gp=vector(1,nlstate);
       }      gm=vector(1,nlstate);
     }  
       for(theta=1; theta <=npar; theta++){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
     free_vector(severity,1,maxwav);        }
     free_imatrix(outcome,1,maxwav+1,1,n);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     free_vector(moisnais,1,n);        for(i=1;i<=nlstate;i++)
     free_vector(annais,1,n);          gp[i] = prlim[i][i];
     /* free_matrix(mint,1,maxwav,1,n);      
        free_matrix(anint,1,maxwav,1,n);*/        for(i=1; i<=npar; i++) /* Computes gradient */
     free_vector(moisdc,1,n);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     free_vector(andc,1,n);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
              gm[i] = prlim[i][i];
     wav=ivector(1,imx);  
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        for(i=1;i<=nlstate;i++)
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
          } /* End theta */
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
       Tcode=ivector(1,100);        for(theta=1; theta <=npar; theta++)
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          trgradg[j][theta]=gradg[theta][j];
       ncodemax[1]=1;  
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      for(i=1;i<=nlstate;i++)
              varpl[i][(int)age] =0.;
    codtab=imatrix(1,100,1,10);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
    h=0;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
    m=pow(2,cptcoveff);      for(i=1;i<=nlstate;i++)
          varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){      fprintf(ficresvpl,"%.0f ",age );
        for(j=1; j <= ncodemax[k]; j++){      for(i=1; i<=nlstate;i++)
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
            h++;      fprintf(ficresvpl,"\n");
            if (h>m) h=1;codtab[h][k]=j;      free_vector(gp,1,nlstate);
          }      free_vector(gm,1,nlstate);
        }      free_matrix(gradg,1,npar,1,nlstate);
      }      free_matrix(trgradg,1,nlstate,1,npar);
    }    } /* End age */
   
     free_vector(xp,1,npar);
    /*for(i=1; i <=m ;i++){    free_matrix(doldm,1,nlstate,1,npar);
      for(k=1; k <=cptcovn; k++){    free_matrix(dnewm,1,nlstate,1,nlstate);
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);  
      }  }
      printf("\n");  
    }  /************ Variance of one-step probabilities  ******************/
    scanf("%d",i);*/  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
      {
    /* Calculates basic frequencies. Computes observed prevalence at single age    int i, j=0,  i1, k1, l1, t, tj;
        and prints on file fileres'p'. */    int k2, l2, j1,  z1;
     int k=0,l, cptcode;
        int first=1, first1;
        double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double **dnewm,**doldm;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double *xp;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double *gp, *gm;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double **gradg, **trgradg;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    double **mu;
          double age,agelim, cov[NCOVMAX];
     /* For Powell, parameters are in a vector p[] starting at p[1]    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    int theta;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     if(mle==1){    char fileresprobcor[FILENAMELENGTH];
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }    double ***varpij;
      
     /*--------- results files --------------*/    strcpy(fileresprob,"prob"); 
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);    strcat(fileresprob,fileres);
      if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
    jk=1;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
    fprintf(ficres,"# Parameters\n");    }
    printf("# Parameters\n");    strcpy(fileresprobcov,"probcov"); 
    for(i=1,jk=1; i <=nlstate; i++){    strcat(fileresprobcov,fileres);
      for(k=1; k <=(nlstate+ndeath); k++){    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
        if (k != i)      printf("Problem with resultfile: %s\n", fileresprobcov);
          {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
            printf("%d%d ",i,k);    }
            fprintf(ficres,"%1d%1d ",i,k);    strcpy(fileresprobcor,"probcor"); 
            for(j=1; j <=ncovmodel; j++){    strcat(fileresprobcor,fileres);
              printf("%f ",p[jk]);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
              fprintf(ficres,"%f ",p[jk]);      printf("Problem with resultfile: %s\n", fileresprobcor);
              jk++;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
            }    }
            printf("\n");    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
            fprintf(ficres,"\n");    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
          }    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      }    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
    }    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
  if(mle==1){    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     /* Computing hessian and covariance matrix */    fprintf(ficresprob, "#Local time at start: %s", strstart);
     ftolhess=ftol; /* Usually correct */    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     hesscov(matcov, p, npar, delti, ftolhess, func);    fprintf(ficresprob,"# Age");
  }    fprintf(ficresprobcov, "#Local time at start: %s", strstart);
     fprintf(ficres,"# Scales\n");    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     printf("# Scales\n");    fprintf(ficresprobcov,"# Age");
      for(i=1,jk=1; i <=nlstate; i++){    fprintf(ficresprobcor, "#Local time at start: %s", strstart);
       for(j=1; j <=nlstate+ndeath; j++){    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
         if (j!=i) {    fprintf(ficresprobcov,"# Age");
           fprintf(ficres,"%1d%1d",i,j);  
           printf("%1d%1d",i,j);  
           for(k=1; k<=ncovmodel;k++){    for(i=1; i<=nlstate;i++)
             printf(" %.5e",delti[jk]);      for(j=1; j<=(nlstate+ndeath);j++){
             fprintf(ficres," %.5e",delti[jk]);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
             jk++;        fprintf(ficresprobcov," p%1d-%1d ",i,j);
           }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
           printf("\n");      }  
           fprintf(ficres,"\n");   /* fprintf(ficresprob,"\n");
         }    fprintf(ficresprobcov,"\n");
       }    fprintf(ficresprobcor,"\n");
      }   */
       xp=vector(1,npar);
     k=1;    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     fprintf(ficres,"# Covariance\n");    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     printf("# Covariance\n");    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     for(i=1;i<=npar;i++){    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
       /*  if (k>nlstate) k=1;    first=1;
       i1=(i-1)/(ncovmodel*nlstate)+1;    fprintf(ficgp,"\n# Routine varprob");
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       printf("%s%d%d",alph[k],i1,tab[i]);*/    fprintf(fichtm,"\n");
       fprintf(ficres,"%3d",i);  
       printf("%3d",i);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
       for(j=1; j<=i;j++){    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
         fprintf(ficres," %.5e",matcov[i][j]);    file %s<br>\n",optionfilehtmcov);
         printf(" %.5e",matcov[i][j]);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
       }  and drawn. It helps understanding how is the covariance between two incidences.\
       fprintf(ficres,"\n");   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
       printf("\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. \
       k++;  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
     }  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
      standard deviations wide on each axis. <br>\
     while((c=getc(ficpar))=='#' && c!= EOF){   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
       ungetc(c,ficpar);   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
       fgets(line, MAXLINE, ficpar);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
       puts(line);  
       fputs(line,ficparo);    cov[1]=1;
     }    tj=cptcoveff;
     ungetc(c,ficpar);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
      j1=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);    for(t=1; t<=tj;t++){
          for(i1=1; i1<=ncodemax[t];i1++){ 
     if (fage <= 2) {        j1++;
       bage = agemin;        if  (cptcovn>0) {
       fage = agemaxpar;          fprintf(ficresprob, "\n#********** Variable "); 
     }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
              fprintf(ficresprob, "**********\n#\n");
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          fprintf(ficresprobcov, "\n#********** Variable "); 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);          fprintf(ficresprobcov, "**********\n#\n");
            
     while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficgp, "\n#********** Variable "); 
     ungetc(c,ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fgets(line, MAXLINE, ficpar);          fprintf(ficgp, "**********\n#\n");
     puts(line);          
     fputs(line,ficparo);          
   }          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   ungetc(c,ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   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);          fprintf(ficresprobcor, "\n#********** Variable ");    
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                fprintf(ficresprobcor, "**********\n#");    
   while((c=getc(ficpar))=='#' && c!= EOF){        }
     ungetc(c,ficpar);        
     fgets(line, MAXLINE, ficpar);        for (age=bage; age<=fage; age ++){ 
     puts(line);          cov[2]=age;
     fputs(line,ficparo);          for (k=1; k<=cptcovn;k++) {
   }            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   ungetc(c,ficpar);          }
            for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
    dateprev1=anprev1+mprev1/12.+jprev1/365.;            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   fscanf(ficpar,"pop_based=%d\n",&popbased);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   fprintf(ficparo,"pop_based=%d\n",popbased);            gp=vector(1,(nlstate)*(nlstate+ndeath));
   fprintf(ficres,"pop_based=%d\n",popbased);            gm=vector(1,(nlstate)*(nlstate+ndeath));
        
   while((c=getc(ficpar))=='#' && c!= EOF){          for(theta=1; theta <=npar; theta++){
     ungetc(c,ficpar);            for(i=1; i<=npar; i++)
     fgets(line, MAXLINE, ficpar);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
     puts(line);            
     fputs(line,ficparo);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   }            
   ungetc(c,ficpar);            k=0;
             for(i=1; i<= (nlstate); i++){
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);              for(j=1; j<=(nlstate+ndeath);j++){
 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);                k=k+1;
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);                gp[k]=pmmij[i][j];
               }
             }
 while((c=getc(ficpar))=='#' && c!= EOF){            
     ungetc(c,ficpar);            for(i=1; i<=npar; i++)
     fgets(line, MAXLINE, ficpar);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     puts(line);      
     fputs(line,ficparo);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   }            k=0;
   ungetc(c,ficpar);            for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);                k=k+1;
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                gm[k]=pmmij[i][j];
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);              }
             }
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
 /*------------ gnuplot -------------*/              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);          }
    
 /*------------ free_vector  -------------*/          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
  chdir(path);            for(theta=1; theta <=npar; theta++)
                trgradg[j][theta]=gradg[theta][j];
  free_ivector(wav,1,imx);          
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
  free_ivector(num,1,n);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
  free_vector(agedc,1,n);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
  /*free_matrix(covar,1,NCOVMAX,1,n);*/          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
  fclose(ficparo);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
  fclose(ficres);  
           pmij(pmmij,cov,ncovmodel,x,nlstate);
 /*--------- index.htm --------*/          
           k=0;
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);          for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
                k=k+1;
   /*--------------- Prevalence limit --------------*/              mu[k][(int) age]=pmmij[i][j];
              }
   strcpy(filerespl,"pl");          }
   strcat(filerespl,fileres);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   if((ficrespl=fopen(filerespl,"w"))==NULL) {            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;              varpij[i][j][(int)age] = doldm[i][j];
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          /*printf("\n%d ",(int)age);
   fprintf(ficrespl,"#Prevalence limit\n");            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   fprintf(ficrespl,"#Age ");            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   fprintf(ficrespl,"\n");            }*/
    
   prlim=matrix(1,nlstate,1,nlstate);          fprintf(ficresprob,"\n%d ",(int)age);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficresprobcov,"\n%d ",(int)age);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficresprobcor,"\n%d ",(int)age);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   k=0;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   agebase=agemin;            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   agelim=agemaxpar;            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   ftolpl=1.e-10;          }
   i1=cptcoveff;          i=0;
   if (cptcovn < 1){i1=1;}          for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
   for(cptcov=1;cptcov<=i1;cptcov++){              i=i++;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
         k=k+1;              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/              for (j=1; j<=i;j++){
         fprintf(ficrespl,"\n#******");                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
         for(j=1;j<=cptcoveff;j++)                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              }
         fprintf(ficrespl,"******\n");            }
                  }/* end of loop for state */
         for (age=agebase; age<=agelim; age++){        } /* end of loop for age */
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
           fprintf(ficrespl,"%.0f",age );        /* Confidence intervalle of pij  */
           for(i=1; i<=nlstate;i++)        /*
           fprintf(ficrespl," %.5f", prlim[i][i]);          fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficrespl,"\n");          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
         }          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       }          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
     }          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   fclose(ficrespl);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   /*------------- h Pij x at various ages ------------*/        */
    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        first1=1;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        for (k2=1; k2<=(nlstate);k2++){
   }          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   printf("Computing pij: result on file '%s' \n", filerespij);            if(l2==k2) continue;
              j=(k2-1)*(nlstate+ndeath)+l2;
   stepsize=(int) (stepm+YEARM-1)/YEARM;            for (k1=1; k1<=(nlstate);k1++){
   /*if (stepm<=24) stepsize=2;*/              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
   agelim=AGESUP;                i=(k1-1)*(nlstate+ndeath)+l1;
   hstepm=stepsize*YEARM; /* Every year of age */                if(i<=j) continue;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */                for (age=bage; age<=fage; age ++){ 
                    if ((int)age %5==0){
   k=0;                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   for(cptcov=1;cptcov<=i1;cptcov++){                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
       k=k+1;                    mu1=mu[i][(int) age]/stepm*YEARM ;
         fprintf(ficrespij,"\n#****** ");                    mu2=mu[j][(int) age]/stepm*YEARM;
         for(j=1;j<=cptcoveff;j++)                    c12=cv12/sqrt(v1*v2);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    /* Computing eigen value of matrix of covariance */
         fprintf(ficrespij,"******\n");                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                            lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                    /* Eigen vectors */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                    /*v21=sqrt(1.-v11*v11); *//* error */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                    v21=(lc1-v1)/cv12*v11;
           oldm=oldms;savm=savms;                    v12=-v21;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                      v22=v11;
           fprintf(ficrespij,"# Age");                    tnalp=v21/v11;
           for(i=1; i<=nlstate;i++)                    if(first1==1){
             for(j=1; j<=nlstate+ndeath;j++)                      first1=0;
               fprintf(ficrespij," %1d-%1d",i,j);                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
           fprintf(ficrespij,"\n");                    }
           for (h=0; h<=nhstepm; h++){                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );                    /*printf(fignu*/
             for(i=1; i<=nlstate;i++)                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
               for(j=1; j<=nlstate+ndeath;j++)                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);                    if(first==1){
             fprintf(ficrespij,"\n");                      first=0;
           }                      fprintf(ficgp,"\nset parametric;unset label");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                      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(ficrespij,"\n");                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
         }                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
     }   :<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,\
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   fclose(ficrespij);                      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);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   /*---------- Forecasting ------------------*/                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   if((stepm == 1) && (strcmp(model,".")==0)){                      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",\
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     free_matrix(mint,1,maxwav,1,n);                    }else{
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);                      first=0;
     free_vector(weight,1,n);}                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
   else{                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     erreur=108;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     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(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   }                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                                mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
   /*---------- Health expectancies and variances ------------*/                  } /* age mod 5 */
                 } /* end loop age */
   strcpy(filerest,"t");                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   strcat(filerest,fileres);                first=1;
   if((ficrest=fopen(filerest,"w"))==NULL) {              } /*l12 */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;            } /* k12 */
   }          } /*l1 */
   printf("Computing Total LEs with variances: file '%s' \n", filerest);        }/* k1 */
       } /* loop covariates */
     }
   strcpy(filerese,"e");    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   strcat(filerese,fileres);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    free_vector(xp,1,npar);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    fclose(ficresprob);
   }    fclose(ficresprobcov);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    fclose(ficresprobcor);
     fflush(ficgp);
  strcpy(fileresv,"v");    fflush(fichtmcov);
   strcat(fileresv,fileres);  }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }  /******************* Printing html file ***********/
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
   k=0;                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   for(cptcov=1;cptcov<=i1;cptcov++){                    int popforecast, int estepm ,\
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    double jprev1, double mprev1,double anprev1, \
       k=k+1;                    double jprev2, double mprev2,double anprev2){
       fprintf(ficrest,"\n#****** ");    int jj1, k1, i1, cpt;
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
       fprintf(ficrest,"******\n");     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
       fprintf(ficreseij,"\n#****** ");     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
       for(j=1;j<=cptcoveff;j++)   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
       fprintf(ficreseij,"******\n");     fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
       fprintf(ficresvij,"\n#****** ");             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
       for(j=1;j<=cptcoveff;j++)     fprintf(fichtm,"\
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
       fprintf(ficresvij,"******\n");             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);   - Life expectancies by age and initial health status (estepm=%2d months): \
       oldm=oldms;savm=savms;     <a href=\"%s\">%s</a> <br>\n</li>",
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);               estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
       m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");   jj1=0;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);   for(k1=1; k1<=m;k1++){
       fprintf(ficrest,"\n");     for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
       hf=1;       if (cptcovn > 0) {
       if (stepm >= YEARM) hf=stepm/YEARM;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       epj=vector(1,nlstate+1);         for (cpt=1; cpt<=cptcoveff;cpt++) 
       for(age=bage; age <=fage ;age++){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         if (popbased==1) {       }
           for(i=1; i<=nlstate;i++)       /* Pij */
             prlim[i][i]=probs[(int)age][i][k];       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);     
               /* Quasi-incidences */
         fprintf(ficrest," %.0f",age);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];         /* Stable prevalence in each health state */
           }         for(cpt=1; cpt<nlstate;cpt++){
           epj[nlstate+1] +=epj[j];           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
         }  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
         for(i=1, vepp=0.;i <=nlstate;i++)         }
           for(j=1;j <=nlstate;j++)       for(cpt=1; cpt<=nlstate;cpt++) {
             vepp += vareij[i][j][(int)age];          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
         for(j=1;j <=nlstate;j++){       }
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));     } /* end i1 */
         }   }/* End k1 */
         fprintf(ficrest,"\n");   fprintf(fichtm,"</ul>");
       }  
     }  
   }   fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
   fclose(ficreseij);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   fclose(ficresvij);  
   fclose(ficrest);   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   fclose(ficpar);           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
   free_vector(epj,1,nlstate+1);   fprintf(fichtm,"\
     - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   /*------- Variance limit prevalence------*/             subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
   strcpy(fileresvpl,"vpl");   fprintf(fichtm,"\
   strcat(fileresvpl,fileres);   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);   fprintf(fichtm,"\
     exit(0);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
   }           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);   fprintf(fichtm,"\
    - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
   k=0;           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
   for(cptcov=1;cptcov<=i1;cptcov++){   fprintf(fichtm,"\
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
       k=k+1;           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
       fprintf(ficresvpl,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)  /*  if(popforecast==1) fprintf(fichtm,"\n */
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
       fprintf(ficresvpl,"******\n");  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
        /*      <br>",fileres,fileres,fileres,fileres); */
       varpl=matrix(1,nlstate,(int) bage, (int) fage);  /*  else  */
       oldm=oldms;savm=savms;  /*    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); */
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);   fflush(fichtm);
     }   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
  }  
    m=cptcoveff;
   fclose(ficresvpl);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
   /*---------- End : free ----------------*/   jj1=0;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);   for(k1=1; k1<=m;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);       jj1++;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);       if (cptcovn > 0) {
           fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           for (cpt=1; cpt<=cptcoveff;cpt++) 
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);       }
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);       for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   free_matrix(matcov,1,npar,1,npar);  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   free_vector(delti,1,npar);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
   free_matrix(agev,1,maxwav,1,imx);       }
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   if(erreur >0)  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
     printf("End of Imach with error %d\n",erreur);     } /* end i1 */
   else   printf("End of Imach\n");   }/* End k1 */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */   fprintf(fichtm,"</ul>");
     fflush(fichtm);
   /* 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);*/  
   /*------ End -----------*/  /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
  end:    char dirfileres[132],optfileres[132];
 #ifdef windows    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   /* chdir(pathcd);*/    int ng;
 #endif  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
  /*system("wgnuplot graph.plt");*/  /*     printf("Problem with file %s",optionfilegnuplot); */
  /*system("../gp37mgw/wgnuplot graph.plt");*/  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
  /*system("cd ../gp37mgw");*/  /*   } */
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  
  strcpy(plotcmd,GNUPLOTPROGRAM);    /*#ifdef windows */
  strcat(plotcmd," ");    fprintf(ficgp,"cd \"%s\" \n",pathc);
  strcat(plotcmd,optionfilegnuplot);      /*#endif */
  system(plotcmd);    m=pow(2,cptcoveff);
   
 #ifdef windows    strcpy(dirfileres,optionfilefiname);
   while (z[0] != 'q') {    strcpy(optfileres,"vpl");
     chdir(path);   /* 1eme*/
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    for (cpt=1; cpt<= nlstate ; cpt ++) {
     scanf("%s",z);     for (k1=1; k1<= m ; k1 ++) {
     if (z[0] == 'c') system("./imach");       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
     else if (z[0] == 'e') {       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
       chdir(path);       fprintf(ficgp,"set xlabel \"Age\" \n\
       system(optionfilehtm);  set ylabel \"Probability\" \n\
     }  set ter png small\n\
     else if (z[0] == 'q') exit(0);  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);
 #endif  
 }       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         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 ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i]==1 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i]==0 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         if (wav[i]>1 & agecens[i]>15) {
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     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>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     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 */
     struct stat info;
     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;
     int agemortsup;
     float  sumlpop=0.;
     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], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",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 parameters 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 || s[m][i]==-4 || s[m][i]==-5){
           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,strstart);
   
     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]));
   
   lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
      
        for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
      
         for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
   
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
   
    tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
          }
      
      
          printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
   
       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,agemortsup);
   
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* 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, "#Local time at start: %s", strstart);
       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, "#Local time at start: %s", strstart);
       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,strstart);
   
       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, strstart);  
    
           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, strstart);
           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, strstart);
           }
   
           fprintf(ficrest, "#Local time at start: %s", strstart);
           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,strstart);
           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\nLocal time 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);
   #ifndef UNIX
     strcpy(plotcmd,"\"");
   #endif
     strcat(plotcmd,pathimach);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     strcat(plotcmd,GNUPLOTPROGRAM);
   #ifndef UNIX
     strcat(plotcmd,"\"");
   #endif
     if(stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
     }
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf(" Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.32  
changed lines
  Added in v.1.107


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