Diff for /imach/src/imach.c between versions 1.23 and 1.115

version 1.23, 2002/02/22 18:08:30 version 1.115, 2006/02/27 12:17:45
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolate Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.115  2006/02/27 12:17:45  brouard
      (Module): One freematrix added in mlikeli! 0.98c
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.114  2006/02/26 12:57:58  brouard
   first survey ("cross") where individuals from different ages are    (Module): Some improvements in processing parameter
   interviewed on their health status or degree of disability (in the    filename with strsep.
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.113  2006/02/24 14:20:24  brouard
   (if any) in individual health status.  Health expectancies are    (Module): Memory leaks checks with valgrind and:
   computed from the time spent in each health state according to a    datafile was not closed, some imatrix were not freed and on matrix
   model. More health states you consider, more time is necessary to reach the    allocation too.
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.112  2006/01/30 09:55:26  brouard
   probabibility to be observed in state j at the second wave    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   conditional to be observed in state i at the first wave. Therefore  
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Revision 1.111  2006/01/25 20:38:18  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    (Module): Lots of cleaning and bugs added (Gompertz)
   complex model than "constant and age", you should modify the program    (Module): Comments can be added in data file. Missing date values
   where the markup *Covariates have to be included here again* invites    can be a simple dot '.'.
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.110  2006/01/25 00:51:50  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.109  2006/01/24 19:37:15  brouard
   identical for each individual. Also, if a individual missed an    (Module): Comments (lines starting with a #) are allowed in data.
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.108  2006/01/19 18:05:42  lievre
     Gnuplot problem appeared...
   hPijx is the probability to be observed in state i at age x+h    To be fixed
   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 1.107  2006/01/19 16:20:37  brouard
   states. This elementary transition (by month or quarter trimester,    Test existence of gnuplot in imach path
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.106  2006/01/19 13:24:36  brouard
   and the contribution of each individual to the likelihood is simply    Some cleaning and links added in html output
   hPijx.  
     Revision 1.105  2006/01/05 20:23:19  lievre
   Also this programme outputs the covariance matrix of the parameters but also    *** empty log message ***
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.104  2005/09/30 16:11:43  lievre
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    (Module): sump fixed, loop imx fixed, and simplifications.
            Institut national d'études démographiques, Paris.    (Module): If the status is missing at the last wave but we know
   This software have been partly granted by Euro-REVES, a concerted action    that the person is alive, then we can code his/her status as -2
   from the European Union.    (instead of missing=-1 in earlier versions) and his/her
   It is copyrighted identically to a GNU software product, ie programme and    contributions to the likelihood is 1 - Prob of dying from last
   software can be distributed freely for non commercial use. Latest version    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   can be accessed at http://euroreves.ined.fr/imach .    the healthy state at last known wave). Version is 0.98
   **********************************************************************/  
      Revision 1.103  2005/09/30 15:54:49  lievre
 #include <math.h>    (Module): sump fixed, loop imx fixed, and simplifications.
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.102  2004/09/15 17:31:30  brouard
 #include <unistd.h>    Add the possibility to read data file including tab characters.
   
 #define MAXLINE 256    Revision 1.101  2004/09/15 10:38:38  brouard
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    Fix on curr_time
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.100  2004/07/12 18:29:06  brouard
 #define windows    Add version for Mac OS X. Just define UNIX in Makefile
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.98  2004/05/16 15:05:56  brouard
     New version 0.97 . First attempt to estimate force of mortality
 #define NINTERVMAX 8    directly from the data i.e. without the need of knowing the health
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    state at each age, but using a Gompertz model: log u =a + b*age .
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    This is the basic analysis of mortality and should be done before any
 #define NCOVMAX 8 /* Maximum number of covariates */    other analysis, in order to test if the mortality estimated from the
 #define MAXN 20000    cross-longitudinal survey is different from the mortality estimated
 #define YEARM 12. /* Number of months per year */    from other sources like vital statistic data.
 #define AGESUP 130  
 #define AGEBASE 40    The same imach parameter file can be used but the option for mle should be -3.
   
     Agnès, who wrote this part of the code, tried to keep most of the
 int erreur; /* Error number */    former routines in order to include the new code within the former code.
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    The output is very simple: only an estimate of the intercept and of
 int npar=NPARMAX;    the slope with 95% confident intervals.
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Current limitations:
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    A) Even if you enter covariates, i.e. with the
 int popbased=0;    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.
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.97  2004/02/20 13:25:42  lievre
 int jmin, jmax; /* min, max spacing between 2 waves */    Version 0.96d. Population forecasting command line is (temporarily)
 int mle, weightopt;    suppressed.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.96  2003/07/15 15:38:55  brouard
 double jmean; /* Mean space between 2 waves */    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 double **oldm, **newm, **savm; /* Working pointers to matrices */    rewritten within the same printf. Workaround: many printfs.
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    Revision 1.95  2003/07/08 07:54:34  brouard
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    * imach.c (Repository):
 FILE *ficreseij;    (Repository): Using imachwizard code to output a more meaningful covariance
   char filerese[FILENAMELENGTH];    matrix (cov(a12,c31) instead of numbers.
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    Revision 1.94  2003/06/27 13:00:02  brouard
  FILE  *ficresvpl;    Just cleaning
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.93  2003/06/25 16:33:55  brouard
 #define NR_END 1    (Module): On windows (cygwin) function asctime_r doesn't
 #define FREE_ARG char*    exist so I changed back to asctime which exists.
 #define FTOL 1.0e-10    (Module): Version 0.96b
   
 #define NRANSI    Revision 1.92  2003/06/25 16:30:45  brouard
 #define ITMAX 200    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 #define TOL 2.0e-4  
     Revision 1.91  2003/06/25 15:30:29  brouard
 #define CGOLD 0.3819660    * imach.c (Repository): Duplicated warning errors corrected.
 #define ZEPS 1.0e-10    (Repository): Elapsed time after each iteration is now output. It
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
 #define GOLD 1.618034    concerning matrix of covariance. It has extension -cov.htm.
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
 static double maxarg1,maxarg2;    mle=-1 a template is output in file "or"mypar.txt with the design
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    of the covariance matrix to be input.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.89  2003/06/24 12:30:52  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    (Module): Some bugs corrected for windows. Also, when
 #define rint(a) floor(a+0.5)    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.88  2003/06/23 17:54:56  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   
 int imx;    Revision 1.87  2003/06/18 12:26:01  brouard
 int stepm;    Version 0.96
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.86  2003/06/17 20:04:08  brouard
 int m,nb;    (Module): Change position of html and gnuplot routines and added
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    routine fileappend.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.85  2003/06/17 13:12:43  brouard
 double dateintmean=0;    * imach.c (Repository): Check when date of death was earlier that
     current date of interview. It may happen when the death was just
 double *weight;    prior to the death. In this case, dh was negative and likelihood
 int **s; /* Status */    was wrong (infinity). We still send an "Error" but patch by
 double *agedc, **covar, idx;    assuming that the date of death was just one stepm after the
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    interview.
     (Repository): Because some people have very long ID (first column)
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    we changed int to long in num[] and we added a new lvector for
 double ftolhess; /* Tolerance for computing hessian */    memory allocation. But we also truncated to 8 characters (left
     truncation)
 /**************** split *************************/    (Repository): No more line truncation errors.
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    Revision 1.84  2003/06/13 21:44:43  brouard
    char *s;                             /* pointer */    * imach.c (Repository): Replace "freqsummary" at a correct
    int  l1, l2;                         /* length counters */    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
    l1 = strlen( path );                 /* length of path */    parcimony.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */    Revision 1.83  2003/06/10 13:39:11  lievre
 #else    *** empty log message ***
    s = strrchr( path, '/' );            /* find last / */  
 #endif    Revision 1.82  2003/06/05 15:57:20  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    Add log in  imach.c and  fullversion number is now printed.
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );  */
   /*
       if ( getwd( dirc ) == NULL ) {     Interpolated Markov Chain
 #else  
       extern char       *getcwd( );    Short summary of the programme:
     
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    This program computes Healthy Life Expectancies from
 #endif    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
          return( GLOCK_ERROR_GETCWD );    first survey ("cross") where individuals from different ages are
       }    interviewed on their health status or degree of disability (in the
       strcpy( name, path );             /* we've got it */    case of a health survey which is our main interest) -2- at least a
    } else {                             /* strip direcotry from path */    second wave of interviews ("longitudinal") which measure each change
       s++;                              /* after this, the filename */    (if any) in individual health status.  Health expectancies are
       l2 = strlen( s );                 /* length of filename */    computed from the time spent in each health state according to a
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    model. More health states you consider, more time is necessary to reach the
       strcpy( name, s );                /* save file name */    Maximum Likelihood of the parameters involved in the model.  The
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    simplest model is the multinomial logistic model where pij is the
       dirc[l1-l2] = 0;                  /* add zero */    probability to be observed in state j at the second wave
    }    conditional to be observed in state i at the first wave. Therefore
    l1 = strlen( dirc );                 /* length of directory */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #ifdef windows    'age' is age and 'sex' is a covariate. If you want to have a more
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    complex model than "constant and age", you should modify the program
 #else    where the markup *Covariates have to be included here again* invites
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    you to do it.  More covariates you add, slower the
 #endif    convergence.
    s = strrchr( name, '.' );            /* find last / */  
    s++;    The advantage of this computer programme, compared to a simple
    strcpy(ext,s);                       /* save extension */    multinomial logistic model, is clear when the delay between waves is not
    l1= strlen( name);    identical for each individual. Also, if a individual missed an
    l2= strlen( s)+1;    intermediate interview, the information is lost, but taken into
    strncpy( finame, name, l1-l2);    account using an interpolation or extrapolation.  
    finame[l1-l2]= 0;  
    return( 0 );                         /* we're done */    hPijx is the probability to be observed in state i at age x+h
 }    conditional to the observed state i at age x. The delay 'h' can be
     split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
 /******************************************/    semester or year) is modelled as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
 void replace(char *s, char*t)    and the contribution of each individual to the likelihood is simply
 {    hPijx.
   int i;  
   int lg=20;    Also this programme outputs the covariance matrix of the parameters but also
   i=0;    of the life expectancies. It also computes the stable prevalence. 
   lg=strlen(t);    
   for(i=0; i<= lg; i++) {    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
     (s[i] = t[i]);             Institut national d'études démographiques, Paris.
     if (t[i]== '\\') s[i]='/';    This software have been partly granted by Euro-REVES, a concerted action
   }    from the European Union.
 }    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 int nbocc(char *s, char occ)    can be accessed at http://euroreves.ined.fr/imach .
 {  
   int i,j=0;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   int lg=20;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   i=0;    
   lg=strlen(s);    **********************************************************************/
   for(i=0; i<= lg; i++) {  /*
   if  (s[i] == occ ) j++;    main
   }    read parameterfile
   return j;    read datafile
 }    concatwav
     freqsummary
 void cutv(char *u,char *v, char*t, char occ)    if (mle >= 1)
 {      mlikeli
   int i,lg,j,p=0;    print results files
   i=0;    if mle==1 
   for(j=0; j<=strlen(t)-1; j++) {       computes hessian
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    read end of parameter file: agemin, agemax, bage, fage, estepm
   }        begin-prev-date,...
     open gnuplot file
   lg=strlen(t);    open html file
   for(j=0; j<p; j++) {    stable prevalence
     (u[j] = t[j]);     for age prevalim()
   }    h Pij x
      u[p]='\0';    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
    for(j=0; j<= lg; j++) {    health expectancies
     if (j>=(p+1))(v[j-p-1] = t[j]);    Variance-covariance of DFLE
   }    prevalence()
 }     movingaverage()
     varevsij() 
 /********************** nrerror ********************/    if popbased==1 varevsij(,popbased)
     total life expectancies
 void nrerror(char error_text[])    Variance of stable prevalence
 {   end
   fprintf(stderr,"ERREUR ...\n");  */
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  
 }  
 /*********************** vector *******************/   
 double *vector(int nl, int nh)  #include <math.h>
 {  #include <stdio.h>
   double *v;  #include <stdlib.h>
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #include <string.h>
   if (!v) nrerror("allocation failure in vector");  #include <unistd.h>
   return v-nl+NR_END;  
 }  #include <limits.h>
   #include <sys/types.h>
 /************************ free vector ******************/  #include <sys/stat.h>
 void free_vector(double*v, int nl, int nh)  #include <errno.h>
 {  extern int errno;
   free((FREE_ARG)(v+nl-NR_END));  
 }  /* #include <sys/time.h> */
   #include <time.h>
 /************************ivector *******************************/  #include "timeval.h"
 int *ivector(long nl,long nh)  
 {  /* #include <libintl.h> */
   int *v;  /* #define _(String) gettext (String) */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");  #define MAXLINE 256
   return v-nl+NR_END;  
 }  #define GNUPLOTPROGRAM "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 /******************free ivector **************************/  #define FILENAMELENGTH 132
 void free_ivector(int *v, long nl, long nh)  
 {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   free((FREE_ARG)(v+nl-NR_END));  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 }  
   #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 /******************* imatrix *******************************/  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  #define NINTERVMAX 8
 {  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   int **m;  #define NCOVMAX 8 /* Maximum number of covariates */
    #define MAXN 20000
   /* allocate pointers to rows */  #define YEARM 12. /* Number of months per year */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #define AGESUP 130
   if (!m) nrerror("allocation failure 1 in matrix()");  #define AGEBASE 40
   m += NR_END;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   m -= nrl;  #ifdef UNIX
    #define DIRSEPARATOR '/'
    #define CHARSEPARATOR "/"
   /* allocate rows and set pointers to them */  #define ODIRSEPARATOR '\\'
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #else
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define DIRSEPARATOR '\\'
   m[nrl] += NR_END;  #define CHARSEPARATOR "\\"
   m[nrl] -= ncl;  #define ODIRSEPARATOR '/'
    #endif
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    /* $Id$ */
   /* return pointer to array of pointers to rows */  /* $State$ */
   return m;  
 }  char version[]="Imach version 0.98c, February 2006, INED-EUROREVES ";
   char fullversion[]="$Revision$ $Date$"; 
 /****************** free_imatrix *************************/  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 void free_imatrix(m,nrl,nrh,ncl,nch)  int nvar;
       int **m;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
       long nch,ncl,nrh,nrl;  int npar=NPARMAX;
      /* free an int matrix allocated by imatrix() */  int nlstate=2; /* Number of live states */
 {  int ndeath=1; /* Number of dead states */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   free((FREE_ARG) (m+nrl-NR_END));  int popbased=0;
 }  
   int *wav; /* Number of waves for this individuual 0 is possible */
 /******************* matrix *******************************/  int maxwav; /* Maxim number of waves */
 double **matrix(long nrl, long nrh, long ncl, long nch)  int jmin, jmax; /* min, max spacing between 2 waves */
 {  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  int gipmx, gsw; /* Global variables on the number of contributions 
   double **m;                     to the likelihood and the sum of weights (done by funcone)*/
   int mle, weightopt;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   if (!m) nrerror("allocation failure 1 in matrix()");  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   m += NR_END;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   m -= nrl;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  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 */
   return m;  long ipmx; /* Number of contributions */
 }  double sw; /* Sum of weights */
   char filerespow[FILENAMELENGTH];
 /*************************free matrix ************************/  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  FILE *ficresilk;
 {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  FILE *ficresprobmorprev;
   free((FREE_ARG)(m+nrl-NR_END));  FILE *fichtm, *fichtmcov; /* Html File */
 }  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 /******************* ma3x *******************************/  FILE  *ficresvij;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  char fileresv[FILENAMELENGTH];
 {  FILE  *ficresvpl;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  char fileresvpl[FILENAMELENGTH];
   double ***m;  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   if (!m) nrerror("allocation failure 1 in matrix()");  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   m += NR_END;  char command[FILENAMELENGTH];
   m -= nrl;  int  outcmd=0;
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  char filelog[FILENAMELENGTH]; /* Log file */
   m[nrl] -= ncl;  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  char popfile[FILENAMELENGTH];
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   m[nrl][ncl] -= nll;  struct timezone tzp;
   for (j=ncl+1; j<=nch; j++)  extern int gettimeofday();
     m[nrl][j]=m[nrl][j-1]+nlay;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
    long time_value;
   for (i=nrl+1; i<=nrh; i++) {  extern long time();
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  char strcurr[80], strfor[80];
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  char *endptr;
   }  long lval;
   return m;  
 }  #define NR_END 1
   #define FREE_ARG char*
 /*************************free ma3x ************************/  #define FTOL 1.0e-10
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {  #define NRANSI 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #define ITMAX 200 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  #define TOL 2.0e-4 
 }  
   #define CGOLD 0.3819660 
 /***************** f1dim *************************/  #define ZEPS 1.0e-10 
 extern int ncom;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);  #define GOLD 1.618034 
    #define GLIMIT 100.0 
 double f1dim(double x)  #define TINY 1.0e-20 
 {  
   int j;  static double maxarg1,maxarg2;
   double f;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   double *xt;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
      
   xt=vector(1,ncom);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #define rint(a) floor(a+0.5)
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);  static double sqrarg;
   return f;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   int agegomp= AGEGOMP;
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  int imx; 
 {  int stepm=1;
   int iter;  /* Stepm, step in month: minimum step interpolation*/
   double a,b,d,etemp;  
   double fu,fv,fw,fx;  int estepm;
   double ftemp;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  int m,nb;
    long *num;
   a=(ax < cx ? ax : cx);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   b=(ax > cx ? ax : cx);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   x=w=v=bx;  double **pmmij, ***probs;
   fw=fv=fx=(*f)(x);  double *ageexmed,*agecens;
   for (iter=1;iter<=ITMAX;iter++) {  double dateintmean=0;
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  double *weight;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  int **s; /* Status */
     printf(".");fflush(stdout);  double *agedc, **covar, idx;
 #ifdef DEBUG  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
     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);  double *lsurv, *lpop, *tpop;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  double ftolhess; /* Tolerance for computing hessian */
       *xmin=x;  
       return fx;  /**************** split *************************/
     }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     ftemp=fu;  {
     if (fabs(e) > tol1) {    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       r=(x-w)*(fx-fv);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       q=(x-v)*(fx-fw);    */ 
       p=(x-v)*q-(x-w)*r;    char  *ss;                            /* pointer */
       q=2.0*(q-r);    int   l1, l2;                         /* length counters */
       if (q > 0.0) p = -p;  
       q=fabs(q);    l1 = strlen(path );                   /* length of path */
       etemp=e;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       e=d;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    if ( ss == NULL ) {                   /* no directory, so determine current directory */
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      strcpy( name, path );               /* we got the fullname name because no directory */
       else {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         d=p/q;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
         u=x+d;      /* get current working directory */
         if (u-a < tol2 || b-u < tol2)      /*    extern  char* getcwd ( char *buf , int len);*/
           d=SIGN(tol1,xm-x);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       }        return( GLOCK_ERROR_GETCWD );
     } else {      }
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      /* got dirc from getcwd*/
     }      printf(" DIRC = %s \n",dirc);
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    } else {                              /* strip direcotry from path */
     fu=(*f)(u);      ss++;                               /* after this, the filename */
     if (fu <= fx) {      l2 = strlen( ss );                  /* length of filename */
       if (u >= x) a=x; else b=x;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       SHFT(v,w,x,u)      strcpy( name, ss );         /* save file name */
         SHFT(fv,fw,fx,fu)      strncpy( dirc, path, l1 - l2 );     /* now the directory */
         } else {      dirc[l1-l2] = 0;                    /* add zero */
           if (u < x) a=u; else b=u;      printf(" DIRC2 = %s \n",dirc);
           if (fu <= fw || w == x) {    }
             v=w;    /* We add a separator at the end of dirc if not exists */
             w=u;    l1 = strlen( dirc );                  /* length of directory */
             fv=fw;    if( dirc[l1-1] != DIRSEPARATOR ){
             fw=fu;      dirc[l1] =  DIRSEPARATOR;
           } else if (fu <= fv || v == x || v == w) {      dirc[l1+1] = 0; 
             v=u;      printf(" DIRC3 = %s \n",dirc);
             fv=fu;    }
           }    ss = strrchr( name, '.' );            /* find last / */
         }    if (ss >0){
   }      ss++;
   nrerror("Too many iterations in brent");      strcpy(ext,ss);                     /* save extension */
   *xmin=x;      l1= strlen( name);
   return fx;      l2= strlen(ss)+1;
 }      strncpy( finame, name, l1-l2);
       finame[l1-l2]= 0;
 /****************** mnbrak ***********************/    }
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    return( 0 );                          /* we're done */
             double (*func)(double))  }
 {  
   double ulim,u,r,q, dum;  
   double fu;  /******************************************/
    
   *fa=(*func)(*ax);  void replace_back_to_slash(char *s, char*t)
   *fb=(*func)(*bx);  {
   if (*fb > *fa) {    int i;
     SHFT(dum,*ax,*bx,dum)    int lg=0;
       SHFT(dum,*fb,*fa,dum)    i=0;
       }    lg=strlen(t);
   *cx=(*bx)+GOLD*(*bx-*ax);    for(i=0; i<= lg; i++) {
   *fc=(*func)(*cx);      (s[i] = t[i]);
   while (*fb > *fc) {      if (t[i]== '\\') s[i]='/';
     r=(*bx-*ax)*(*fb-*fc);    }
     q=(*bx-*cx)*(*fb-*fa);  }
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  int nbocc(char *s, char occ)
     ulim=(*bx)+GLIMIT*(*cx-*bx);  {
     if ((*bx-u)*(u-*cx) > 0.0) {    int i,j=0;
       fu=(*func)(u);    int lg=20;
     } else if ((*cx-u)*(u-ulim) > 0.0) {    i=0;
       fu=(*func)(u);    lg=strlen(s);
       if (fu < *fc) {    for(i=0; i<= lg; i++) {
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    if  (s[i] == occ ) j++;
           SHFT(*fb,*fc,fu,(*func)(u))    }
           }    return j;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  }
       u=ulim;  
       fu=(*func)(u);  void cutv(char *u,char *v, char*t, char occ)
     } else {  {
       u=(*cx)+GOLD*(*cx-*bx);    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
       fu=(*func)(u);       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
     }       gives u="abcedf" and v="ghi2j" */
     SHFT(*ax,*bx,*cx,u)    int i,lg,j,p=0;
       SHFT(*fa,*fb,*fc,fu)    i=0;
       }    for(j=0; j<=strlen(t)-1; j++) {
 }      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     }
 /*************** linmin ************************/  
     lg=strlen(t);
 int ncom;    for(j=0; j<p; j++) {
 double *pcom,*xicom;      (u[j] = t[j]);
 double (*nrfunc)(double []);    }
         u[p]='\0';
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {     for(j=0; j<= lg; j++) {
   double brent(double ax, double bx, double cx,      if (j>=(p+1))(v[j-p-1] = t[j]);
                double (*f)(double), double tol, double *xmin);    }
   double f1dim(double x);  }
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  
               double *fc, double (*func)(double));  /********************** nrerror ********************/
   int j;  
   double xx,xmin,bx,ax;  void nrerror(char error_text[])
   double fx,fb,fa;  {
      fprintf(stderr,"ERREUR ...\n");
   ncom=n;    fprintf(stderr,"%s\n",error_text);
   pcom=vector(1,n);    exit(EXIT_FAILURE);
   xicom=vector(1,n);  }
   nrfunc=func;  /*********************** vector *******************/
   for (j=1;j<=n;j++) {  double *vector(int nl, int nh)
     pcom[j]=p[j];  {
     xicom[j]=xi[j];    double *v;
   }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   ax=0.0;    if (!v) nrerror("allocation failure in vector");
   xx=1.0;    return v-nl+NR_END;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  }
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  /************************ free vector ******************/
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  void free_vector(double*v, int nl, int nh)
 #endif  {
   for (j=1;j<=n;j++) {    free((FREE_ARG)(v+nl-NR_END));
     xi[j] *= xmin;  }
     p[j] += xi[j];  
   }  /************************ivector *******************************/
   free_vector(xicom,1,n);  int *ivector(long nl,long nh)
   free_vector(pcom,1,n);  {
 }    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 /*************** powell ************************/    if (!v) nrerror("allocation failure in ivector");
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    return v-nl+NR_END;
             double (*func)(double []))  }
 {  
   void linmin(double p[], double xi[], int n, double *fret,  /******************free ivector **************************/
               double (*func)(double []));  void free_ivector(int *v, long nl, long nh)
   int i,ibig,j;  {
   double del,t,*pt,*ptt,*xit;    free((FREE_ARG)(v+nl-NR_END));
   double fp,fptt;  }
   double *xits;  
   pt=vector(1,n);  /************************lvector *******************************/
   ptt=vector(1,n);  long *lvector(long nl,long nh)
   xit=vector(1,n);  {
   xits=vector(1,n);    long *v;
   *fret=(*func)(p);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   for (j=1;j<=n;j++) pt[j]=p[j];    if (!v) nrerror("allocation failure in ivector");
   for (*iter=1;;++(*iter)) {    return v-nl+NR_END;
     fp=(*fret);  }
     ibig=0;  
     del=0.0;  /******************free lvector **************************/
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  void free_lvector(long *v, long nl, long nh)
     for (i=1;i<=n;i++)  {
       printf(" %d %.12f",i, p[i]);    free((FREE_ARG)(v+nl-NR_END));
     printf("\n");  }
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  /******************* imatrix *******************************/
       fptt=(*fret);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
 #ifdef DEBUG       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       printf("fret=%lf \n",*fret);  { 
 #endif    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       printf("%d",i);fflush(stdout);    int **m; 
       linmin(p,xit,n,fret,func);    
       if (fabs(fptt-(*fret)) > del) {    /* allocate pointers to rows */ 
         del=fabs(fptt-(*fret));    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
         ibig=i;    if (!m) nrerror("allocation failure 1 in matrix()"); 
       }    m += NR_END; 
 #ifdef DEBUG    m -= nrl; 
       printf("%d %.12e",i,(*fret));    
       for (j=1;j<=n;j++) {    
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    /* allocate rows and set pointers to them */ 
         printf(" x(%d)=%.12e",j,xit[j]);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       for(j=1;j<=n;j++)    m[nrl] += NR_END; 
         printf(" p=%.12e",p[j]);    m[nrl] -= ncl; 
       printf("\n");    
 #endif    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     }    
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    /* return pointer to array of pointers to rows */ 
 #ifdef DEBUG    return m; 
       int k[2],l;  } 
       k[0]=1;  
       k[1]=-1;  /****************** free_imatrix *************************/
       printf("Max: %.12e",(*func)(p));  void free_imatrix(m,nrl,nrh,ncl,nch)
       for (j=1;j<=n;j++)        int **m;
         printf(" %.12e",p[j]);        long nch,ncl,nrh,nrl; 
       printf("\n");       /* free an int matrix allocated by imatrix() */ 
       for(l=0;l<=1;l++) {  { 
         for (j=1;j<=n;j++) {    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    free((FREE_ARG) (m+nrl-NR_END)); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  } 
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  /******************* matrix *******************************/
       }  double **matrix(long nrl, long nrh, long ncl, long nch)
 #endif  {
     long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     double **m;
       free_vector(xit,1,n);  
       free_vector(xits,1,n);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       free_vector(ptt,1,n);    if (!m) nrerror("allocation failure 1 in matrix()");
       free_vector(pt,1,n);    m += NR_END;
       return;    m -= nrl;
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    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()");
       ptt[j]=2.0*p[j]-pt[j];    m[nrl] += NR_END;
       xit[j]=p[j]-pt[j];    m[nrl] -= ncl;
       pt[j]=p[j];  
     }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     fptt=(*func)(ptt);    return m;
     if (fptt < fp) {    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       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);  
         for (j=1;j<=n;j++) {  /*************************free matrix ************************/
           xi[j][ibig]=xi[j][n];  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
           xi[j][n]=xit[j];  {
         }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 #ifdef DEBUG    free((FREE_ARG)(m+nrl-NR_END));
         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]);  /******************* ma3x *******************************/
         printf("\n");  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 #endif  {
       }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     }    double ***m;
   }  
 }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 /**** Prevalence limit ****************/    m += NR_END;
     m -= nrl;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  
 {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
      matrix by transitions matrix until convergence is reached */    m[nrl] += NR_END;
     m[nrl] -= ncl;
   int i, ii,j,k;  
   double min, max, maxmin, maxmax,sumnew=0.;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   double **newm;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   double agefin, delaymax=50 ; /* Max number of years to converge */    m[nrl][ncl] += NR_END;
     m[nrl][ncl] -= nll;
   for (ii=1;ii<=nlstate+ndeath;ii++)    for (j=ncl+1; j<=nch; j++) 
     for (j=1;j<=nlstate+ndeath;j++){      m[nrl][j]=m[nrl][j-1]+nlay;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    
     }    for (i=nrl+1; i<=nrh; i++) {
       m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
    cov[1]=1.;      for (j=ncl+1; j<=nch; j++) 
          m[i][j]=m[i][j-1]+nlay;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    }
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    return m; 
     newm=savm;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     /* Covariates have to be included here again */             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
      cov[2]=agefin;    */
    }
       for (k=1; k<=cptcovn;k++) {  
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  /*************************free ma3x ************************/
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       }  {
       for (k=1; k<=cptcovage;k++)    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       for (k=1; k<=cptcovprod;k++)    free((FREE_ARG)(m+nrl-NR_END));
         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]);*/  /*************** function subdirf ***********/
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  char *subdirf(char fileres[])
   {
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
     savm=oldm;    strcat(tmpout,"/"); /* Add to the right */
     oldm=newm;    strcat(tmpout,fileres);
     maxmax=0.;    return tmpout;
     for(j=1;j<=nlstate;j++){  }
       min=1.;  
       max=0.;  /*************** function subdirf2 ***********/
       for(i=1; i<=nlstate; i++) {  char *subdirf2(char fileres[], char *preop)
         sumnew=0;  {
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    
         prlim[i][j]= newm[i][j]/(1-sumnew);    /* Caution optionfilefiname is hidden */
         max=FMAX(max,prlim[i][j]);    strcpy(tmpout,optionfilefiname);
         min=FMIN(min,prlim[i][j]);    strcat(tmpout,"/");
       }    strcat(tmpout,preop);
       maxmin=max-min;    strcat(tmpout,fileres);
       maxmax=FMAX(maxmax,maxmin);    return tmpout;
     }  }
     if(maxmax < ftolpl){  
       return prlim;  /*************** function subdirf3 ***********/
     }  char *subdirf3(char fileres[], char *preop, char *preop2)
   }  {
 }    
     /* Caution optionfilefiname is hidden */
 /*************** transition probabilities ***************/    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    strcat(tmpout,preop);
 {    strcat(tmpout,preop2);
   double s1, s2;    strcat(tmpout,fileres);
   /*double t34;*/    return tmpout;
   int i,j,j1, nc, ii, jj;  }
   
     for(i=1; i<= nlstate; i++){  /***************** f1dim *************************/
     for(j=1; j<i;j++){  extern int ncom; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  extern double *pcom,*xicom;
         /*s2 += param[i][j][nc]*cov[nc];*/  extern double (*nrfunc)(double []); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];   
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  double f1dim(double x) 
       }  { 
       ps[i][j]=s2;    int j; 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    double f;
     }    double *xt; 
     for(j=i+1; j<=nlstate+ndeath;j++){   
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    xt=vector(1,ncom); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    f=(*nrfunc)(xt); 
       }    free_vector(xt,1,ncom); 
       ps[i][j]=s2;    return f; 
     }  } 
   }  
     /*ps[3][2]=1;*/  /*****************brent *************************/
   double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   for(i=1; i<= nlstate; i++){  { 
      s1=0;    int iter; 
     for(j=1; j<i; j++)    double a,b,d,etemp;
       s1+=exp(ps[i][j]);    double fu,fv,fw,fx;
     for(j=i+1; j<=nlstate+ndeath; j++)    double ftemp;
       s1+=exp(ps[i][j]);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     ps[i][i]=1./(s1+1.);    double e=0.0; 
     for(j=1; j<i; j++)   
       ps[i][j]= exp(ps[i][j])*ps[i][i];    a=(ax < cx ? ax : cx); 
     for(j=i+1; j<=nlstate+ndeath; j++)    b=(ax > cx ? ax : cx); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    x=w=v=bx; 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    fw=fv=fx=(*f)(x); 
   } /* end i */    for (iter=1;iter<=ITMAX;iter++) { 
       xm=0.5*(a+b); 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     for(jj=1; jj<= nlstate+ndeath; jj++){      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       ps[ii][jj]=0;      printf(".");fflush(stdout);
       ps[ii][ii]=1;      fprintf(ficlog,".");fflush(ficlog);
     }  #ifdef DEBUG
   }      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  #endif
     for(jj=1; jj<= nlstate+ndeath; jj++){      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
      printf("%lf ",ps[ii][jj]);        *xmin=x; 
    }        return fx; 
     printf("\n ");      } 
     }      ftemp=fu;
     printf("\n ");printf("%lf ",cov[2]);*/      if (fabs(e) > tol1) { 
 /*        r=(x-w)*(fx-fv); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        q=(x-v)*(fx-fw); 
   goto end;*/        p=(x-v)*q-(x-w)*r; 
     return ps;        q=2.0*(q-r); 
 }        if (q > 0.0) p = -p; 
         q=fabs(q); 
 /**************** Product of 2 matrices ******************/        etemp=e; 
         e=d; 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        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)); 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        else { 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          d=p/q; 
   /* in, b, out are matrice of pointers which should have been initialized          u=x+d; 
      before: only the contents of out is modified. The function returns          if (u-a < tol2 || b-u < tol2) 
      a pointer to pointers identical to out */            d=SIGN(tol1,xm-x); 
   long i, j, k;        } 
   for(i=nrl; i<= nrh; i++)      } else { 
     for(k=ncolol; k<=ncoloh; k++)        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      } 
         out[i][k] +=in[i][j]*b[j][k];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       fu=(*f)(u); 
   return out;      if (fu <= fx) { 
 }        if (u >= x) a=x; else b=x; 
         SHFT(v,w,x,u) 
           SHFT(fv,fw,fx,fu) 
 /************* Higher Matrix Product ***************/          } else { 
             if (u < x) a=u; else b=u; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )            if (fu <= fw || w == x) { 
 {              v=w; 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month              w=u; 
      duration (i.e. until              fv=fw; 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.              fw=fu; 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step            } else if (fu <= fv || v == x || v == w) { 
      (typically every 2 years instead of every month which is too big).              v=u; 
      Model is determined by parameters x and covariates have to be              fv=fu; 
      included manually here.            } 
           } 
      */    } 
     nrerror("Too many iterations in brent"); 
   int i, j, d, h, k;    *xmin=x; 
   double **out, cov[NCOVMAX];    return fx; 
   double **newm;  } 
   
   /* Hstepm could be zero and should return the unit matrix */  /****************** mnbrak ***********************/
   for (i=1;i<=nlstate+ndeath;i++)  
     for (j=1;j<=nlstate+ndeath;j++){  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       oldm[i][j]=(i==j ? 1.0 : 0.0);              double (*func)(double)) 
       po[i][j][0]=(i==j ? 1.0 : 0.0);  { 
     }    double ulim,u,r,q, dum;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    double fu; 
   for(h=1; h <=nhstepm; h++){   
     for(d=1; d <=hstepm; d++){    *fa=(*func)(*ax); 
       newm=savm;    *fb=(*func)(*bx); 
       /* Covariates have to be included here again */    if (*fb > *fa) { 
       cov[1]=1.;      SHFT(dum,*ax,*bx,dum) 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        SHFT(dum,*fb,*fa,dum) 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        } 
       for (k=1; k<=cptcovage;k++)    *cx=(*bx)+GOLD*(*bx-*ax); 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    *fc=(*func)(*cx); 
       for (k=1; k<=cptcovprod;k++)    while (*fb > *fc) { 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      if ((*bx-u)*(u-*cx) > 0.0) { 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        fu=(*func)(u); 
       savm=oldm;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       oldm=newm;        fu=(*func)(u); 
     }        if (fu < *fc) { 
     for(i=1; i<=nlstate+ndeath; i++)          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       for(j=1;j<=nlstate+ndeath;j++) {            SHFT(*fb,*fc,fu,(*func)(u)) 
         po[i][j][h]=newm[i][j];            } 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
          */        u=ulim; 
       }        fu=(*func)(u); 
   } /* end h */      } else { 
   return po;        u=(*cx)+GOLD*(*cx-*bx); 
 }        fu=(*func)(u); 
       } 
       SHFT(*ax,*bx,*cx,u) 
 /*************** log-likelihood *************/        SHFT(*fa,*fb,*fc,fu) 
 double func( double *x)        } 
 {  } 
   int i, ii, j, k, mi, d, kk;  
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  /*************** linmin ************************/
   double **out;  
   double sw; /* Sum of weights */  int ncom; 
   double lli; /* Individual log likelihood */  double *pcom,*xicom;
   long ipmx;  double (*nrfunc)(double []); 
   /*extern weight */   
   /* We are differentiating ll according to initial status */  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  { 
   /*for(i=1;i<imx;i++)    double brent(double ax, double bx, double cx, 
     printf(" %d\n",s[4][i]);                 double (*f)(double), double tol, double *xmin); 
   */    double f1dim(double x); 
   cov[1]=1.;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
   for(k=1; k<=nlstate; k++) ll[k]=0.;    int j; 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    double xx,xmin,bx,ax; 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    double fx,fb,fa;
     for(mi=1; mi<= wav[i]-1; mi++){   
       for (ii=1;ii<=nlstate+ndeath;ii++)    ncom=n; 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    pcom=vector(1,n); 
       for(d=0; d<dh[mi][i]; d++){    xicom=vector(1,n); 
         newm=savm;    nrfunc=func; 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    for (j=1;j<=n;j++) { 
         for (kk=1; kk<=cptcovage;kk++) {      pcom[j]=p[j]; 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      xicom[j]=xi[j]; 
         }    } 
            ax=0.0; 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    xx=1.0; 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         savm=oldm;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
         oldm=newm;  #ifdef DEBUG
            printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
            fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       } /* end mult */  #endif
          for (j=1;j<=n;j++) { 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      xi[j] *= xmin; 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      p[j] += xi[j]; 
       ipmx +=1;    } 
       sw += weight[i];    free_vector(xicom,1,n); 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    free_vector(pcom,1,n); 
     } /* end of wave */  } 
   } /* end of individual */  
   char *asc_diff_time(long time_sec, char ascdiff[])
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  {
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    long sec_left, days, hours, minutes;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    days = (time_sec) / (60*60*24);
   return -l;    sec_left = (time_sec) % (60*60*24);
 }    hours = (sec_left) / (60*60) ;
     sec_left = (sec_left) %(60*60);
     minutes = (sec_left) /60;
 /*********** Maximum Likelihood Estimation ***************/    sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    return ascdiff;
 {  }
   int i,j, iter;  
   double **xi,*delti;  /*************** powell ************************/
   double fret;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   xi=matrix(1,npar,1,npar);              double (*func)(double [])) 
   for (i=1;i<=npar;i++)  { 
     for (j=1;j<=npar;j++)    void linmin(double p[], double xi[], int n, double *fret, 
       xi[i][j]=(i==j ? 1.0 : 0.0);                double (*func)(double [])); 
   printf("Powell\n");    int i,ibig,j; 
   powell(p,xi,npar,ftol,&iter,&fret,func);    double del,t,*pt,*ptt,*xit;
     double fp,fptt;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    double *xits;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    int niterf, itmp;
   
 }    pt=vector(1,n); 
     ptt=vector(1,n); 
 /**** Computes Hessian and covariance matrix ***/    xit=vector(1,n); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    xits=vector(1,n); 
 {    *fret=(*func)(p); 
   double  **a,**y,*x,pd;    for (j=1;j<=n;j++) pt[j]=p[j]; 
   double **hess;    for (*iter=1;;++(*iter)) { 
   int i, j,jk;      fp=(*fret); 
   int *indx;      ibig=0; 
       del=0.0; 
   double hessii(double p[], double delta, int theta, double delti[]);      last_time=curr_time;
   double hessij(double p[], double delti[], int i, int j);      (void) gettimeofday(&curr_time,&tzp);
   void lubksb(double **a, int npar, int *indx, double b[]) ;      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);
   void ludcmp(double **a, int npar, int *indx, double *d) ;      /*    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
       fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   hess=matrix(1,npar,1,npar);      */
      for (i=1;i<=n;i++) {
   printf("\nCalculation of the hessian matrix. Wait...\n");        printf(" %d %.12f",i, p[i]);
   for (i=1;i<=npar;i++){        fprintf(ficlog," %d %.12lf",i, p[i]);
     printf("%d",i);fflush(stdout);        fprintf(ficrespow," %.12lf", p[i]);
     hess[i][i]=hessii(p,ftolhess,i,delti);      }
     /*printf(" %f ",p[i]);*/      printf("\n");
     /*printf(" %lf ",hess[i][i]);*/      fprintf(ficlog,"\n");
   }      fprintf(ficrespow,"\n");fflush(ficrespow);
        if(*iter <=3){
   for (i=1;i<=npar;i++) {        tm = *localtime(&curr_time.tv_sec);
     for (j=1;j<=npar;j++)  {        strcpy(strcurr,asctime(&tm));
       if (j>i) {  /*       asctime_r(&tm,strcurr); */
         printf(".%d%d",i,j);fflush(stdout);        forecast_time=curr_time; 
         hess[i][j]=hessij(p,delti,i,j);        itmp = strlen(strcurr);
         hess[j][i]=hess[i][j];            if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         /*printf(" %lf ",hess[i][j]);*/          strcurr[itmp-1]='\0';
       }        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     }        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){
   printf("\n");          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
           tmf = *localtime(&forecast_time.tv_sec);
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  /*      asctime_r(&tmf,strfor); */
            strcpy(strfor,asctime(&tmf));
   a=matrix(1,npar,1,npar);          itmp = strlen(strfor);
   y=matrix(1,npar,1,npar);          if(strfor[itmp-1]=='\n')
   x=vector(1,npar);          strfor[itmp-1]='\0';
   indx=ivector(1,npar);          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);
   for (i=1;i<=npar;i++)          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        }
   ludcmp(a,npar,indx,&pd);      }
       for (i=1;i<=n;i++) { 
   for (j=1;j<=npar;j++) {        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     for (i=1;i<=npar;i++) x[i]=0;        fptt=(*fret); 
     x[j]=1;  #ifdef DEBUG
     lubksb(a,npar,indx,x);        printf("fret=%lf \n",*fret);
     for (i=1;i<=npar;i++){        fprintf(ficlog,"fret=%lf \n",*fret);
       matcov[i][j]=x[i];  #endif
     }        printf("%d",i);fflush(stdout);
   }        fprintf(ficlog,"%d",i);fflush(ficlog);
         linmin(p,xit,n,fret,func); 
   printf("\n#Hessian matrix#\n");        if (fabs(fptt-(*fret)) > del) { 
   for (i=1;i<=npar;i++) {          del=fabs(fptt-(*fret)); 
     for (j=1;j<=npar;j++) {          ibig=i; 
       printf("%.3e ",hess[i][j]);        } 
     }  #ifdef DEBUG
     printf("\n");        printf("%d %.12e",i,(*fret));
   }        fprintf(ficlog,"%d %.12e",i,(*fret));
         for (j=1;j<=n;j++) {
   /* Recompute Inverse */          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   for (i=1;i<=npar;i++)          printf(" x(%d)=%.12e",j,xit[j]);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   ludcmp(a,npar,indx,&pd);        }
         for(j=1;j<=n;j++) {
   /*  printf("\n#Hessian matrix recomputed#\n");          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
   for (j=1;j<=npar;j++) {        }
     for (i=1;i<=npar;i++) x[i]=0;        printf("\n");
     x[j]=1;        fprintf(ficlog,"\n");
     lubksb(a,npar,indx,x);  #endif
     for (i=1;i<=npar;i++){      } 
       y[i][j]=x[i];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       printf("%.3e ",y[i][j]);  #ifdef DEBUG
     }        int k[2],l;
     printf("\n");        k[0]=1;
   }        k[1]=-1;
   */        printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
   free_matrix(a,1,npar,1,npar);        for (j=1;j<=n;j++) {
   free_matrix(y,1,npar,1,npar);          printf(" %.12e",p[j]);
   free_vector(x,1,npar);          fprintf(ficlog," %.12e",p[j]);
   free_ivector(indx,1,npar);        }
   free_matrix(hess,1,npar,1,npar);        printf("\n");
         fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
 }          for (j=1;j<=n;j++) {
             ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 /*************** hessian matrix ****************/            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 double hessii( double x[], double delta, int theta, double delti[])            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 {          }
   int i;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   int l=1, lmax=20;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double k1,k2;        }
   double p2[NPARMAX+1];  #endif
   double res;  
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  
   double fx;        free_vector(xit,1,n); 
   int k=0,kmax=10;        free_vector(xits,1,n); 
   double l1;        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
   fx=func(x);        return; 
   for (i=1;i<=npar;i++) p2[i]=x[i];      } 
   for(l=0 ; l <=lmax; l++){      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     l1=pow(10,l);      for (j=1;j<=n;j++) { 
     delts=delt;        ptt[j]=2.0*p[j]-pt[j]; 
     for(k=1 ; k <kmax; k=k+1){        xit[j]=p[j]-pt[j]; 
       delt = delta*(l1*k);        pt[j]=p[j]; 
       p2[theta]=x[theta] +delt;      } 
       k1=func(p2)-fx;      fptt=(*func)(ptt); 
       p2[theta]=x[theta]-delt;      if (fptt < fp) { 
       k2=func(p2)-fx;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       /*res= (k1-2.0*fx+k2)/delt/delt; */        if (t < 0.0) { 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          linmin(p,xit,n,fret,func); 
                for (j=1;j<=n;j++) { 
 #ifdef DEBUG            xi[j][ibig]=xi[j][n]; 
       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);            xi[j][n]=xit[j]; 
 #endif          }
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  #ifdef DEBUG
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         k=kmax;          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++){
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */            printf(" %.12e",xit[j]);
         k=kmax; l=lmax*10.;            fprintf(ficlog," %.12e",xit[j]);
       }          }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          printf("\n");
         delts=delt;          fprintf(ficlog,"\n");
       }  #endif
     }        }
   }      } 
   delti[theta]=delts;    } 
   return res;  } 
    
 }  /**** Prevalence limit (stable prevalence)  ****************/
   
 double hessij( double x[], double delti[], int thetai,int thetaj)  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
 {  {
   int i;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   int l=1, l1, lmax=20;       matrix by transitions matrix until convergence is reached */
   double k1,k2,k3,k4,res,fx;  
   double p2[NPARMAX+1];    int i, ii,j,k;
   int k;    double min, max, maxmin, maxmax,sumnew=0.;
     double **matprod2();
   fx=func(x);    double **out, cov[NCOVMAX], **pmij();
   for (k=1; k<=2; k++) {    double **newm;
     for (i=1;i<=npar;i++) p2[i]=x[i];    double agefin, delaymax=50 ; /* Max number of years to converge */
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    for (ii=1;ii<=nlstate+ndeath;ii++)
     k1=func(p2)-fx;      for (j=1;j<=nlstate+ndeath;j++){
          oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetai]=x[thetai]+delti[thetai]/k;      }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k2=func(p2)-fx;     cov[1]=1.;
     
     p2[thetai]=x[thetai]-delti[thetai]/k;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     k3=func(p2)-fx;      newm=savm;
        /* Covariates have to be included here again */
     p2[thetai]=x[thetai]-delti[thetai]/k;       cov[2]=agefin;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    
     k4=func(p2)-fx;        for (k=1; k<=cptcovn;k++) {
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 #ifdef DEBUG          /*      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]]);*/
     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        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   }        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]);*/
 /************** Inverse of matrix **************/        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
 void ludcmp(double **a, int n, int *indx, double *d)        /*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,imax,j,k;  
   double big,dum,sum,temp;      savm=oldm;
   double *vv;      oldm=newm;
        maxmax=0.;
   vv=vector(1,n);      for(j=1;j<=nlstate;j++){
   *d=1.0;        min=1.;
   for (i=1;i<=n;i++) {        max=0.;
     big=0.0;        for(i=1; i<=nlstate; i++) {
     for (j=1;j<=n;j++)          sumnew=0;
       if ((temp=fabs(a[i][j])) > big) big=temp;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          prlim[i][j]= newm[i][j]/(1-sumnew);
     vv[i]=1.0/big;          max=FMAX(max,prlim[i][j]);
   }          min=FMIN(min,prlim[i][j]);
   for (j=1;j<=n;j++) {        }
     for (i=1;i<j;i++) {        maxmin=max-min;
       sum=a[i][j];        maxmax=FMAX(maxmax,maxmin);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      }
       a[i][j]=sum;      if(maxmax < ftolpl){
     }        return prlim;
     big=0.0;      }
     for (i=j;i<=n;i++) {    }
       sum=a[i][j];  }
       for (k=1;k<j;k++)  
         sum -= a[i][k]*a[k][j];  /*************** transition probabilities ***************/ 
       a[i][j]=sum;  
       if ( (dum=vv[i]*fabs(sum)) >= big) {  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         big=dum;  {
         imax=i;    double s1, s2;
       }    /*double t34;*/
     }    int i,j,j1, nc, ii, jj;
     if (j != imax) {  
       for (k=1;k<=n;k++) {      for(i=1; i<= nlstate; i++){
         dum=a[imax][k];        for(j=1; j<i;j++){
         a[imax][k]=a[j][k];          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         a[j][k]=dum;            /*s2 += param[i][j][nc]*cov[nc];*/
       }            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       *d = -(*d);  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
       vv[imax]=vv[j];          }
     }          ps[i][j]=s2;
     indx[j]=imax;  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
     if (a[j][j] == 0.0) a[j][j]=TINY;        }
     if (j != n) {        for(j=i+1; j<=nlstate+ndeath;j++){
       dum=1.0/(a[j][j]);          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       for (i=j+1;i<=n;i++) a[i][j] *= dum;            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     }  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
   }          }
   free_vector(vv,1,n);  /* Doesn't work */          ps[i][j]=s2;
 ;        }
 }      }
       /*ps[3][2]=1;*/
 void lubksb(double **a, int n, int *indx, double b[])      
 {      for(i=1; i<= nlstate; i++){
   int i,ii=0,ip,j;        s1=0;
   double sum;        for(j=1; j<i; j++)
            s1+=exp(ps[i][j]);
   for (i=1;i<=n;i++) {        for(j=i+1; j<=nlstate+ndeath; j++)
     ip=indx[i];          s1+=exp(ps[i][j]);
     sum=b[ip];        ps[i][i]=1./(s1+1.);
     b[ip]=b[i];        for(j=1; j<i; j++)
     if (ii)          ps[i][j]= exp(ps[i][j])*ps[i][i];
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        for(j=i+1; j<=nlstate+ndeath; j++)
     else if (sum) ii=i;          ps[i][j]= exp(ps[i][j])*ps[i][i];
     b[i]=sum;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   }      } /* end i */
   for (i=n;i>=1;i--) {      
     sum=b[i];      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        for(jj=1; jj<= nlstate+ndeath; jj++){
     b[i]=sum/a[i][i];          ps[ii][jj]=0;
   }          ps[ii][ii]=1;
 }        }
       }
 /************ 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)  
 {  /* Some frequencies */  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
    /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  /*         printf("ddd %lf ",ps[ii][jj]); */
   double ***freq; /* Frequencies */  /*       } */
   double *pp;  /*       printf("\n "); */
   double pos, k2, dateintsum=0,k2cpt=0;  /*        } */
   FILE *ficresp;  /*        printf("\n ");printf("%lf ",cov[2]); */
   char fileresp[FILENAMELENGTH];         /*
         for(i=1; i<= npar; i++) printf("%f ",x[i]);
   pp=vector(1,nlstate);        goto end;*/
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      return ps;
   strcpy(fileresp,"p");  }
   strcat(fileresp,fileres);  
   if((ficresp=fopen(fileresp,"w"))==NULL) {  /**************** Product of 2 matrices ******************/
     printf("Problem with prevalence resultfile: %s\n", fileresp);  
     exit(0);  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   }  {
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   j1=0;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
   j=cptcoveff;       before: only the contents of out is modified. The function returns
   if (cptcovn<1) {j=1;ncodemax[1]=1;}       a pointer to pointers identical to out */
     long i, j, k;
   for(k1=1; k1<=j;k1++){    for(i=nrl; i<= nrh; i++)
    for(i1=1; i1<=ncodemax[k1];i1++){      for(k=ncolol; k<=ncoloh; k++)
        j1++;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          out[i][k] +=in[i][j]*b[j][k];
          scanf("%d", i);*/  
         for (i=-1; i<=nlstate+ndeath; i++)      return out;
          for (jk=-1; jk<=nlstate+ndeath; jk++)    }
            for(m=agemin; m <= agemax+3; m++)  
              freq[i][jk][m]=0;  
   /************* Higher Matrix Product ***************/
         dateintsum=0;  
         k2cpt=0;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
        for (i=1; i<=imx; i++) {  {
          bool=1;    /* Computes the transition matrix starting at age 'age' over 
          if  (cptcovn>0) {       'nhstepm*hstepm*stepm' months (i.e. until
            for (z1=1; z1<=cptcoveff; z1++)       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])       nhstepm*hstepm matrices. 
                bool=0;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
          }       (typically every 2 years instead of every month which is too big 
          if (bool==1) {       for the memory).
            for(m=firstpass; m<=lastpass; m++){       Model is determined by parameters x and covariates have to be 
              k2=anint[m][i]+(mint[m][i]/12.);       included manually here. 
              if ((k2>=dateprev1) && (k2<=dateprev2)) {  
                if(agev[m][i]==0) agev[m][i]=agemax+1;       */
                if(agev[m][i]==1) agev[m][i]=agemax+2;  
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    int i, j, d, h, k;
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    double **out, cov[NCOVMAX];
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    double **newm;
                  dateintsum=dateintsum+k2;  
                  k2cpt++;    /* Hstepm could be zero and should return the unit matrix */
                }    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
              }        oldm[i][j]=(i==j ? 1.0 : 0.0);
            }        po[i][j][0]=(i==j ? 1.0 : 0.0);
          }      }
        }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         if  (cptcovn>0) {    for(h=1; h <=nhstepm; h++){
          fprintf(ficresp, "\n#********** Variable ");      for(d=1; d <=hstepm; d++){
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        newm=savm;
        fprintf(ficresp, "**********\n#");        /* Covariates have to be included here again */
         }        cov[1]=1.;
        for(i=1; i<=nlstate;i++)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
        fprintf(ficresp, "\n");        for (k=1; k<=cptcovage;k++)
                  cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   for(i=(int)agemin; i <= (int)agemax+3; i++){        for (k=1; k<=cptcovprod;k++)
     if(i==(int)agemax+3)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       printf("Total");  
     else  
       printf("Age %d", i);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     for(jk=1; jk <=nlstate ; jk++){        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         pp[jk] += freq[jk][m][i];                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     }        savm=oldm;
     for(jk=1; jk <=nlstate ; jk++){        oldm=newm;
       for(m=-1, pos=0; m <=0 ; m++)      }
         pos += freq[jk][m][i];      for(i=1; i<=nlstate+ndeath; i++)
       if(pp[jk]>=1.e-10)        for(j=1;j<=nlstate+ndeath;j++) {
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          po[i][j][h]=newm[i][j];
       else          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);           */
     }        }
     } /* end h */
      for(jk=1; jk <=nlstate ; jk++){    return po;
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  }
         pp[jk] += freq[jk][m][i];  
      }  
   /*************** log-likelihood *************/
     for(jk=1,pos=0; jk <=nlstate ; jk++)  double func( double *x)
       pos += pp[jk];  {
     for(jk=1; jk <=nlstate ; jk++){    int i, ii, j, k, mi, d, kk;
       if(pos>=1.e-5)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    double **out;
       else    double sw; /* Sum of weights */
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    double lli; /* Individual log likelihood */
       if( i <= (int) agemax){    int s1, s2;
         if(pos>=1.e-5){    double bbh, survp;
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    long ipmx;
           probs[i][jk][j1]= pp[jk]/pos;    /*extern weight */
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    /* We are differentiating ll according to initial status */
         }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       else    /*for(i=1;i<imx;i++) 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      printf(" %d\n",s[4][i]);
       }    */
     }    cov[1]=1.;
     for(jk=-1; jk <=nlstate+ndeath; jk++)  
       for(m=-1; m <=nlstate+ndeath; m++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  
     if(i <= (int) agemax)    if(mle==1){
       fprintf(ficresp,"\n");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     printf("\n");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
  }            for (j=1;j<=nlstate+ndeath;j++){
   dateintmean=dateintsum/k2cpt;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
   fclose(ficresp);            }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          for(d=0; d<dh[mi][i]; d++){
   free_vector(pp,1,nlstate);            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /* End of Freq */            for (kk=1; kk<=cptcovage;kk++) {
 }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
 /************ Prevalence ********************/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 void prevalence(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 calagedate)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 {  /* Some frequencies */            savm=oldm;
              oldm=newm;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          } /* end mult */
   double ***freq; /* Frequencies */        
   double *pp;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   double pos, k2;          /* But now since version 0.9 we anticipate for bias at large stepm.
            * If stepm is larger than one month (smallest stepm) and if the exact delay 
   pp=vector(1,nlstate);           * (in months) between two waves is not a multiple of stepm, we rounded to 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);           * the nearest (and in case of equal distance, to the lowest) interval but now
             * we keep into memory the bias bh[mi][i] and also the previous matrix product
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   j1=0;           * probability in order to take into account the bias as a fraction of the way
             * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   j=cptcoveff;           * -stepm/2 to stepm/2 .
   if (cptcovn<1) {j=1;ncodemax[1]=1;}           * For stepm=1 the results are the same as for previous versions of Imach.
             * For stepm > 1 the results are less biased than in previous versions. 
  for(k1=1; k1<=j;k1++){           */
     for(i1=1; i1<=ncodemax[k1];i1++){          s1=s[mw[mi][i]][i];
       j1++;          s2=s[mw[mi+1][i]][i];
            bbh=(double)bh[mi][i]/(double)stepm; 
       for (i=-1; i<=nlstate+ndeath; i++)            /* bias bh is positive if real duration
         for (jk=-1; jk<=nlstate+ndeath; jk++)             * is higher than the multiple of stepm and negative otherwise.
           for(m=agemin; m <= agemax+3; m++)           */
             freq[i][jk][m]=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]));*/
                if( s2 > nlstate){ 
       for (i=1; i<=imx; i++) {            /* i.e. if s2 is a death state and if the date of death is known 
         bool=1;               then the contribution to the likelihood is the probability to 
         if  (cptcovn>0) {               die between last step unit time and current  step unit time, 
           for (z1=1; z1<=cptcoveff; z1++)               which is also equal to probability to die before dh 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])               minus probability to die before dh-stepm . 
               bool=0;               In version up to 0.92 likelihood was computed
         }          as if date of death was unknown. Death was treated as any other
         if (bool==1) {          health state: the date of the interview describes the actual state
           for(m=firstpass; m<=lastpass; m++){          and not the date of a change in health state. The former idea was
             k2=anint[m][i]+(mint[m][i]/12.);          to consider that at each interview the state was recorded
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          (healthy, disable or death) and IMaCh was corrected; but when we
               if(agev[m][i]==0) agev[m][i]=agemax+1;          introduced the exact date of death then we should have modified
               if(agev[m][i]==1) agev[m][i]=agemax+2;          the contribution of an exact death to the likelihood. This new
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          contribution is smaller and very dependent of the step unit
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];            stepm. It is no more the probability to die between last interview
             }          and month of death but the probability to survive from last
           }          interview up to one month before death multiplied by the
         }          probability to die within a month. Thanks to Chris
       }          Jackson for correcting this bug.  Former versions increased
                mortality artificially. The bad side is that we add another loop
         for(i=(int)agemin; i <= (int)agemax+3; i++){          which slows down the processing. The difference can be up to 10%
           for(jk=1; jk <=nlstate ; jk++){          lower mortality.
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            */
               pp[jk] += freq[jk][m][i];            lli=log(out[s1][s2] - savm[s1][s2]);
           }  
           for(jk=1; jk <=nlstate ; jk++){  
             for(m=-1, pos=0; m <=0 ; m++)          } else if  (s2==-2) {
             pos += freq[jk][m][i];            for (j=1,survp=0. ; j<=nlstate; j++) 
         }              survp += out[s1][j];
                    lli= survp;
          for(jk=1; jk <=nlstate ; jk++){          }
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          
              pp[jk] += freq[jk][m][i];          else if  (s2==-4) {
          }            for (j=3,survp=0. ; j<=nlstate; j++) 
                        survp += out[s1][j];
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];            lli= survp;
           }
          for(jk=1; jk <=nlstate ; jk++){                    
            if( i <= (int) agemax){          else if  (s2==-5) {
              if(pos>=1.e-5){            for (j=1,survp=0. ; j<=2; j++) 
                probs[i][jk][j1]= pp[jk]/pos;              survp += out[s1][j];
              }            lli= survp;
            }          }
          }  
            
         }          else{
     }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
            } 
            /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          /*if(lli ==000.0)*/
   free_vector(pp,1,nlstate);          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
            ipmx +=1;
 }  /* End of Freq */          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 /************* Waves Concatenation ***************/        } /* end of wave */
       } /* end of individual */
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    }  else if(mle==2){
 {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      Death is a valid wave (if date is known).        for(mi=1; mi<= wav[i]-1; mi++){
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          for (ii=1;ii<=nlstate+ndeath;ii++)
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            for (j=1;j<=nlstate+ndeath;j++){
      and mw[mi+1][i]. dh depends on stepm.              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   int i, mi, m;          for(d=0; d<=dh[mi][i]; d++){
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;            newm=savm;
      double sum=0., jmean=0.;*/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   int j, k=0,jk, ju, jl;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double sum=0.;            }
   jmin=1e+5;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   jmax=-1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   jmean=0.;            savm=oldm;
   for(i=1; i<=imx; i++){            oldm=newm;
     mi=0;          } /* end mult */
     m=firstpass;        
     while(s[m][i] <= nlstate){          s1=s[mw[mi][i]][i];
       if(s[m][i]>=1)          s2=s[mw[mi+1][i]][i];
         mw[++mi][i]=m;          bbh=(double)bh[mi][i]/(double)stepm; 
       if(m >=lastpass)          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 */
         break;          ipmx +=1;
       else          sw += weight[i];
         m++;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }/* end while */        } /* end of wave */
     if (s[m][i] > nlstate){      } /* end of individual */
       mi++;     /* Death is another wave */    }  else if(mle==3){  /* exponential inter-extrapolation */
       /* if(mi==0)  never been interviewed correctly before death */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          /* Only death is a correct wave */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       mw[mi][i]=m;        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
     wav[i]=mi;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     if(mi==0)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            }
   }          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   for(i=1; i<=imx; i++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(mi=1; mi<wav[i];mi++){            for (kk=1; kk<=cptcovage;kk++) {
       if (stepm <=0)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         dh[mi][i]=1;            }
       else{            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         if (s[mw[mi+1][i]][i] > nlstate) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           if (agedc[i] < 2*AGESUP) {            savm=oldm;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);            oldm=newm;
           if(j==0) j=1;  /* Survives at least one month after exam */          } /* end mult */
           k=k+1;        
           if (j >= jmax) jmax=j;          s1=s[mw[mi][i]][i];
           if (j <= jmin) jmin=j;          s2=s[mw[mi+1][i]][i];
           sum=sum+j;          bbh=(double)bh[mi][i]/(double)stepm; 
           /* if (j<10) printf("j=%d num=%d ",j,i); */          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
           }          ipmx +=1;
         }          sw += weight[i];
         else{          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        } /* end of wave */
           k=k+1;      } /* end of individual */
           if (j >= jmax) jmax=j;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
           else if (j <= jmin)jmin=j;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           sum=sum+j;        for(mi=1; mi<= wav[i]-1; mi++){
         }          for (ii=1;ii<=nlstate+ndeath;ii++)
         jk= j/stepm;            for (j=1;j<=nlstate+ndeath;j++){
         jl= j -jk*stepm;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         ju= j -(jk+1)*stepm;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         if(jl <= -ju)            }
           dh[mi][i]=jk;          for(d=0; d<dh[mi][i]; d++){
         else            newm=savm;
           dh[mi][i]=jk+1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         if(dh[mi][i]==0)            for (kk=1; kk<=cptcovage;kk++) {
           dh[mi][i]=1; /* At least one step */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
     }          
   }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   jmean=sum/k;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            savm=oldm;
  }            oldm=newm;
 /*********** Tricode ****************************/          } /* end mult */
 void tricode(int *Tvar, int **nbcode, int imx)        
 {          s1=s[mw[mi][i]][i];
   int Ndum[20],ij=1, k, j, i;          s2=s[mw[mi+1][i]][i];
   int cptcode=0;          if( s2 > nlstate){ 
   cptcoveff=0;            lli=log(out[s1][s2] - savm[s1][s2]);
            }else{
   for (k=0; k<19; k++) Ndum[k]=0;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   for (k=1; k<=7; k++) ncodemax[k]=0;          }
           ipmx +=1;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          sw += weight[i];
     for (i=1; i<=imx; i++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       ij=(int)(covar[Tvar[j]][i]);  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       Ndum[ij]++;        } /* end of wave */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      } /* end of individual */
       if (ij > cptcode) cptcode=ij;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for (i=0; i<=cptcode; i++) {        for(mi=1; mi<= wav[i]-1; mi++){
       if(Ndum[i]!=0) ncodemax[j]++;          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);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
     for (i=1; i<=ncodemax[j]; i++) {          for(d=0; d<dh[mi][i]; d++){
       for (k=0; k<=19; k++) {            newm=savm;
         if (Ndum[k] != 0) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           nbcode[Tvar[j]][ij]=k;            for (kk=1; kk<=cptcovage;kk++) {
           ij++;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }            }
         if (ij > ncodemax[j]) break;          
       }              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }              savm=oldm;
             oldm=newm;
  for (k=0; k<19; k++) Ndum[k]=0;          } /* end mult */
         
  for (i=1; i<=ncovmodel-2; i++) {          s1=s[mw[mi][i]][i];
       ij=Tvar[i];          s2=s[mw[mi+1][i]][i];
       Ndum[ij]++;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     }          ipmx +=1;
           sw += weight[i];
  ij=1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
  for (i=1; i<=10; i++) {          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
    if((Ndum[i]!=0) && (i<=ncov)){        } /* end of wave */
      Tvaraff[ij]=i;      } /* end of individual */
      ij++;    } /* End of if */
    }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
  }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
      l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     cptcoveff=ij-1;    return -l;
 }  }
   
 /*********** Health Expectancies ****************/  /*************** log-likelihood *************/
   double funcone( double *x)
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)  {
 {    /* Same as likeli but slower because of a lot of printf and if */
   /* Health expectancies */    int i, ii, j, k, mi, d, kk;
   int i, j, nhstepm, hstepm, h;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   double age, agelim,hf;    double **out;
   double ***p3mat;    double lli; /* Individual log likelihood */
      double llt;
   fprintf(ficreseij,"# Health expectancies\n");    int s1, s2;
   fprintf(ficreseij,"# Age");    double bbh, survp;
   for(i=1; i<=nlstate;i++)    /*extern weight */
     for(j=1; j<=nlstate;j++)    /* We are differentiating ll according to initial status */
       fprintf(ficreseij," %1d-%1d",i,j);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   fprintf(ficreseij,"\n");    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
   hstepm=1*YEARM; /*  Every j years of age (in month) */    */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    cov[1]=1.;
   
   agelim=AGESUP;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     /* nhstepm age range expressed in number of stepm */    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     /* Typically if 20 years = 20*12/6=40 stepm */      for(mi=1; mi<= wav[i]-1; mi++){
     if (stepm >= YEARM) hstepm=1;        for (ii=1;ii<=nlstate+ndeath;ii++)
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */          for (j=1;j<=nlstate+ndeath;j++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            savm[ii][j]=(ii==j ? 1.0 : 0.0);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          }
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          for(d=0; d<dh[mi][i]; d++){
           newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(i=1; i<=nlstate;i++)          for (kk=1; kk<=cptcovage;kk++) {
       for(j=1; j<=nlstate;j++)            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          }
           eij[i][j][(int)age] +=p3mat[i][j][h];          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
     hf=1;          oldm=newm;
     if (stepm >= YEARM) hf=stepm/YEARM;        } /* end mult */
     fprintf(ficreseij,"%.0f",age );        
     for(i=1; i<=nlstate;i++)        s1=s[mw[mi][i]][i];
       for(j=1; j<=nlstate;j++){        s2=s[mw[mi+1][i]][i];
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);        bbh=(double)bh[mi][i]/(double)stepm; 
       }        /* bias is positive if real duration
     fprintf(ficreseij,"\n");         * is higher than the multiple of stepm and negative otherwise.
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         */
   }        if( s2 > nlstate && (mle <5) ){  /* Jackson */
 }          lli=log(out[s1][s2] - savm[s1][s2]);
         } else if (mle==1){
 /************ Variance ******************/          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 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)        } 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 */
   /* Variance of health expectancies */        } else if(mle==3){  /* exponential inter-extrapolation */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          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 */
   double **newm;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   double **dnewm,**doldm;          lli=log(out[s1][s2]); /* Original formula */
   int i, j, nhstepm, hstepm, h;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   int k, cptcode;          lli=log(out[s1][s2]); /* Original formula */
   double *xp;        } /* End of if */
   double **gp, **gm;        ipmx +=1;
   double ***gradg, ***trgradg;        sw += weight[i];
   double ***p3mat;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double age,agelim;  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   int theta;        if(globpr){
           fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
    fprintf(ficresvij,"# Covariances of life expectancies\n");   %10.6f %10.6f %10.6f ", \
   fprintf(ficresvij,"# Age");                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   for(i=1; i<=nlstate;i++)                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     for(j=1; j<=nlstate;j++)          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            llt +=ll[k]*gipmx/gsw;
   fprintf(ficresvij,"\n");            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
   xp=vector(1,npar);          fprintf(ficresilk," %10.6f\n", -llt);
   dnewm=matrix(1,nlstate,1,npar);        }
   doldm=matrix(1,nlstate,1,nlstate);      } /* end of wave */
      } /* end of individual */
   hstepm=1*YEARM; /* Every year of age */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   agelim = AGESUP;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    if(globpr==0){ /* First time we count the contributions and weights */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      gipmx=ipmx;
     if (stepm >= YEARM) hstepm=1;      gsw=sw;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    return -l;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  }
     gp=matrix(0,nhstepm,1,nlstate);  
     gm=matrix(0,nhstepm,1,nlstate);  
   /*************** function likelione ***********/
     for(theta=1; theta <=npar; theta++){  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
       for(i=1; i<=npar; i++){ /* Computes gradient */  {
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    /* This routine should help understanding what is done with 
       }       the selection of individuals/waves and
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);         to check the exact contribution to the likelihood.
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       Plotting could be done.
      */
       if (popbased==1) {    int k;
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];    if(*globpri !=0){ /* Just counts and sums, no printings */
       }      strcpy(fileresilk,"ilk"); 
            strcat(fileresilk,fileres);
       for(j=1; j<= nlstate; j++){      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         for(h=0; h<=nhstepm; h++){        printf("Problem with resultfile: %s\n", fileresilk);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      }
         }      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
       }      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
          /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(i=1; i<=npar; i++) /* Computes gradient */      for(k=1; k<=nlstate; k++) 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    }
   
       if (popbased==1) {    *fretone=(*funcone)(p);
         for(i=1; i<=nlstate;i++)    if(*globpri !=0){
           prlim[i][i]=probs[(int)age][i][ij];      fclose(ficresilk);
       }      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       fflush(fichtm); 
       for(j=1; j<= nlstate; j++){    } 
         for(h=0; h<=nhstepm; h++){    return;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  }
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }  
       }  /*********** Maximum Likelihood Estimation ***************/
   
       for(j=1; j<= nlstate; j++)  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
         for(h=0; h<=nhstepm; h++){  {
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    int i,j, iter;
         }    double **xi;
     } /* End theta */    double fret;
     double fretone; /* Only one call to likelihood */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    /*  char filerespow[FILENAMELENGTH];*/
     xi=matrix(1,npar,1,npar);
     for(h=0; h<=nhstepm; h++)    for (i=1;i<=npar;i++)
       for(j=1; j<=nlstate;j++)      for (j=1;j<=npar;j++)
         for(theta=1; theta <=npar; theta++)        xi[i][j]=(i==j ? 1.0 : 0.0);
           trgradg[h][j][theta]=gradg[h][theta][j];    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
     for(i=1;i<=nlstate;i++)    strcat(filerespow,fileres);
       for(j=1;j<=nlstate;j++)    if((ficrespow=fopen(filerespow,"w"))==NULL) {
         vareij[i][j][(int)age] =0.;      printf("Problem with resultfile: %s\n", filerespow);
     for(h=0;h<=nhstepm;h++){      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       for(k=0;k<=nhstepm;k++){    }
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    for (i=1;i<=nlstate;i++)
         for(i=1;i<=nlstate;i++)      for(j=1;j<=nlstate+ndeath;j++)
           for(j=1;j<=nlstate;j++)        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
             vareij[i][j][(int)age] += doldm[i][j];    fprintf(ficrespow,"\n");
       }  
     }    powell(p,xi,npar,ftol,&iter,&fret,func);
     h=1;  
     if (stepm >= YEARM) h=stepm/YEARM;    free_matrix(xi,1,npar,1,npar);
     fprintf(ficresvij,"%.0f ",age );    fclose(ficrespow);
     for(i=1; i<=nlstate;i++)    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       for(j=1; j<=nlstate;j++){    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       }  
     fprintf(ficresvij,"\n");  }
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);  /**** Computes Hessian and covariance matrix ***/
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  {
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double  **a,**y,*x,pd;
   } /* End age */    double **hess;
      int i, j,jk;
   free_vector(xp,1,npar);    int *indx;
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
 }    void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
 /************ Variance of prevlim ******************/    double gompertz(double p[]);
 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)    hess=matrix(1,npar,1,npar);
 {  
   /* Variance of prevalence limit */    printf("\nCalculation of the hessian matrix. Wait...\n");
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   double **newm;    for (i=1;i<=npar;i++){
   double **dnewm,**doldm;      printf("%d",i);fflush(stdout);
   int i, j, nhstepm, hstepm;      fprintf(ficlog,"%d",i);fflush(ficlog);
   int k, cptcode;     
   double *xp;       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   double *gp, *gm;      
   double **gradg, **trgradg;      /*  printf(" %f ",p[i]);
   double age,agelim;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   int theta;    }
        
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    for (i=1;i<=npar;i++) {
   fprintf(ficresvpl,"# Age");      for (j=1;j<=npar;j++)  {
   for(i=1; i<=nlstate;i++)        if (j>i) { 
       fprintf(ficresvpl," %1d-%1d",i,i);          printf(".%d%d",i,j);fflush(stdout);
   fprintf(ficresvpl,"\n");          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,delti,i,j,func,npar);
   xp=vector(1,npar);          
   dnewm=matrix(1,nlstate,1,npar);          hess[j][i]=hess[i][j];    
   doldm=matrix(1,nlstate,1,nlstate);          /*printf(" %lf ",hess[i][j]);*/
          }
   hstepm=1*YEARM; /* Every year of age */      }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    }
   agelim = AGESUP;    printf("\n");
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    fprintf(ficlog,"\n");
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
     if (stepm >= YEARM) hstepm=1;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     gradg=matrix(1,npar,1,nlstate);    
     gp=vector(1,nlstate);    a=matrix(1,npar,1,npar);
     gm=vector(1,nlstate);    y=matrix(1,npar,1,npar);
     x=vector(1,npar);
     for(theta=1; theta <=npar; theta++){    indx=ivector(1,npar);
       for(i=1; i<=npar; i++){ /* Computes gradient */    for (i=1;i<=npar;i++)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       }    ludcmp(a,npar,indx,&pd);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    for (j=1;j<=npar;j++) {
         gp[i] = prlim[i][i];      for (i=1;i<=npar;i++) x[i]=0;
          x[j]=1;
       for(i=1; i<=npar; i++) /* Computes gradient */      lubksb(a,npar,indx,x);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (i=1;i<=npar;i++){ 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        matcov[i][j]=x[i];
       for(i=1;i<=nlstate;i++)      }
         gm[i] = prlim[i][i];    }
   
       for(i=1;i<=nlstate;i++)    printf("\n#Hessian matrix#\n");
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    fprintf(ficlog,"\n#Hessian matrix#\n");
     } /* End theta */    for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
     trgradg =matrix(1,nlstate,1,npar);        printf("%.3e ",hess[i][j]);
         fprintf(ficlog,"%.3e ",hess[i][j]);
     for(j=1; j<=nlstate;j++)      }
       for(theta=1; theta <=npar; theta++)      printf("\n");
         trgradg[j][theta]=gradg[theta][j];      fprintf(ficlog,"\n");
     }
     for(i=1;i<=nlstate;i++)  
       varpl[i][(int)age] =0.;    /* Recompute Inverse */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    for (i=1;i<=npar;i++)
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     for(i=1;i<=nlstate;i++)    ludcmp(a,npar,indx,&pd);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  
     /*  printf("\n#Hessian matrix recomputed#\n");
     fprintf(ficresvpl,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)    for (j=1;j<=npar;j++) {
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      for (i=1;i<=npar;i++) x[i]=0;
     fprintf(ficresvpl,"\n");      x[j]=1;
     free_vector(gp,1,nlstate);      lubksb(a,npar,indx,x);
     free_vector(gm,1,nlstate);      for (i=1;i<=npar;i++){ 
     free_matrix(gradg,1,npar,1,nlstate);        y[i][j]=x[i];
     free_matrix(trgradg,1,nlstate,1,npar);        printf("%.3e ",y[i][j]);
   } /* End age */        fprintf(ficlog,"%.3e ",y[i][j]);
       }
   free_vector(xp,1,npar);      printf("\n");
   free_matrix(doldm,1,nlstate,1,npar);      fprintf(ficlog,"\n");
   free_matrix(dnewm,1,nlstate,1,nlstate);    }
     */
 }  
     free_matrix(a,1,npar,1,npar);
 /************ Variance of one-step probabilities  ******************/    free_matrix(y,1,npar,1,npar);
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    free_vector(x,1,npar);
 {    free_ivector(indx,1,npar);
   int i, j;    free_matrix(hess,1,npar,1,npar);
   int k=0, cptcode;  
   double **dnewm,**doldm;  
   double *xp;  }
   double *gp, *gm;  
   double **gradg, **trgradg;  /*************** hessian matrix ****************/
   double age,agelim, cov[NCOVMAX];  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   int theta;  {
   char fileresprob[FILENAMELENGTH];    int i;
     int l=1, lmax=20;
   strcpy(fileresprob,"prob");    double k1,k2;
   strcat(fileresprob,fileres);    double p2[NPARMAX+1];
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    double res;
     printf("Problem with resultfile: %s\n", fileresprob);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   }    double fx;
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    int k=0,kmax=10;
      double l1;
   
   xp=vector(1,npar);    fx=func(x);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    for (i=1;i<=npar;i++) p2[i]=x[i];
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    for(l=0 ; l <=lmax; l++){
        l1=pow(10,l);
   cov[1]=1;      delts=delt;
   for (age=bage; age<=fage; age ++){      for(k=1 ; k <kmax; k=k+1){
     cov[2]=age;        delt = delta*(l1*k);
     gradg=matrix(1,npar,1,9);        p2[theta]=x[theta] +delt;
     trgradg=matrix(1,9,1,npar);        k1=func(p2)-fx;
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        p2[theta]=x[theta]-delt;
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        k2=func(p2)-fx;
            /*res= (k1-2.0*fx+k2)/delt/delt; */
     for(theta=1; theta <=npar; theta++){        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       for(i=1; i<=npar; i++)        
         xp[i] = x[i] + (i==theta ?delti[theta]: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);
       pmij(pmmij,cov,ncovmodel,xp,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);
      #endif
       k=0;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       for(i=1; i<= (nlstate+ndeath); i++){        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         for(j=1; j<=(nlstate+ndeath);j++){          k=kmax;
            k=k+1;        }
           gp[k]=pmmij[i][j];        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         }          k=kmax; l=lmax*10.;
       }        }
         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       for(i=1; i<=npar; i++)          delts=delt;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        }
          }
     }
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    delti[theta]=delts;
       k=0;    return res; 
       for(i=1; i<=(nlstate+ndeath); i++){    
         for(j=1; j<=(nlstate+ndeath);j++){  }
           k=k+1;  
           gm[k]=pmmij[i][j];  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
         }  {
       }    int i;
          int l=1, l1, lmax=20;
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    double k1,k2,k3,k4,res,fx;
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      double p2[NPARMAX+1];
     }    int k;
   
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    fx=func(x);
       for(theta=1; theta <=npar; theta++)    for (k=1; k<=2; k++) {
       trgradg[j][theta]=gradg[theta][j];      for (i=1;i<=npar;i++) p2[i]=x[i];
        p2[thetai]=x[thetai]+delti[thetai]/k;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);      k1=func(p2)-fx;
     
      pmij(pmmij,cov,ncovmodel,x,nlstate);      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
      k=0;      k2=func(p2)-fx;
      for(i=1; i<=(nlstate+ndeath); i++){    
        for(j=1; j<=(nlstate+ndeath);j++){      p2[thetai]=x[thetai]-delti[thetai]/k;
          k=k+1;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
          gm[k]=pmmij[i][j];      k3=func(p2)-fx;
         }    
      }      p2[thetai]=x[thetai]-delti[thetai]/k;
            p2[thetaj]=x[thetaj]-delti[thetaj]/k;
      /*printf("\n%d ",(int)age);      k4=func(p2)-fx;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
          #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);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      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
     }
   fprintf(ficresprob,"\n%d ",(int)age);    return res;
   }
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  /************** Inverse of matrix **************/
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  void ludcmp(double **a, int n, int *indx, double *d) 
   }  { 
     int i,imax,j,k; 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    double big,dum,sum,temp; 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    double *vv; 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);   
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    vv=vector(1,n); 
 }    *d=1.0; 
  free_vector(xp,1,npar);    for (i=1;i<=n;i++) { 
 fclose(ficresprob);      big=0.0; 
  exit(0);      for (j=1;j<=n;j++) 
 }        if ((temp=fabs(a[i][j])) > big) big=temp; 
       if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 /***********************************************/      vv[i]=1.0/big; 
 /**************** Main Program *****************/    } 
 /***********************************************/    for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
 int main(int argc, char *argv[])        sum=a[i][j]; 
 {        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      } 
   double agedeb, agefin,hf;      big=0.0; 
   double agemin=1.e20, agemax=-1.e20;      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
   double fret;        for (k=1;k<j;k++) 
   double **xi,tmp,delta;          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
   double dum; /* Dummy variable */        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   double ***p3mat;          big=dum; 
   int *indx;          imax=i; 
   char line[MAXLINE], linepar[MAXLINE];        } 
   char title[MAXLINE];      } 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];      if (j != imax) { 
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];        for (k=1;k<=n;k++) { 
            dum=a[imax][k]; 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];          a[imax][k]=a[j][k]; 
           a[j][k]=dum; 
   char filerest[FILENAMELENGTH];        } 
   char fileregp[FILENAMELENGTH];        *d = -(*d); 
   char popfile[FILENAMELENGTH];        vv[imax]=vv[j]; 
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      } 
   int firstobs=1, lastobs=10;      indx[j]=imax; 
   int sdeb, sfin; /* Status at beginning and end */      if (a[j][j] == 0.0) a[j][j]=TINY; 
   int c,  h , cpt,l;      if (j != n) { 
   int ju,jl, mi;        dum=1.0/(a[j][j]); 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      } 
   int mobilav=0,popforecast=0;    } 
   int hstepm, nhstepm;    free_vector(vv,1,n);  /* Doesn't work */
   int *popage;/*boolprev=0 if date and zero if wave*/  ;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;  } 
   
   double bage, fage, age, agelim, agebase;  void lubksb(double **a, int n, int *indx, double b[]) 
   double ftolpl=FTOL;  { 
   double **prlim;    int i,ii=0,ip,j; 
   double *severity;    double sum; 
   double ***param; /* Matrix of parameters */   
   double  *p;    for (i=1;i<=n;i++) { 
   double **matcov; /* Matrix of covariance */      ip=indx[i]; 
   double ***delti3; /* Scale */      sum=b[ip]; 
   double *delti; /* Scale */      b[ip]=b[i]; 
   double ***eij, ***vareij;      if (ii) 
   double **varpl; /* Variances of prevalence limits by age */        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   double *epj, vepp;      else if (sum) ii=i; 
   double kk1, kk2;      b[i]=sum; 
   double *popeffectif,*popcount;    } 
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;    for (i=n;i>=1;i--) { 
   double yp,yp1,yp2;      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";      b[i]=sum/a[i][i]; 
   char *alph[]={"a","a","b","c","d","e"}, str[4];    } 
   } 
   
   char z[1]="c", occ;  /************ Frequencies ********************/
 #include <sys/time.h>  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[])
 #include <time.h>  {  /* Some frequencies */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    
      int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   /* long total_usecs;    int first;
   struct timeval start_time, end_time;    double ***freq; /* Frequencies */
      double *pp, **prop;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     FILE *ficresp;
     char fileresp[FILENAMELENGTH];
   printf("\n%s",version);    
   if(argc <=1){    pp=vector(1,nlstate);
     printf("\nEnter the parameter file name: ");    prop=matrix(1,nlstate,iagemin,iagemax+3);
     scanf("%s",pathtot);    strcpy(fileresp,"p");
   }    strcat(fileresp,fileres);
   else{    if((ficresp=fopen(fileresp,"w"))==NULL) {
     strcpy(pathtot,argv[1]);      printf("Problem with prevalence resultfile: %s\n", fileresp);
   }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/      exit(0);
   /*cygwin_split_path(pathtot,path,optionfile);    }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   /* cutv(path,optionfile,pathtot,'\\');*/    j1=0;
     
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    j=cptcoveff;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   chdir(path);  
   replace(pathc,path);    first=1;
   
 /*-------- arguments in the command line --------*/    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
   strcpy(fileres,"r");        j1++;
   strcat(fileres, optionfilefiname);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   strcat(fileres,".txt");    /* Other files have txt extension */          scanf("%d", i);*/
         for (i=-5; i<=nlstate+ndeath; i++)  
   /*---------arguments file --------*/          for (jk=-5; jk<=nlstate+ndeath; jk++)  
             for(m=iagemin; m <= iagemax+3; m++)
   if((ficpar=fopen(optionfile,"r"))==NULL)    {              freq[i][jk][m]=0;
     printf("Problem with optionfile %s\n",optionfile);  
     goto end;      for (i=1; i<=nlstate; i++)  
   }        for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
   strcpy(filereso,"o");        
   strcat(filereso,fileres);        dateintsum=0;
   if((ficparo=fopen(filereso,"w"))==NULL) {        k2cpt=0;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        for (i=1; i<=imx; i++) {
   }          bool=1;
           if  (cptcovn>0) {
   /* Reads comments: lines beginning with '#' */            for (z1=1; z1<=cptcoveff; z1++) 
   while((c=getc(ficpar))=='#' && c!= EOF){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     ungetc(c,ficpar);                bool=0;
     fgets(line, MAXLINE, ficpar);          }
     puts(line);          if (bool==1){
     fputs(line,ficparo);            for(m=firstpass; m<=lastpass; m++){
   }              k2=anint[m][i]+(mint[m][i]/12.);
   ungetc(c,ficpar);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
   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);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   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);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   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);                if (m<lastpass) {
 while((c=getc(ficpar))=='#' && c!= EOF){                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     ungetc(c,ficpar);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     fgets(line, MAXLINE, ficpar);                }
     puts(line);                
     fputs(line,ficparo);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   }                  dateintsum=dateintsum+k2;
   ungetc(c,ficpar);                  k2cpt++;
                  }
                    /*}*/
   covar=matrix(0,NCOVMAX,1,n);            }
   cptcovn=0;          }
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;        }
          
   ncovmodel=2+cptcovn;        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  fprintf(ficresp, "#Local time at start: %s", strstart);
          if  (cptcovn>0) {
   /* Read guess parameters */          fprintf(ficresp, "\n#********** Variable "); 
   /* Reads comments: lines beginning with '#' */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresp, "**********\n#");
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);        for(i=1; i<=nlstate;i++) 
     puts(line);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     fputs(line,ficparo);        fprintf(ficresp, "\n");
   }        
   ungetc(c,ficpar);        for(i=iagemin; i <= iagemax+3; i++){
            if(i==iagemax+3){
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            fprintf(ficlog,"Total");
     for(i=1; i <=nlstate; i++)          }else{
     for(j=1; j <=nlstate+ndeath-1; j++){            if(first==1){
       fscanf(ficpar,"%1d%1d",&i1,&j1);              first=0;
       fprintf(ficparo,"%1d%1d",i1,j1);              printf("See log file for details...\n");
       printf("%1d%1d",i,j);            }
       for(k=1; k<=ncovmodel;k++){            fprintf(ficlog,"Age %d", i);
         fscanf(ficpar," %lf",&param[i][j][k]);          }
         printf(" %lf",param[i][j][k]);          for(jk=1; jk <=nlstate ; jk++){
         fprintf(ficparo," %lf",param[i][j][k]);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       }              pp[jk] += freq[jk][m][i]; 
       fscanf(ficpar,"\n");          }
       printf("\n");          for(jk=1; jk <=nlstate ; jk++){
       fprintf(ficparo,"\n");            for(m=-1, pos=0; m <=0 ; m++)
     }              pos += freq[jk][m][i];
              if(pp[jk]>=1.e-10){
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;              if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   p=param[1][1];              }
                fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   /* Reads comments: lines beginning with '#' */            }else{
   while((c=getc(ficpar))=='#' && c!= EOF){              if(first==1)
     ungetc(c,ficpar);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     fgets(line, MAXLINE, ficpar);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     puts(line);            }
     fputs(line,ficparo);          }
   }  
   ungetc(c,ficpar);          for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              pp[jk] += freq[jk][m][i];
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          }       
   for(i=1; i <=nlstate; i++){          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     for(j=1; j <=nlstate+ndeath-1; j++){            pos += pp[jk];
       fscanf(ficpar,"%1d%1d",&i1,&j1);            posprop += prop[jk][i];
       printf("%1d%1d",i,j);          }
       fprintf(ficparo,"%1d%1d",i1,j1);          for(jk=1; jk <=nlstate ; jk++){
       for(k=1; k<=ncovmodel;k++){            if(pos>=1.e-5){
         fscanf(ficpar,"%le",&delti3[i][j][k]);              if(first==1)
         printf(" %le",delti3[i][j][k]);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         fprintf(ficparo," %le",delti3[i][j][k]);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       }            }else{
       fscanf(ficpar,"\n");              if(first==1)
       printf("\n");                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       fprintf(ficparo,"\n");              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     }            }
   }            if( i <= iagemax){
   delti=delti3[1][1];              if(pos>=1.e-5){
                  fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   /* Reads comments: lines beginning with '#' */                /*probs[i][jk][j1]= pp[jk]/pos;*/
   while((c=getc(ficpar))=='#' && c!= EOF){                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     ungetc(c,ficpar);              }
     fgets(line, MAXLINE, ficpar);              else
     puts(line);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     fputs(line,ficparo);            }
   }          }
   ungetc(c,ficpar);          
            for(jk=-1; jk <=nlstate+ndeath; jk++)
   matcov=matrix(1,npar,1,npar);            for(m=-1; m <=nlstate+ndeath; m++)
   for(i=1; i <=npar; i++){              if(freq[jk][m][i] !=0 ) {
     fscanf(ficpar,"%s",&str);              if(first==1)
     printf("%s",str);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     fprintf(ficparo,"%s",str);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     for(j=1; j <=i; j++){              }
       fscanf(ficpar," %le",&matcov[i][j]);          if(i <= iagemax)
       printf(" %.5le",matcov[i][j]);            fprintf(ficresp,"\n");
       fprintf(ficparo," %.5le",matcov[i][j]);          if(first==1)
     }            printf("Others in log...\n");
     fscanf(ficpar,"\n");          fprintf(ficlog,"\n");
     printf("\n");        }
     fprintf(ficparo,"\n");      }
   }    }
   for(i=1; i <=npar; i++)    dateintmean=dateintsum/k2cpt; 
     for(j=i+1;j<=npar;j++)   
       matcov[i][j]=matcov[j][i];    fclose(ficresp);
        free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   printf("\n");    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
     /*-------- data file ----------*/  }
     if((ficres =fopen(fileres,"w"))==NULL) {  
       printf("Problem with resultfile: %s\n", fileres);goto end;  /************ Prevalence ********************/
     }  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
     fprintf(ficres,"#%s\n",version);  {  
        /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     if((fic=fopen(datafile,"r"))==NULL)    {       in each health status at the date of interview (if between dateprev1 and dateprev2).
       printf("Problem with datafile: %s\n", datafile);goto end;       We still use firstpass and lastpass as another selection.
     }    */
    
     n= lastobs;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     severity = vector(1,maxwav);    double ***freq; /* Frequencies */
     outcome=imatrix(1,maxwav+1,1,n);    double *pp, **prop;
     num=ivector(1,n);    double pos,posprop; 
     moisnais=vector(1,n);    double  y2; /* in fractional years */
     annais=vector(1,n);    int iagemin, iagemax;
     moisdc=vector(1,n);  
     andc=vector(1,n);    iagemin= (int) agemin;
     agedc=vector(1,n);    iagemax= (int) agemax;
     cod=ivector(1,n);    /*pp=vector(1,nlstate);*/
     weight=vector(1,n);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     mint=matrix(1,maxwav,1,n);    j1=0;
     anint=matrix(1,maxwav,1,n);    
     s=imatrix(1,maxwav+1,1,n);    j=cptcoveff;
     adl=imatrix(1,maxwav+1,1,n);        if (cptcovn<1) {j=1;ncodemax[1]=1;}
     tab=ivector(1,NCOVMAX);    
     ncodemax=ivector(1,8);    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
     i=1;        j1++;
     while (fgets(line, MAXLINE, fic) != NULL)    {        
       if ((i >= firstobs) && (i <=lastobs)) {        for (i=1; i<=nlstate; i++)  
                  for(m=iagemin; m <= iagemax+3; m++)
         for (j=maxwav;j>=1;j--){            prop[i][m]=0.0;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);       
           strcpy(line,stra);        for (i=1; i<=imx; i++) { /* Each individual */
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          bool=1;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          if  (cptcovn>0) {
         }            for (z1=1; z1<=cptcoveff; z1++) 
                      if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);                bool=0;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          } 
           if (bool==1) { 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         for (j=ncov;j>=1;j--){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
         }                if (s[m][i]>0 && s[m][i]<=nlstate) { 
         num[i]=atol(stra);                  /*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];
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){                  prop[s[m][i]][iagemax+3] += weight[i]; 
           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;            } /* end selection of waves */
       }          }
     }        }
     /* printf("ii=%d", ij);        for(i=iagemin; i <= iagemax+3; i++){  
        scanf("%d",i);*/          
   imx=i-1; /* Number of individuals */          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
   /* for (i=1; i<=imx; i++){          } 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;  
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;          for(jk=1; jk <=nlstate ; jk++){     
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;            if( i <=  iagemax){ 
     }              if(posprop>=1.e-5){ 
                 probs[i][jk][j1]= prop[jk][i]/posprop;
     for (i=1; i<=imx; i++)              } 
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/            } 
           }/* end jk */ 
   /* Calculation of the number of parameter from char model*/        }/* end i */ 
   Tvar=ivector(1,15);      } /* end i1 */
   Tprod=ivector(1,15);    } /* end k1 */
   Tvaraff=ivector(1,15);    
   Tvard=imatrix(1,15,1,2);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   Tage=ivector(1,15);          /*free_vector(pp,1,nlstate);*/
        free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   if (strlen(model) >1){  }  /* End of prevalence */
     j=0, j1=0, k1=1, k2=1;  
     j=nbocc(model,'+');  /************* Waves Concatenation ***************/
     j1=nbocc(model,'*');  
     cptcovn=j+1;  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
     cptcovprod=j1;  {
        /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
           Death is a valid wave (if date is known).
     strcpy(modelsav,model);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       printf("Error. Non available option model=%s ",model);       and mw[mi+1][i]. dh depends on stepm.
       goto end;       */
     }  
        int i, mi, m;
     for(i=(j+1); i>=1;i--){    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       cutv(stra,strb,modelsav,'+');       double sum=0., jmean=0.;*/
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    int first;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    int j, k=0,jk, ju, jl;
       /*scanf("%d",i);*/    double sum=0.;
       if (strchr(strb,'*')) {    first=0;
         cutv(strd,strc,strb,'*');    jmin=1e+5;
         if (strcmp(strc,"age")==0) {    jmax=-1;
           cptcovprod--;    jmean=0.;
           cutv(strb,stre,strd,'V');    for(i=1; i<=imx; i++){
           Tvar[i]=atoi(stre);      mi=0;
           cptcovage++;      m=firstpass;
             Tage[cptcovage]=i;      while(s[m][i] <= nlstate){
             /*printf("stre=%s ", stre);*/        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
         }          mw[++mi][i]=m;
         else if (strcmp(strd,"age")==0) {        if(m >=lastpass)
           cptcovprod--;          break;
           cutv(strb,stre,strc,'V');        else
           Tvar[i]=atoi(stre);          m++;
           cptcovage++;      }/* end while */
           Tage[cptcovage]=i;      if (s[m][i] > nlstate){
         }        mi++;     /* Death is another wave */
         else {        /* if(mi==0)  never been interviewed correctly before death */
           cutv(strb,stre,strc,'V');           /* Only death is a correct wave */
           Tvar[i]=ncov+k1;        mw[mi][i]=m;
           cutv(strb,strc,strd,'V');      }
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc);      wav[i]=mi;
           Tvard[k1][2]=atoi(stre);      if(mi==0){
           Tvar[cptcovn+k2]=Tvard[k1][1];        nbwarn++;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        if(first==0){
           for (k=1; k<=lastobs;k++)          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];          first=1;
           k1++;        }
           k2=k2+2;        if(first==1){
         }          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
       }        }
       else {      } /* end mi==0 */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    } /* End individuals */
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');    for(i=1; i<=imx; i++){
       Tvar[i]=atoi(strc);      for(mi=1; mi<wav[i];mi++){
       }        if (stepm <=0)
       strcpy(modelsav,stra);            dh[mi][i]=1;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        else{
         scanf("%d",i);*/          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     }            if (agedc[i] < 2*AGESUP) {
 }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                if(j==0) j=1;  /* Survives at least one month after exam */
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);              else if(j<0){
   printf("cptcovprod=%d ", cptcovprod);                nberr++;
   scanf("%d ",i);*/                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]);
     fclose(fic);                j=1; /* Temporary Dangerous patch */
                 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);
     /*  if(mle==1){*/                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     if (weightopt != 1) { /* Maximisation without weights*/                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);
       for(i=1;i<=n;i++) weight[i]=1.0;              }
     }              k=k+1;
     /*-calculation of age at interview from date of interview and age at death -*/              if (j >= jmax){
     agev=matrix(1,maxwav,1,imx);                jmax=j;
                 ijmax=i;
    for (i=1; i<=imx; i++)              }
      for(m=2; (m<= maxwav); m++)              if (j <= jmin){
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){                jmin=j;
          anint[m][i]=9999;                ijmin=i;
          s[m][i]=-1;              }
        }              sum=sum+j;
                  /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     for (i=1; i<=imx; i++)  {              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);            }
       for(m=1; (m<= maxwav); m++){          }
         if(s[m][i] >0){          else{
           if (s[m][i] == nlstate+1) {            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
             if(agedc[i]>0)  /*        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]); */
               if(moisdc[i]!=99 && andc[i]!=9999)  
               agev[m][i]=agedc[i];            k=k+1;
             else {            if (j >= jmax) {
               if (andc[i]!=9999){              jmax=j;
               printf("Warning negative age at death: %d line:%d\n",num[i],i);              ijmax=i;
               agev[m][i]=-1;            }
               }            else if (j <= jmin){
             }              jmin=j;
           }              ijmin=i;
           else if(s[m][i] !=9){ /* Should no more exist */            }
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             if(mint[m][i]==99 || anint[m][i]==9999)            /*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]);*/
               agev[m][i]=1;            if(j<0){
             else if(agev[m][i] <agemin){              nberr++;
               agemin=agev[m][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]);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/              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]);
             }            }
             else if(agev[m][i] >agemax){            sum=sum+j;
               agemax=agev[m][i];          }
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/          jk= j/stepm;
             }          jl= j -jk*stepm;
             /*agev[m][i]=anint[m][i]-annais[i];*/          ju= j -(jk+1)*stepm;
             /*   agev[m][i] = age[i]+2*m;*/          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           }            if(jl==0){
           else { /* =9 */              dh[mi][i]=jk;
             agev[m][i]=1;              bh[mi][i]=0;
             s[m][i]=-1;            }else{ /* We want a negative bias in order to only have interpolation ie
           }                    * at the price of an extra matrix product in likelihood */
         }              dh[mi][i]=jk+1;
         else /*= 0 Unknown */              bh[mi][i]=ju;
           agev[m][i]=1;            }
       }          }else{
                if(jl <= -ju){
     }              dh[mi][i]=jk;
     for (i=1; i<=imx; i++)  {              bh[mi][i]=jl;       /* bias is positive if real duration
       for(m=1; (m<= maxwav); m++){                                   * is higher than the multiple of stepm and negative otherwise.
         if (s[m][i] > (nlstate+ndeath)) {                                   */
           printf("Error: Wrong value in nlstate or ndeath\n");              }
           goto end;            else{
         }              dh[mi][i]=jk+1;
       }              bh[mi][i]=ju;
     }            }
             if(dh[mi][i]==0){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);              dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
     free_vector(severity,1,maxwav);              /*  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);*/
     free_imatrix(outcome,1,maxwav+1,1,n);            }
     free_vector(moisnais,1,n);          } /* end if mle */
     free_vector(annais,1,n);        }
     /* free_matrix(mint,1,maxwav,1,n);      } /* end wave */
        free_matrix(anint,1,maxwav,1,n);*/    }
     free_vector(moisdc,1,n);    jmean=sum/k;
     free_vector(andc,1,n);    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
     fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
       }
     wav=ivector(1,imx);  
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  /*********** Tricode ****************************/
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  void tricode(int *Tvar, int **nbcode, int imx)
      {
     /* Concatenates waves */    
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    int Ndum[20],ij=1, k, j, i, maxncov=19;
     int cptcode=0;
     cptcoveff=0; 
       Tcode=ivector(1,100);   
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    for (k=0; k<maxncov; k++) Ndum[k]=0;
       ncodemax[1]=1;    for (k=1; k<=7; k++) ncodemax[k]=0;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  
          for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
    codtab=imatrix(1,100,1,10);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
    h=0;                                 modality*/ 
    m=pow(2,cptcoveff);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
          Ndum[ij]++; /*store the modality */
    for(k=1;k<=cptcoveff; k++){        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
      for(i=1; i <=(m/pow(2,k));i++){        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
        for(j=1; j <= ncodemax[k]; j++){                                         Tvar[j]. If V=sex and male is 0 and 
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){                                         female is 1, then  cptcode=1.*/
            h++;      }
            if (h>m) h=1;codtab[h][k]=j;  
          }      for (i=0; i<=cptcode; i++) {
        }        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 */
      }      }
    }  
       ij=1; 
       for (i=1; i<=ncodemax[j]; i++) {
    /*for(i=1; i <=m ;i++){        for (k=0; k<= maxncov; k++) {
      for(k=1; k <=cptcovn; k++){          if (Ndum[k] != 0) {
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);            nbcode[Tvar[j]][ij]=k; 
      }            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
      printf("\n");            
    }            ij++;
    scanf("%d",i);*/          }
              if (ij > ncodemax[j]) break; 
    /* Calculates basic frequencies. Computes observed prevalence at single age        }  
        and prints on file fileres'p'. */      } 
     }  
      
       for (k=0; k< maxncov; k++) Ndum[k]=0;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   for (i=1; i<=ncovmodel-2; i++) { 
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     ij=Tvar[i];
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */     Ndum[ij]++;
         }
     /* 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] */   ij=1;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */   for (i=1; i<= maxncov; i++) {
      if((Ndum[i]!=0) && (i<=ncovcol)){
     if(mle==1){       Tvaraff[ij]=i; /*For printing */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);       ij++;
     }     }
       }
     /*--------- results files --------------*/   
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);   cptcoveff=ij-1; /*Number of simple covariates*/
    }
   
    jk=1;  /*********** Health Expectancies ****************/
    fprintf(ficres,"# Parameters\n");  
    printf("# Parameters\n");  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[] )
    for(i=1,jk=1; i <=nlstate; i++){  
      for(k=1; k <=(nlstate+ndeath); k++){  {
        if (k != i)    /* Health expectancies */
          {    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
            printf("%d%d ",i,k);    double age, agelim, hf;
            fprintf(ficres,"%1d%1d ",i,k);    double ***p3mat,***varhe;
            for(j=1; j <=ncovmodel; j++){    double **dnewm,**doldm;
              printf("%f ",p[jk]);    double *xp;
              fprintf(ficres,"%f ",p[jk]);    double **gp, **gm;
              jk++;    double ***gradg, ***trgradg;
            }    int theta;
            printf("\n");  
            fprintf(ficres,"\n");    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
          }    xp=vector(1,npar);
      }    dnewm=matrix(1,nlstate*nlstate,1,npar);
    }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
  if(mle==1){    
     /* Computing hessian and covariance matrix */    fprintf(ficreseij,"# Local time at start: %s", strstart);
     ftolhess=ftol; /* Usually correct */    fprintf(ficreseij,"# Health expectancies\n");
     hesscov(matcov, p, npar, delti, ftolhess, func);    fprintf(ficreseij,"# Age");
  }    for(i=1; i<=nlstate;i++)
     fprintf(ficres,"# Scales\n");      for(j=1; j<=nlstate;j++)
     printf("# Scales\n");        fprintf(ficreseij," %1d-%1d (SE)",i,j);
      for(i=1,jk=1; i <=nlstate; i++){    fprintf(ficreseij,"\n");
       for(j=1; j <=nlstate+ndeath; j++){  
         if (j!=i) {    if(estepm < stepm){
           fprintf(ficres,"%1d%1d",i,j);      printf ("Problem %d lower than %d\n",estepm, stepm);
           printf("%1d%1d",i,j);    }
           for(k=1; k<=ncovmodel;k++){    else  hstepm=estepm;   
             printf(" %.5e",delti[jk]);    /* We compute the life expectancy from trapezoids spaced every estepm months
             fprintf(ficres," %.5e",delti[jk]);     * This is mainly to measure the difference between two models: for example
             jk++;     * 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 
           printf("\n");     * progression in between and thus overestimating or underestimating according
           fprintf(ficres,"\n");     * to the curvature of the survival function. If, for the same date, we 
         }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       }     * to compare the new estimate of Life expectancy with the same linear 
      }     * hypothesis. A more precise result, taking into account a more precise
         * curvature will be obtained if estepm is as small as stepm. */
     k=1;  
     fprintf(ficres,"# Covariance\n");    /* For example we decided to compute the life expectancy with the smallest unit */
     printf("# Covariance\n");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     for(i=1;i<=npar;i++){       nhstepm is the number of hstepm from age to agelim 
       /*  if (k>nlstate) k=1;       nstepm is the number of stepm from age to agelin. 
       i1=(i-1)/(ncovmodel*nlstate)+1;       Look at hpijx to understand the reason of that which relies in memory size
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);       and note for a fixed period like estepm months */
       printf("%s%d%d",alph[k],i1,tab[i]);*/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       fprintf(ficres,"%3d",i);       survival function given by stepm (the optimization length). Unfortunately it
       printf("%3d",i);       means that if the survival funtion is printed only each two years of age and if
       for(j=1; j<=i;j++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         fprintf(ficres," %.5e",matcov[i][j]);       results. So we changed our mind and took the option of the best precision.
         printf(" %.5e",matcov[i][j]);    */
       }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       fprintf(ficres,"\n");  
       printf("\n");    agelim=AGESUP;
       k++;    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); 
     while((c=getc(ficpar))=='#' && c!= EOF){      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       ungetc(c,ficpar);      /* if (stepm >= YEARM) hstepm=1;*/
       fgets(line, MAXLINE, ficpar);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       puts(line);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fputs(line,ficparo);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     }      gp=matrix(0,nhstepm,1,nlstate*nlstate);
     ungetc(c,ficpar);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
    
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
             in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     if (fage <= 2) {      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
       bage = agemin;   
       fage = agemax;  
     }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      /* Computing  Variances of health expectancies */
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);       for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ 
     while((c=getc(ficpar))=='#' && c!= EOF){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     puts(line);    
     fputs(line,ficparo);        cptj=0;
   }        for(j=1; j<= nlstate; j++){
   ungetc(c,ficpar);          for(i=1; i<=nlstate; i++){
              cptj=cptj+1;
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_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);        for(i=1; i<=npar; i++) 
     fputs(line,ficparo);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   ungetc(c,ficpar);        
          cptj=0;
         for(j=1; j<= nlstate; j++){
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          for(i=1;i<=nlstate;i++){
    dateprev2=anprev2+mprev2/12.+jprev2/365.;            cptj=cptj+1;
             for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   fscanf(ficpar,"pop_based=%d\n",&popbased);  
    fprintf(ficparo,"pop_based=%d\n",popbased);                gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
    fprintf(ficres,"pop_based=%d\n",popbased);              }
           }
   while((c=getc(ficpar))=='#' && c!= EOF){        }
     ungetc(c,ficpar);        for(j=1; j<= nlstate*nlstate; j++)
     fgets(line, MAXLINE, ficpar);          for(h=0; h<=nhstepm-1; h++){
     puts(line);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     fputs(line,ficparo);          }
   }       } 
   ungetc(c,ficpar);     
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);  /* End theta */
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);  
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
              for(theta=1; theta <=npar; theta++)
     /*------------ gnuplot -------------*/            trgradg[h][j][theta]=gradg[h][theta][j];
     /*chdir(pathcd);*/       
     strcpy(optionfilegnuplot,optionfilefiname);  
     strcat(optionfilegnuplot,".plt");       for(i=1;i<=nlstate*nlstate;i++)
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        for(j=1;j<=nlstate*nlstate;j++)
       printf("Problem with file %s",optionfilegnuplot);goto end;          varhe[i][j][(int)age] =0.;
     }  
 #ifdef windows       printf("%d|",(int)age);fflush(stdout);
     fprintf(ficgp,"cd \"%s\" \n",pathc);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 #endif       for(h=0;h<=nhstepm-1;h++){
 m=pow(2,cptcoveff);        for(k=0;k<=nhstepm-1;k++){
            matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
  /* 1eme*/          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   for (cpt=1; cpt<= nlstate ; cpt ++) {          for(i=1;i<=nlstate*nlstate;i++)
    for (k1=1; k1<= m ; k1 ++) {            for(j=1;j<=nlstate*nlstate;j++)
               varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
 #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);      }
 #endif      /* Computing expectancies */
 #ifdef unix      for(i=1; i<=nlstate;i++)
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);        for(j=1; j<=nlstate;j++)
 #endif          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;
 for (i=1; i<= nlstate ; i ++) {            
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  /* 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]);*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }          }
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  
     for (i=1; i<= nlstate ; i ++) {      fprintf(ficreseij,"%3.0f",age );
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      cptj=0;
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(i=1; i<=nlstate;i++)
 }        for(j=1; j<=nlstate;j++){
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          cptj++;
      for (i=1; i<= nlstate ; i ++) {          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(ficreseij,"\n");
 }       
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
 #ifdef unix      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
 fprintf(ficgp,"\nset ter gif small size 400,300");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
 #endif      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    }    }
   }    printf("\n");
   /*2 eme*/    fprintf(ficlog,"\n");
   
   for (k1=1; k1<= m ; k1 ++) {    free_vector(xp,1,npar);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
        free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     for (i=1; i<= nlstate+1 ; i ++) {    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
       k=2*i;  }
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {  /************ Variance ******************/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  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[])
   else fprintf(ficgp," \%%*lf (\%%*lf)");  {
 }      /* Variance of health expectancies */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    /* double **newm;*/
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    double **dnewm,**doldm;
       for (j=1; j<= nlstate+1 ; j ++) {    double **dnewmp,**doldmp;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    int i, j, nhstepm, hstepm, h, nstepm ;
         else fprintf(ficgp," \%%*lf (\%%*lf)");    int k, cptcode;
 }      double *xp;
       fprintf(ficgp,"\" t\"\" w l 0,");    double **gp, **gm;  /* for var eij */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    double ***gradg, ***trgradg; /*for var eij */
       for (j=1; j<= nlstate+1 ; j ++) {    double **gradgp, **trgradgp; /* for var p point j */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double *gpp, *gmp; /* for var p point j */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
 }      double ***p3mat;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    double age,agelim, hf;
       else fprintf(ficgp,"\" t\"\" w l 0,");    double ***mobaverage;
     }    int theta;
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    char digit[4];
   }    char digitp[25];
    
   /*3eme*/    char fileresprobmorprev[FILENAMELENGTH];
   
   for (k1=1; k1<= m ; k1 ++) {    if(popbased==1){
     for (cpt=1; cpt<= nlstate ; cpt ++) {      if(mobilav!=0)
       k=2+nlstate*(cpt-1);        strcpy(digitp,"-populbased-mobilav-");
       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);      else strcpy(digitp,"-populbased-nomobil-");
       for (i=1; i< nlstate ; i ++) {    }
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);    else 
       }      strcpy(digitp,"-stablbased-");
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }    if (mobilav!=0) {
   }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   /* CV preval stat */        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   for (k1=1; k1<= m ; k1 ++) {        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     for (cpt=1; cpt<nlstate ; cpt ++) {      }
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);  
       for (i=1; i< nlstate ; i ++)    strcpy(fileresprobmorprev,"prmorprev"); 
         fprintf(ficgp,"+$%d",k+i+1);    sprintf(digit,"%-d",ij);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
          strcat(fileresprobmorprev,digit); /* Tvar to be done */
       l=3+(nlstate+ndeath)*cpt;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    strcat(fileresprobmorprev,fileres);
       for (i=1; i< nlstate ; i ++) {    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
         l=3+(nlstate+ndeath)*cpt;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
         fprintf(ficgp,"+$%d",l+i+1);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       }    }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);   
     }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   }      fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
     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);
   /* proba elementaires */    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
    for(i=1,jk=1; i <=nlstate; i++){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     for(k=1; k <=(nlstate+ndeath); k++){      fprintf(ficresprobmorprev," p.%-d SE",j);
       if (k != i) {      for(i=1; i<=nlstate;i++)
         for(j=1; j <=ncovmodel; j++){        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/    }  
           /*fprintf(ficgp,"%s",alph[1]);*/    fprintf(ficresprobmorprev,"\n");
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    fprintf(ficgp,"\n# Routine varevsij");
           jk++;    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
           fprintf(ficgp,"\n");    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
         }    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
       }  /*   } */
     }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     }   fprintf(ficresvij, "#Local time at start: %s", strstart);
     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");
   for(jk=1; jk <=m; jk++) {    fprintf(ficresvij,"# Age");
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    for(i=1; i<=nlstate;i++)
    i=1;      for(j=1; j<=nlstate;j++)
    for(k2=1; k2<=nlstate; k2++) {        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
      k3=i;    fprintf(ficresvij,"\n");
      for(k=1; k<=(nlstate+ndeath); k++) {  
        if (k != k2){    xp=vector(1,npar);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    dnewm=matrix(1,nlstate,1,npar);
 ij=1;    doldm=matrix(1,nlstate,1,nlstate);
         for(j=3; j <=ncovmodel; j++) {    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
           }    gpp=vector(nlstate+1,nlstate+ndeath);
           else    gmp=vector(nlstate+1,nlstate+ndeath);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         }    
           fprintf(ficgp,")/(1");    if(estepm < stepm){
              printf ("Problem %d lower than %d\n",estepm, stepm);
         for(k1=1; k1 <=nlstate; k1++){      }
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    else  hstepm=estepm;   
 ij=1;    /* For example we decided to compute the life expectancy with the smallest unit */
           for(j=3; j <=ncovmodel; j++){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {       nhstepm is the number of hstepm from age to agelim 
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);       nstepm is the number of stepm from age to agelin. 
             ij++;       Look at hpijx to understand the reason of that which relies in memory size
           }       and note for a fixed period like k years */
           else    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);       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
           fprintf(ficgp,")");       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.
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    */
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         i=i+ncovmodel;    agelim = AGESUP;
        }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
      }      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
    }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
          gp=matrix(0,nhstepm,1,nlstate);
   fclose(ficgp);      gm=matrix(0,nhstepm,1,nlstate);
   /* end gnuplot */  
      
 chdir(path);      for(theta=1; theta <=npar; theta++){
            for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     free_ivector(wav,1,imx);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        }
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     free_ivector(num,1,n);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     free_vector(agedc,1,n);  
     /*free_matrix(covar,1,NCOVMAX,1,n);*/        if (popbased==1) {
     fclose(ficparo);          if(mobilav ==0){
     fclose(ficres);            for(i=1; i<=nlstate;i++)
     /*  }*/              prlim[i][i]=probs[(int)age][i][ij];
              }else{ /* mobilav */ 
    /*________fin mle=1_________*/            for(i=1; i<=nlstate;i++)
                  prlim[i][i]=mobaverage[(int)age][i][ij];
           }
          }
     /* No more information from the sample is required now */    
   /* Reads comments: lines beginning with '#' */        for(j=1; j<= nlstate; j++){
   while((c=getc(ficpar))=='#' && c!= EOF){          for(h=0; h<=nhstepm; h++){
     ungetc(c,ficpar);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     puts(line);          }
     fputs(line,ficparo);        }
   }        /* This for computing probability of death (h=1 means
   ungetc(c,ficpar);           computed over hstepm matrices product = hstepm*stepm months) 
             as a weighted average of prlim.
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);        */
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
 /*--------- index.htm --------*/            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
   strcpy(optionfilehtm,optionfile);        /* end probability of death */
   strcat(optionfilehtm,".htm");  
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     printf("Problem with %s \n",optionfilehtm);goto end;          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);
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">   
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>        if (popbased==1) {
 Total number of observations=%d <br>          if(mobilav ==0){
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>            for(i=1; i<=nlstate;i++)
 <hr  size=\"2\" color=\"#EC5E5E\">              prlim[i][i]=probs[(int)age][i][ij];
 <li>Outputs files<br><br>\n          }else{ /* mobilav */ 
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n            for(i=1; i<=nlstate;i++)
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>              prlim[i][i]=mobaverage[(int)age][i][ij];
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>          }
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>        }
         - 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>        for(j=1; j<= nlstate; j++){
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>          for(h=0; h<=nhstepm; h++){
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>          }
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);        }
         /* This for computing probability of death (h=1 means
  fprintf(fichtm," <li>Graphs</li><p>");           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
  m=cptcoveff;        */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
  j1=0;           gmp[j] += prlim[i][i]*p3mat[i][j][1];
  for(k1=1; k1<=m;k1++){        }    
    for(i1=1; i1<=ncodemax[k1];i1++){        /* end probability of death */
        j1++;  
        if (cptcovn > 0) {        for(j=1; j<= nlstate; j++) /* vareij */
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          for(h=0; h<=nhstepm; h++){
          for (cpt=1; cpt<=cptcoveff;cpt++)            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);          }
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  
        }        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            }
        for(cpt=1; cpt<nlstate;cpt++){  
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      } /* End theta */
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);  
        }      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     for(cpt=1; cpt<=nlstate;cpt++) {  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      for(h=0; h<=nhstepm; h++) /* veij */
 interval) in state (%d): v%s%d%d.gif <br>        for(j=1; j<=nlstate;j++)
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);            for(theta=1; theta <=npar; theta++)
      }            trgradg[h][j][theta]=gradg[h][theta][j];
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        for(theta=1; theta <=npar; theta++)
      }          trgradgp[j][theta]=gradgp[theta][j];
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    
 health expectancies in states (1) and (2): e%s%d.gif<br>  
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 fprintf(fichtm,"\n</body>");      for(i=1;i<=nlstate;i++)
    }        for(j=1;j<=nlstate;j++)
  }          vareij[i][j][(int)age] =0.;
 fclose(fichtm);  
       for(h=0;h<=nhstepm;h++){
   /*--------------- Prevalence limit --------------*/        for(k=0;k<=nhstepm;k++){
            matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   strcpy(filerespl,"pl");          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   strcat(filerespl,fileres);          for(i=1;i<=nlstate;i++)
   if((ficrespl=fopen(filerespl,"w"))==NULL) {            for(j=1;j<=nlstate;j++)
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   }        }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      }
   fprintf(ficrespl,"#Prevalence limit\n");    
   fprintf(ficrespl,"#Age ");      /* pptj */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   fprintf(ficrespl,"\n");      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
        for(j=nlstate+1;j<=nlstate+ndeath;j++)
   prlim=matrix(1,nlstate,1,nlstate);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          varppt[j][i]=doldmp[j][i];
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      /* end ppptj */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      /*  x centered again */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   k=0;   
   agebase=agemin;      if (popbased==1) {
   agelim=agemax;        if(mobilav ==0){
   ftolpl=1.e-10;          for(i=1; i<=nlstate;i++)
   i1=cptcoveff;            prlim[i][i]=probs[(int)age][i][ij];
   if (cptcovn < 1){i1=1;}        }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
   for(cptcov=1;cptcov<=i1;cptcov++){            prlim[i][i]=mobaverage[(int)age][i][ij];
     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#******");      /* This for computing probability of death (h=1 means
         for(j=1;j<=cptcoveff;j++)         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         as a weighted average of prlim.
         fprintf(ficrespl,"******\n");      */
              for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for (age=agebase; age<=agelim; age++){        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           fprintf(ficrespl,"%.0f",age );      }    
           for(i=1; i<=nlstate;i++)      /* end probability of death */
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
         }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       }        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     }        for(i=1; i<=nlstate;i++){
   fclose(ficrespl);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
   /*------------- h Pij x at various ages ------------*/      } 
        fprintf(ficresprobmorprev,"\n");
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      fprintf(ficresvij,"%.0f ",age );
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      for(i=1; i<=nlstate;i++)
   }        for(j=1; j<=nlstate;j++){
   printf("Computing pij: result on file '%s' \n", filerespij);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
          }
   stepsize=(int) (stepm+YEARM-1)/YEARM;      fprintf(ficresvij,"\n");
   /*if (stepm<=24) stepsize=2;*/      free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
   agelim=AGESUP;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   hstepm=stepsize*YEARM; /* Every year of age */      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      } /* End age */
   k=0;    free_vector(gpp,nlstate+1,nlstate+ndeath);
   for(cptcov=1;cptcov<=i1;cptcov++){    free_vector(gmp,nlstate+1,nlstate+ndeath);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
       k=k+1;    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         fprintf(ficrespij,"\n#****** ");    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
         for(j=1;j<=cptcoveff;j++)    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
         fprintf(ficrespij,"******\n");  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
          /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
           oldm=oldms;savm=savms;    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
           fprintf(ficrespij,"# Age");    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
           for(i=1; i<=nlstate;i++)  */
             for(j=1; j<=nlstate+ndeath;j++)  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
               fprintf(ficrespij," %1d-%1d",i,j);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
           fprintf(ficrespij,"\n");  
           for (h=0; h<=nhstepm; h++){    free_vector(xp,1,npar);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    free_matrix(doldm,1,nlstate,1,nlstate);
             for(i=1; i<=nlstate;i++)    free_matrix(dnewm,1,nlstate,1,npar);
               for(j=1; j<=nlstate+ndeath;j++)    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
             fprintf(ficrespij,"\n");    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fclose(ficresprobmorprev);
           fprintf(ficrespij,"\n");    fflush(ficgp);
         }    fflush(fichtm); 
     }  }  /* end varevsij */
   }  
   /************ Variance of prevlim ******************/
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/  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[])
   {
   fclose(ficrespij);    /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   if(stepm == 1) {    double **newm;
   /*---------- Forecasting ------------------*/    double **dnewm,**doldm;
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    int i, j, nhstepm, hstepm;
     int k, cptcode;
   /*printf("calage= %f", calagedate);*/    double *xp;
      double *gp, *gm;
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    double **gradg, **trgradg;
     double age,agelim;
     int theta;
   strcpy(fileresf,"f");    fprintf(ficresvpl, "#Local time at start: %s", strstart); 
   strcat(fileresf,fileres);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   if((ficresf=fopen(fileresf,"w"))==NULL) {    fprintf(ficresvpl,"# Age");
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;    for(i=1; i<=nlstate;i++)
   }        fprintf(ficresvpl," %1d-%1d",i,i);
   printf("Computing forecasting: result on file '%s' \n", fileresf);    fprintf(ficresvpl,"\n");
   
   free_matrix(mint,1,maxwav,1,n);    xp=vector(1,npar);
   free_matrix(anint,1,maxwav,1,n);    dnewm=matrix(1,nlstate,1,npar);
   free_matrix(agev,1,maxwav,1,imx);    doldm=matrix(1,nlstate,1,nlstate);
   /* Mobile average */    
     hstepm=1*YEARM; /* Every year of age */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
   if (mobilav==1) {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)      if (stepm >= YEARM) hstepm=1;
       for (i=1; i<=nlstate;i++)      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      gradg=matrix(1,npar,1,nlstate);
           mobaverage[(int)agedeb][i][cptcod]=0.;      gp=vector(1,nlstate);
          gm=vector(1,nlstate);
     for (agedeb=bage+4; agedeb<=fage; agedeb++){  
       for (i=1; i<=nlstate;i++){      for(theta=1; theta <=npar; theta++){
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        for(i=1; i<=npar; i++){ /* Computes gradient */
           for (cpt=0;cpt<=4;cpt++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        }
           }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        for(i=1;i<=nlstate;i++)
         }          gp[i] = prlim[i][i];
       }      
     }          for(i=1; i<=npar; i++) /* Computes gradient */
   }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   stepsize=(int) (stepm+YEARM-1)/YEARM;        for(i=1;i<=nlstate;i++)
   if (stepm<=12) stepsize=1;          gm[i] = prlim[i][i];
   
   agelim=AGESUP;        for(i=1;i<=nlstate;i++)
   /*hstepm=stepsize*YEARM; *//* Every year of age */          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   hstepm=1;      } /* End theta */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */  
   yp1=modf(dateintmean,&yp);      trgradg =matrix(1,nlstate,1,npar);
   anprojmean=yp;  
   yp2=modf((yp1*12),&yp);      for(j=1; j<=nlstate;j++)
   mprojmean=yp;        for(theta=1; theta <=npar; theta++)
   yp1=modf((yp2*30.5),&yp);          trgradg[j][theta]=gradg[theta][j];
   jprojmean=yp;  
   if(jprojmean==0) jprojmean=1;      for(i=1;i<=nlstate;i++)
   if(mprojmean==0) jprojmean=1;        varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
   if (popforecast==1) {        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     if((ficpop=fopen(popfile,"r"))==NULL)    {  
       printf("Problem with population file : %s\n",popfile);goto end;      fprintf(ficresvpl,"%.0f ",age );
     }      for(i=1; i<=nlstate;i++)
     popage=ivector(0,AGESUP);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
     popeffectif=vector(0,AGESUP);      fprintf(ficresvpl,"\n");
     popcount=vector(0,AGESUP);      free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
     i=1;        free_matrix(gradg,1,npar,1,nlstate);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)      free_matrix(trgradg,1,nlstate,1,npar);
       {    } /* End age */
         i=i+1;  
       }    free_vector(xp,1,npar);
     imx=i;    free_matrix(doldm,1,nlstate,1,npar);
        free_matrix(dnewm,1,nlstate,1,nlstate);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];  
   }  }
   
   for(cptcov=1;cptcov<=i1;cptcov++){  /************ Variance of one-step probabilities  ******************/
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  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[])
       k=k+1;  {
       fprintf(ficresf,"\n#******");    int i, j=0,  i1, k1, l1, t, tj;
       for(j=1;j<=cptcoveff;j++) {    int k2, l2, j1,  z1;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int k=0,l, cptcode;
       }    int first=1, first1;
       fprintf(ficresf,"******\n");    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
       fprintf(ficresf,"# StartingAge FinalAge");    double **dnewm,**doldm;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    double *xp;
       if (popforecast==1)  fprintf(ficresf," [Population]");    double *gp, *gm;
        double **gradg, **trgradg;
       for (cpt=0; cpt<4;cpt++) {    double **mu;
         fprintf(ficresf,"\n");    double age,agelim, cov[NCOVMAX];
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */    char fileresprob[FILENAMELENGTH];
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    char fileresprobcov[FILENAMELENGTH];
         nhstepm = nhstepm/hstepm;    char fileresprobcor[FILENAMELENGTH];
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/  
     double ***varpij;
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         oldm=oldms;savm=savms;    strcpy(fileresprob,"prob"); 
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      strcat(fileresprob,fileres);
            if((ficresprob=fopen(fileresprob,"w"))==NULL) {
         for (h=0; h<=nhstepm; h++){      printf("Problem with resultfile: %s\n", fileresprob);
           if (h==(int) (calagedate+YEARM*cpt)) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);    }
           }    strcpy(fileresprobcov,"probcov"); 
           for(j=1; j<=nlstate+ndeath;j++) {    strcat(fileresprobcov,fileres);
             kk1=0.;kk2=0;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
             for(i=1; i<=nlstate;i++) {              printf("Problem with resultfile: %s\n", fileresprobcov);
               if (mobilav==1)      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    }
               else {    strcpy(fileresprobcor,"probcor"); 
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    strcat(fileresprobcor,fileres);
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
               }      printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];    }
             }    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
              fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
             if (h==(int)(calagedate+12*cpt)){    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
               fprintf(ficresf," %.3f", kk1);    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 (popforecast==1) fprintf(ficresf," [%.f]", kk2);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
             }    fprintf(ficresprob, "#Local time at start: %s", strstart);
           }    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
         }    fprintf(ficresprob,"# Age");
         /*      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);*/    fprintf(ficresprobcov, "#Local time at start: %s", strstart);
       }    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
       }    fprintf(ficresprobcov,"# Age");
     }    fprintf(ficresprobcor, "#Local time at start: %s", strstart);
   }    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   /*  if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficresprobcov,"# Age");
   if (popforecast==1) {  
     free_ivector(popage,0,AGESUP);  
     free_vector(popeffectif,0,AGESUP);    for(i=1; i<=nlstate;i++)
     free_vector(popcount,0,AGESUP);      for(j=1; j<=(nlstate+ndeath);j++){
   }        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   free_imatrix(s,1,maxwav+1,1,n);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   free_vector(weight,1,n);*/        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   fclose(ficresf);      }  
   }/* End forecasting */   /* fprintf(ficresprob,"\n");
   else{    fprintf(ficresprobcov,"\n");
     erreur=108;    fprintf(ficresprobcor,"\n");
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);   */
   }   xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   /*---------- Health expectancies and variances ------------*/    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   strcpy(filerest,"t");    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   strcat(filerest,fileres);    first=1;
   if((ficrest=fopen(filerest,"w"))==NULL) {    fprintf(ficgp,"\n# Routine varprob");
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   }    fprintf(fichtm,"\n");
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
   strcpy(filerese,"e");    file %s<br>\n",optionfilehtmcov);
   strcat(filerese,fileres);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   if((ficreseij=fopen(filerese,"w"))==NULL) {  and drawn. It helps understanding how is the covariance between two incidences.\
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   }    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  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 \
  strcpy(fileresv,"v");  standard deviations wide on each axis. <br>\
   strcat(fileresv,fileres);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
   if((ficresvij=fopen(fileresv,"w"))==NULL) {   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   }  
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    cov[1]=1;
     tj=cptcoveff;
   k=0;    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   for(cptcov=1;cptcov<=i1;cptcov++){    j1=0;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    for(t=1; t<=tj;t++){
       k=k+1;      for(i1=1; i1<=ncodemax[t];i1++){ 
       fprintf(ficrest,"\n#****** ");        j1++;
       for(j=1;j<=cptcoveff;j++)        if  (cptcovn>0) {
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficresprob, "\n#********** Variable "); 
       fprintf(ficrest,"******\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
       fprintf(ficreseij,"\n#****** ");          fprintf(ficresprobcov, "\n#********** Variable "); 
       for(j=1;j<=cptcoveff;j++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          fprintf(ficresprobcov, "**********\n#\n");
       fprintf(ficreseij,"******\n");          
           fprintf(ficgp, "\n#********** Variable "); 
       fprintf(ficresvij,"\n#****** ");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       for(j=1;j<=cptcoveff;j++)          fprintf(ficgp, "**********\n#\n");
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          
       fprintf(ficresvij,"******\n");          
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       oldm=oldms;savm=savms;          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);            
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          fprintf(ficresprobcor, "\n#********** Variable ");    
       oldm=oldms;savm=savms;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          fprintf(ficresprobcor, "**********\n#");    
              }
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        for (age=bage; age<=fage; age ++){ 
       fprintf(ficrest,"\n");          cov[2]=age;
                  for (k=1; k<=cptcovn;k++) {
       hf=1;            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
       if (stepm >= YEARM) hf=stepm/YEARM;          }
       epj=vector(1,nlstate+1);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       for(age=bage; age <=fage ;age++){          for (k=1; k<=cptcovprod;k++)
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         if (popbased==1) {          
           for(i=1; i<=nlstate;i++)          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
             prlim[i][i]=probs[(int)age][i][k];          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         }          gp=vector(1,(nlstate)*(nlstate+ndeath));
                  gm=vector(1,(nlstate)*(nlstate+ndeath));
         fprintf(ficrest," %.0f",age);      
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          for(theta=1; theta <=npar; theta++){
           for(i=1, epj[j]=0.;i <=nlstate;i++) {            for(i=1; i<=npar; i++)
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
           }            
           epj[nlstate+1] +=epj[j];            pmij(pmmij,cov,ncovmodel,xp,nlstate);
         }            
         for(i=1, vepp=0.;i <=nlstate;i++)            k=0;
           for(j=1;j <=nlstate;j++)            for(i=1; i<= (nlstate); i++){
             vepp += vareij[i][j][(int)age];              for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));                k=k+1;
         for(j=1;j <=nlstate;j++){                gp[k]=pmmij[i][j];
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));              }
         }            }
         fprintf(ficrest,"\n");            
       }            for(i=1; i<=npar; i++)
     }              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   }      
                    pmij(pmmij,cov,ncovmodel,xp,nlstate);
                    k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
  fclose(ficreseij);                k=k+1;
  fclose(ficresvij);                gm[k]=pmmij[i][j];
   fclose(ficrest);              }
   fclose(ficpar);            }
   free_vector(epj,1,nlstate+1);       
   /*  scanf("%d ",i); */            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
   /*------- Variance limit prevalence------*/            }
   
 strcpy(fileresvpl,"vpl");          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   strcat(fileresvpl,fileres);            for(theta=1; theta <=npar; theta++)
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {              trgradg[j][theta]=gradg[theta][j];
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);          
     exit(0);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   }          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
  k=0;          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
  for(cptcov=1;cptcov<=i1;cptcov++){          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
      k=k+1;          pmij(pmmij,cov,ncovmodel,x,nlstate);
      fprintf(ficresvpl,"\n#****** ");          
      for(j=1;j<=cptcoveff;j++)          k=0;
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for(i=1; i<=(nlstate); i++){
      fprintf(ficresvpl,"******\n");            for(j=1; j<=(nlstate+ndeath);j++){
                    k=k+1;
      varpl=matrix(1,nlstate,(int) bage, (int) fage);              mu[k][(int) age]=pmmij[i][j];
      oldm=oldms;savm=savms;            }
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          }
    }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
  }            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   fclose(ficresvpl);  
           /*printf("\n%d ",(int)age);
   /*---------- End : free ----------------*/            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
              fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);            }*/
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
            fprintf(ficresprob,"\n%d ",(int)age);
            fprintf(ficresprobcov,"\n%d ",(int)age);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          fprintf(ficresprobcor,"\n%d ",(int)age);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   free_matrix(matcov,1,npar,1,npar);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   free_vector(delti,1,npar);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
            }
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);          i=0;
           for (k=1; k<=(nlstate);k++){
   if(erreur >0)            for (l=1; l<=(nlstate+ndeath);l++){ 
     printf("End of Imach with error %d\n",erreur);              i=i++;
   else   printf("End of Imach\n");              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                for (j=1; j<=i;j++){
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   /*printf("Total time was %d uSec.\n", total_usecs);*/                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   /*------ End -----------*/              }
             }
           }/* end of loop for state */
  end:        } /* end of loop for age */
 #ifdef windows  
   /* chdir(pathcd);*/        /* Confidence intervalle of pij  */
 #endif        /*
  /*system("wgnuplot graph.plt");*/          fprintf(ficgp,"\nset noparametric;unset label");
  /*system("../gp37mgw/wgnuplot graph.plt");*/          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
  /*system("cd ../gp37mgw");*/          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/          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);
  strcpy(plotcmd,GNUPLOTPROGRAM);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
  strcat(plotcmd," ");          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
  strcat(plotcmd,optionfilegnuplot);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
  system(plotcmd);        */
   
 #ifdef windows        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   while (z[0] != 'q') {        first1=1;
     chdir(path);        for (k2=1; k2<=(nlstate);k2++){
     printf("\nType e to edit output files, c to start again, and q for exiting: ");          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     scanf("%s",z);            if(l2==k2) continue;
     if (z[0] == 'c') system("./imach");            j=(k2-1)*(nlstate+ndeath)+l2;
     else if (z[0] == 'e') {            for (k1=1; k1<=(nlstate);k1++){
       chdir(path);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
       system(optionfilehtm);                if(l1==k1) continue;
     }                i=(k1-1)*(nlstate+ndeath)+l1;
     else if (z[0] == 'q') exit(0);                if(i<=j) continue;
   }                for (age=bage; age<=fage; age ++){ 
 #endif                  if ((int)age %5==0){
 }                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     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.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       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,\
                               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);
                       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);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       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 */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   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 rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - Life expectancies by age and initial health status (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            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(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(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;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          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) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           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 linei, month, year,iout;
     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];
     char dummy[]="                         ";
     /*  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]; 
     char **bp, *tok, *val; /* pathtot */
     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: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Un peu sale */
       }
     }
     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;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
           exit(1);
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           exit(1);
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         exit(1);
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         exit(1);
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       lval=strtol(strb,&endptr,10); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight.  Exiting.\n",lval, i,line,linei);
         exit(1);
       }
       weight[i]=(double)(lval); 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self).  Exiting.\n",lval,linei, i,line,j);
           exit(1);
         }
         covar[j][i]=(double)(lval);
         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;
     } /* End loop reading  data */
     fclose(fic);
     /* 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);*/
   
       /*  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 (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    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;
           }else 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]=0.0268; p[NDIM]=0.083;
       /*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(prlim,1,nlstate,1,nlstate);
       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);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     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);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n 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.1.23  
changed lines
  Added in v.1.115


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