Diff for /imach/src/imach.c between versions 1.32 and 1.108

version 1.32, 2002/03/11 14:17:15 version 1.108, 2006/01/19 18:05:42
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.108  2006/01/19 18:05:42  lievre
      Gnuplot problem appeared...
   This program computes Healthy Life Expectancies from    To be fixed
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  
   first survey ("cross") where individuals from different ages are    Revision 1.107  2006/01/19 16:20:37  brouard
   interviewed on their health status or degree of disability (in the    Test existence of gnuplot in imach path
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.106  2006/01/19 13:24:36  brouard
   (if any) in individual health status.  Health expectancies are    Some cleaning and links added in html output
   computed from the time spent in each health state according to a  
   model. More health states you consider, more time is necessary to reach the    Revision 1.105  2006/01/05 20:23:19  lievre
   Maximum Likelihood of the parameters involved in the model.  The    *** empty log message ***
   simplest model is the multinomial logistic model where pij is the  
   probabibility to be observed in state j at the second wave    Revision 1.104  2005/09/30 16:11:43  lievre
   conditional to be observed in state i at the first wave. Therefore    (Module): sump fixed, loop imx fixed, and simplifications.
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    (Module): If the status is missing at the last wave but we know
   'age' is age and 'sex' is a covariate. If you want to have a more    that the person is alive, then we can code his/her status as -2
   complex model than "constant and age", you should modify the program    (instead of missing=-1 in earlier versions) and his/her
   where the markup *Covariates have to be included here again* invites    contributions to the likelihood is 1 - Prob of dying from last
   you to do it.  More covariates you add, slower the    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   convergence.    the healthy state at last known wave). Version is 0.98
   
   The advantage of this computer programme, compared to a simple    Revision 1.103  2005/09/30 15:54:49  lievre
   multinomial logistic model, is clear when the delay between waves is not    (Module): sump fixed, loop imx fixed, and simplifications.
   identical for each individual. Also, if a individual missed an  
   intermediate interview, the information is lost, but taken into    Revision 1.102  2004/09/15 17:31:30  brouard
   account using an interpolation or extrapolation.      Add the possibility to read data file including tab characters.
   
   hPijx is the probability to be observed in state i at age x+h    Revision 1.101  2004/09/15 10:38:38  brouard
   conditional to the observed state i at age x. The delay 'h' can be    Fix on curr_time
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    Revision 1.100  2004/07/12 18:29:06  brouard
   semester or year) is model as a multinomial logistic.  The hPx    Add version for Mac OS X. Just define UNIX in Makefile
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.99  2004/06/05 08:57:40  brouard
   hPijx.    *** empty log message ***
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.98  2004/05/16 15:05:56  brouard
   of the life expectancies. It also computes the prevalence limits.    New version 0.97 . First attempt to estimate force of mortality
      directly from the data i.e. without the need of knowing the health
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    state at each age, but using a Gompertz model: log u =a + b*age .
            Institut national d'études démographiques, Paris.    This is the basic analysis of mortality and should be done before any
   This software have been partly granted by Euro-REVES, a concerted action    other analysis, in order to test if the mortality estimated from the
   from the European Union.    cross-longitudinal survey is different from the mortality estimated
   It is copyrighted identically to a GNU software product, ie programme and    from other sources like vital statistic data.
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    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
 #include <math.h>    former routines in order to include the new code within the former code.
 #include <stdio.h>  
 #include <stdlib.h>    The output is very simple: only an estimate of the intercept and of
 #include <unistd.h>    the slope with 95% confident intervals.
   
 #define MAXLINE 256    Current limitations:
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    A) Even if you enter covariates, i.e. with the
 #define FILENAMELENGTH 80    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 /*#define DEBUG*/    B) There is no computation of Life Expectancy nor Life Table.
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.97  2004/02/20 13:25:42  lievre
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.96  2003/07/15 15:38:55  brouard
     * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #define NINTERVMAX 8    rewritten within the same printf. Workaround: many printfs.
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.95  2003/07/08 07:54:34  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    * imach.c (Repository):
 #define MAXN 20000    (Repository): Using imachwizard code to output a more meaningful covariance
 #define YEARM 12. /* Number of months per year */    matrix (cov(a12,c31) instead of numbers.
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
   
 int erreur; /* Error number */    Revision 1.93  2003/06/25 16:33:55  brouard
 int nvar;    (Module): On windows (cygwin) function asctime_r doesn't
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    exist so I changed back to asctime which exists.
 int npar=NPARMAX;    (Module): Version 0.96b
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.92  2003/06/25 16:30:45  brouard
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    (Module): On windows (cygwin) function asctime_r doesn't
 int popbased=0;    exist so I changed back to asctime which exists.
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.91  2003/06/25 15:30:29  brouard
 int maxwav; /* Maxim number of waves */    * imach.c (Repository): Duplicated warning errors corrected.
 int jmin, jmax; /* min, max spacing between 2 waves */    (Repository): Elapsed time after each iteration is now output. It
 int mle, weightopt;    helps to forecast when convergence will be reached. Elapsed time
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    is stamped in powell.  We created a new html file for the graphs
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    concerning matrix of covariance. It has extension -cov.htm.
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.90  2003/06/24 12:34:15  brouard
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    (Module): Some bugs corrected for windows. Also, when
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    mle=-1 a template is output in file "or"mypar.txt with the design
 FILE *ficgp,*ficresprob,*ficpop;    of the covariance matrix to be input.
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.89  2003/06/24 12:30:52  brouard
  FILE  *ficresvij;    (Module): Some bugs corrected for windows. Also, when
   char fileresv[FILENAMELENGTH];    mle=-1 a template is output in file "or"mypar.txt with the design
  FILE  *ficresvpl;    of the covariance matrix to be input.
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.88  2003/06/23 17:54:56  brouard
 #define NR_END 1    * 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.
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
 #define NRANSI  
 #define ITMAX 200    Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
 #define TOL 2.0e-4    routine fileappend.
   
 #define CGOLD 0.3819660    Revision 1.85  2003/06/17 13:12:43  brouard
 #define ZEPS 1.0e-10    * imach.c (Repository): Check when date of death was earlier that
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
 #define GOLD 1.618034    was wrong (infinity). We still send an "Error" but patch by
 #define GLIMIT 100.0    assuming that the date of death was just one stepm after the
 #define TINY 1.0e-20    interview.
     (Repository): Because some people have very long ID (first column)
 static double maxarg1,maxarg2;    we changed int to long in num[] and we added a new lvector for
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    memory allocation. But we also truncated to 8 characters (left
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    truncation)
      (Repository): No more line truncation errors.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
 static double sqrarg;    place. It differs from routine "prevalence" which may be called
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    many times. Probs is memory consuming and must be used with
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 int imx;  
 int stepm;    Revision 1.83  2003/06/10 13:39:11  lievre
 /* Stepm, step in month: minimum step interpolation*/    *** empty log message ***
   
 int m,nb;    Revision 1.82  2003/06/05 15:57:20  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Add log in  imach.c and  fullversion number is now printed.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;  */
 double dateintmean=0;  /*
      Interpolated Markov Chain
 double *weight;  
 int **s; /* Status */    Short summary of the programme:
 double *agedc, **covar, idx;    
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    first survey ("cross") where individuals from different ages are
 double ftolhess; /* Tolerance for computing hessian */    interviewed on their health status or degree of disability (in the
     case of a health survey which is our main interest) -2- at least a
 /**************** split *************************/    second wave of interviews ("longitudinal") which measure each change
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    (if any) in individual health status.  Health expectancies are
 {    computed from the time spent in each health state according to a
    char *s;                             /* pointer */    model. More health states you consider, more time is necessary to reach the
    int  l1, l2;                         /* length counters */    Maximum Likelihood of the parameters involved in the model.  The
     simplest model is the multinomial logistic model where pij is the
    l1 = strlen( path );                 /* length of path */    probability to be observed in state j at the second wave
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    conditional to be observed in state i at the first wave. Therefore
 #ifdef windows    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
    s = strrchr( path, '\\' );           /* find last / */    'age' is age and 'sex' is a covariate. If you want to have a more
 #else    complex model than "constant and age", you should modify the program
    s = strrchr( path, '/' );            /* find last / */    where the markup *Covariates have to be included here again* invites
 #endif    you to do it.  More covariates you add, slower the
    if ( s == NULL ) {                   /* no directory, so use current */    convergence.
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    The advantage of this computer programme, compared to a simple
     multinomial logistic model, is clear when the delay between waves is not
       if ( getwd( dirc ) == NULL ) {    identical for each individual. Also, if a individual missed an
 #else    intermediate interview, the information is lost, but taken into
       extern char       *getcwd( );    account using an interpolation or extrapolation.  
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    hPijx is the probability to be observed in state i at age x+h
 #endif    conditional to the observed state i at age x. The delay 'h' can be
          return( GLOCK_ERROR_GETCWD );    split into an exact number (nh*stepm) of unobserved intermediate
       }    states. This elementary transition (by month, quarter,
       strcpy( name, path );             /* we've got it */    semester or year) is modelled as a multinomial logistic.  The hPx
    } else {                             /* strip direcotry from path */    matrix is simply the matrix product of nh*stepm elementary matrices
       s++;                              /* after this, the filename */    and the contribution of each individual to the likelihood is simply
       l2 = strlen( s );                 /* length of filename */    hPijx.
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Also this programme outputs the covariance matrix of the parameters but also
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    of the life expectancies. It also computes the stable prevalence. 
       dirc[l1-l2] = 0;                  /* add zero */    
    }    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
    l1 = strlen( dirc );                 /* length of directory */             Institut national d'études démographiques, Paris.
 #ifdef windows    This software have been partly granted by Euro-REVES, a concerted action
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    from the European Union.
 #else    It is copyrighted identically to a GNU software product, ie programme and
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    software can be distributed freely for non commercial use. Latest version
 #endif    can be accessed at http://euroreves.ined.fr/imach .
    s = strrchr( name, '.' );            /* find last / */  
    s++;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
    strcpy(ext,s);                       /* save extension */    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
    l1= strlen( name);    
    l2= strlen( s)+1;    **********************************************************************/
    strncpy( finame, name, l1-l2);  /*
    finame[l1-l2]= 0;    main
    return( 0 );                         /* we're done */    read parameterfile
 }    read datafile
     concatwav
     freqsummary
 /******************************************/    if (mle >= 1)
       mlikeli
 void replace(char *s, char*t)    print results files
 {    if mle==1 
   int i;       computes hessian
   int lg=20;    read end of parameter file: agemin, agemax, bage, fage, estepm
   i=0;        begin-prev-date,...
   lg=strlen(t);    open gnuplot file
   for(i=0; i<= lg; i++) {    open html file
     (s[i] = t[i]);    stable prevalence
     if (t[i]== '\\') s[i]='/';     for age prevalim()
   }    h Pij x
 }    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
 int nbocc(char *s, char occ)    health expectancies
 {    Variance-covariance of DFLE
   int i,j=0;    prevalence()
   int lg=20;     movingaverage()
   i=0;    varevsij() 
   lg=strlen(s);    if popbased==1 varevsij(,popbased)
   for(i=0; i<= lg; i++) {    total life expectancies
   if  (s[i] == occ ) j++;    Variance of stable prevalence
   }   end
   return j;  */
 }  
   
 void cutv(char *u,char *v, char*t, char occ)  
 {   
   int i,lg,j,p=0;  #include <math.h>
   i=0;  #include <stdio.h>
   for(j=0; j<=strlen(t)-1; j++) {  #include <stdlib.h>
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  #include <string.h>
   }  #include <unistd.h>
   
   lg=strlen(t);  #include <sys/types.h>
   for(j=0; j<p; j++) {  #include <sys/stat.h>
     (u[j] = t[j]);  #include <errno.h>
   }  extern int errno;
      u[p]='\0';  
   /* #include <sys/time.h> */
    for(j=0; j<= lg; j++) {  #include <time.h>
     if (j>=(p+1))(v[j-p-1] = t[j]);  #include "timeval.h"
   }  
 }  /* #include <libintl.h> */
   /* #define _(String) gettext (String) */
 /********************** nrerror ********************/  
   #define MAXLINE 256
 void nrerror(char error_text[])  
 {  #define GNUPLOTPROGRAM "gnuplot"
   fprintf(stderr,"ERREUR ...\n");  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   fprintf(stderr,"%s\n",error_text);  #define FILENAMELENGTH 132
   exit(1);  
 }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 /*********************** vector *******************/  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 double *vector(int nl, int nh)  
 {  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   double *v;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  #define NINTERVMAX 8
   return v-nl+NR_END;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 }  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 8 /* Maximum number of covariates */
 /************************ free vector ******************/  #define MAXN 20000
 void free_vector(double*v, int nl, int nh)  #define YEARM 12. /* Number of months per year */
 {  #define AGESUP 130
   free((FREE_ARG)(v+nl-NR_END));  #define AGEBASE 40
 }  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   #ifdef UNIX
 /************************ivector *******************************/  #define DIRSEPARATOR '/'
 int *ivector(long nl,long nh)  #define CHARSEPARATOR "/"
 {  #define ODIRSEPARATOR '\\'
   int *v;  #else
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #define DIRSEPARATOR '\\'
   if (!v) nrerror("allocation failure in ivector");  #define CHARSEPARATOR "\\"
   return v-nl+NR_END;  #define ODIRSEPARATOR '/'
 }  #endif
   
 /******************free ivector **************************/  /* $Id$ */
 void free_ivector(int *v, long nl, long nh)  /* $State$ */
 {  
   free((FREE_ARG)(v+nl-NR_END));  char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";
 }  char fullversion[]="$Revision$ $Date$"; 
   int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 /******************* imatrix *******************************/  int nvar;
 int **imatrix(long nrl, long nrh, long ncl, long nch)  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  int npar=NPARMAX;
 {  int nlstate=2; /* Number of live states */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  int ndeath=1; /* Number of dead states */
   int **m;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
    int popbased=0;
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  int *wav; /* Number of waves for this individuual 0 is possible */
   if (!m) nrerror("allocation failure 1 in matrix()");  int maxwav; /* Maxim number of waves */
   m += NR_END;  int jmin, jmax; /* min, max spacing between 2 waves */
   m -= nrl;  int gipmx, gsw; /* Global variables on the number of contributions 
                       to the likelihood and the sum of weights (done by funcone)*/
    int mle, weightopt;
   /* allocate rows and set pointers to them */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   m[nrl] += NR_END;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   m[nrl] -= ncl;  double jmean; /* Mean space between 2 waves */
    double **oldm, **newm, **savm; /* Working pointers to matrices */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
    FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   /* return pointer to array of pointers to rows */  FILE *ficlog, *ficrespow;
   return m;  int globpr; /* Global variable for printing or not */
 }  double fretone; /* Only one call to likelihood */
   long ipmx; /* Number of contributions */
 /****************** free_imatrix *************************/  double sw; /* Sum of weights */
 void free_imatrix(m,nrl,nrh,ncl,nch)  char filerespow[FILENAMELENGTH];
       int **m;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       long nch,ncl,nrh,nrl;  FILE *ficresilk;
      /* free an int matrix allocated by imatrix() */  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 {  FILE *ficresprobmorprev;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  FILE *fichtm, *fichtmcov; /* Html File */
   free((FREE_ARG) (m+nrl-NR_END));  FILE *ficreseij;
 }  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
 /******************* matrix *******************************/  char fileresv[FILENAMELENGTH];
 double **matrix(long nrl, long nrh, long ncl, long nch)  FILE  *ficresvpl;
 {  char fileresvpl[FILENAMELENGTH];
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  char title[MAXLINE];
   double **m;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   if (!m) nrerror("allocation failure 1 in matrix()");  char command[FILENAMELENGTH];
   m += NR_END;  int  outcmd=0;
   m -= nrl;  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  char filelog[FILENAMELENGTH]; /* Log file */
   m[nrl] += NR_END;  char filerest[FILENAMELENGTH];
   m[nrl] -= ncl;  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 }  
   struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 /*************************free matrix ************************/  struct timezone tzp;
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  extern int gettimeofday();
 {  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  long time_value;
   free((FREE_ARG)(m+nrl-NR_END));  extern long time();
 }  char strcurr[80], strfor[80];
   
 /******************* ma3x *******************************/  #define NR_END 1
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  #define FREE_ARG char*
 {  #define FTOL 1.0e-10
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  #define NRANSI 
   #define ITMAX 200 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  #define TOL 2.0e-4 
   m += NR_END;  
   m -= nrl;  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  #define GOLD 1.618034 
   m[nrl] -= ncl;  #define GLIMIT 100.0 
   #define TINY 1.0e-20 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   static double maxarg1,maxarg2;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   m[nrl][ncl] += NR_END;    
   m[nrl][ncl] -= nll;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   for (j=ncl+1; j<=nch; j++)  #define rint(a) floor(a+0.5)
     m[nrl][j]=m[nrl][j-1]+nlay;  
    static double sqrarg;
   for (i=nrl+1; i<=nrh; i++) {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
     for (j=ncl+1; j<=nch; j++)  int agegomp= AGEGOMP;
       m[i][j]=m[i][j-1]+nlay;  
   }  int imx; 
   return m;  int stepm=1;
 }  /* Stepm, step in month: minimum step interpolation*/
   
 /*************************free ma3x ************************/  int estepm;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  int m,nb;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  long *num;
   free((FREE_ARG)(m+nrl-NR_END));  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 }  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs;
 /***************** f1dim *************************/  double *ageexmed,*agecens;
 extern int ncom;  double dateintmean=0;
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);  double *weight;
    int **s; /* Status */
 double f1dim(double x)  double *agedc, **covar, idx;
 {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   int j;  double *lsurv, *lpop, *tpop;
   double f;  
   double *xt;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
    double ftolhess; /* Tolerance for computing hessian */
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  /**************** split *************************/
   f=(*nrfunc)(xt);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   free_vector(xt,1,ncom);  {
   return f;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
 }       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     */ 
 /*****************brent *************************/    char  *ss;                            /* pointer */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    int   l1, l2;                         /* length counters */
 {  
   int iter;    l1 = strlen(path );                   /* length of path */
   double a,b,d,etemp;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   double fu,fv,fw,fx;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   double ftemp;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   double p,q,r,tol1,tol2,u,v,w,x,xm;      strcpy( name, path );               /* we got the fullname name because no directory */
   double e=0.0;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
          printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   a=(ax < cx ? ax : cx);      /* get current working directory */
   b=(ax > cx ? ax : cx);      /*    extern  char* getcwd ( char *buf , int len);*/
   x=w=v=bx;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   fw=fv=fx=(*f)(x);        return( GLOCK_ERROR_GETCWD );
   for (iter=1;iter<=ITMAX;iter++) {      }
     xm=0.5*(a+b);      /* got dirc from getcwd*/
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);      printf(" DIRC = %s \n",dirc);
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    } else {                              /* strip direcotry from path */
     printf(".");fflush(stdout);      ss++;                               /* after this, the filename */
 #ifdef DEBUG      l2 = strlen( ss );                  /* length of filename */
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */      strcpy( name, ss );         /* save file name */
 #endif      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){      dirc[l1-l2] = 0;                    /* add zero */
       *xmin=x;      printf(" DIRC2 = %s \n",dirc);
       return fx;    }
     }    /* We add a separator at the end of dirc if not exists */
     ftemp=fu;    l1 = strlen( dirc );                  /* length of directory */
     if (fabs(e) > tol1) {    if( dirc[l1-1] != DIRSEPARATOR ){
       r=(x-w)*(fx-fv);      dirc[l1] =  DIRSEPARATOR;
       q=(x-v)*(fx-fw);      dirc[l1+1] = 0; 
       p=(x-v)*q-(x-w)*r;      printf(" DIRC3 = %s \n",dirc);
       q=2.0*(q-r);    }
       if (q > 0.0) p = -p;    ss = strrchr( name, '.' );            /* find last / */
       q=fabs(q);    if (ss >0){
       etemp=e;      ss++;
       e=d;      strcpy(ext,ss);                     /* save extension */
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))      l1= strlen( name);
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      l2= strlen(ss)+1;
       else {      strncpy( finame, name, l1-l2);
         d=p/q;      finame[l1-l2]= 0;
         u=x+d;    }
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);    return( 0 );                          /* we're done */
       }  }
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  /******************************************/
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);  void replace_back_to_slash(char *s, char*t)
     if (fu <= fx) {  {
       if (u >= x) a=x; else b=x;    int i;
       SHFT(v,w,x,u)    int lg=0;
         SHFT(fv,fw,fx,fu)    i=0;
         } else {    lg=strlen(t);
           if (u < x) a=u; else b=u;    for(i=0; i<= lg; i++) {
           if (fu <= fw || w == x) {      (s[i] = t[i]);
             v=w;      if (t[i]== '\\') s[i]='/';
             w=u;    }
             fv=fw;  }
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {  int nbocc(char *s, char occ)
             v=u;  {
             fv=fu;    int i,j=0;
           }    int lg=20;
         }    i=0;
   }    lg=strlen(s);
   nrerror("Too many iterations in brent");    for(i=0; i<= lg; i++) {
   *xmin=x;    if  (s[i] == occ ) j++;
   return fx;    }
 }    return j;
   }
 /****************** mnbrak ***********************/  
   void cutv(char *u,char *v, char*t, char occ)
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  {
             double (*func)(double))    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
 {       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
   double ulim,u,r,q, dum;       gives u="abcedf" and v="ghi2j" */
   double fu;    int i,lg,j,p=0;
      i=0;
   *fa=(*func)(*ax);    for(j=0; j<=strlen(t)-1; j++) {
   *fb=(*func)(*bx);      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   if (*fb > *fa) {    }
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)    lg=strlen(t);
       }    for(j=0; j<p; j++) {
   *cx=(*bx)+GOLD*(*bx-*ax);      (u[j] = t[j]);
   *fc=(*func)(*cx);    }
   while (*fb > *fc) {       u[p]='\0';
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);     for(j=0; j<= lg; j++) {
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      if (j>=(p+1))(v[j-p-1] = t[j]);
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    }
     ulim=(*bx)+GLIMIT*(*cx-*bx);  }
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);  /********************** nrerror ********************/
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  void nrerror(char error_text[])
       if (fu < *fc) {  {
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    fprintf(stderr,"ERREUR ...\n");
           SHFT(*fb,*fc,fu,(*func)(u))    fprintf(stderr,"%s\n",error_text);
           }    exit(EXIT_FAILURE);
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  }
       u=ulim;  /*********************** vector *******************/
       fu=(*func)(u);  double *vector(int nl, int nh)
     } else {  {
       u=(*cx)+GOLD*(*cx-*bx);    double *v;
       fu=(*func)(u);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     }    if (!v) nrerror("allocation failure in vector");
     SHFT(*ax,*bx,*cx,u)    return v-nl+NR_END;
       SHFT(*fa,*fb,*fc,fu)  }
       }  
 }  /************************ free vector ******************/
   void free_vector(double*v, int nl, int nh)
 /*************** linmin ************************/  {
     free((FREE_ARG)(v+nl-NR_END));
 int ncom;  }
 double *pcom,*xicom;  
 double (*nrfunc)(double []);  /************************ivector *******************************/
    int *ivector(long nl,long nh)
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  {
 {    int *v;
   double brent(double ax, double bx, double cx,    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
                double (*f)(double), double tol, double *xmin);    if (!v) nrerror("allocation failure in ivector");
   double f1dim(double x);    return v-nl+NR_END;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  }
               double *fc, double (*func)(double));  
   int j;  /******************free ivector **************************/
   double xx,xmin,bx,ax;  void free_ivector(int *v, long nl, long nh)
   double fx,fb,fa;  {
      free((FREE_ARG)(v+nl-NR_END));
   ncom=n;  }
   pcom=vector(1,n);  
   xicom=vector(1,n);  /************************lvector *******************************/
   nrfunc=func;  long *lvector(long nl,long nh)
   for (j=1;j<=n;j++) {  {
     pcom[j]=p[j];    long *v;
     xicom[j]=xi[j];    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   }    if (!v) nrerror("allocation failure in ivector");
   ax=0.0;    return v-nl+NR_END;
   xx=1.0;  }
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  /******************free lvector **************************/
 #ifdef DEBUG  void free_lvector(long *v, long nl, long nh)
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  {
 #endif    free((FREE_ARG)(v+nl-NR_END));
   for (j=1;j<=n;j++) {  }
     xi[j] *= xmin;  
     p[j] += xi[j];  /******************* imatrix *******************************/
   }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   free_vector(xicom,1,n);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   free_vector(pcom,1,n);  { 
 }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     int **m; 
 /*************** powell ************************/    
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    /* allocate pointers to rows */ 
             double (*func)(double []))    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 {    if (!m) nrerror("allocation failure 1 in matrix()"); 
   void linmin(double p[], double xi[], int n, double *fret,    m += NR_END; 
               double (*func)(double []));    m -= nrl; 
   int i,ibig,j;    
   double del,t,*pt,*ptt,*xit;    
   double fp,fptt;    /* allocate rows and set pointers to them */ 
   double *xits;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   pt=vector(1,n);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   ptt=vector(1,n);    m[nrl] += NR_END; 
   xit=vector(1,n);    m[nrl] -= ncl; 
   xits=vector(1,n);    
   *fret=(*func)(p);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   for (j=1;j<=n;j++) pt[j]=p[j];    
   for (*iter=1;;++(*iter)) {    /* return pointer to array of pointers to rows */ 
     fp=(*fret);    return m; 
     ibig=0;  } 
     del=0.0;  
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  /****************** free_imatrix *************************/
     for (i=1;i<=n;i++)  void free_imatrix(m,nrl,nrh,ncl,nch)
       printf(" %d %.12f",i, p[i]);        int **m;
     printf("\n");        long nch,ncl,nrh,nrl; 
     for (i=1;i<=n;i++) {       /* free an int matrix allocated by imatrix() */ 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  { 
       fptt=(*fret);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 #ifdef DEBUG    free((FREE_ARG) (m+nrl-NR_END)); 
       printf("fret=%lf \n",*fret);  } 
 #endif  
       printf("%d",i);fflush(stdout);  /******************* matrix *******************************/
       linmin(p,xit,n,fret,func);  double **matrix(long nrl, long nrh, long ncl, long nch)
       if (fabs(fptt-(*fret)) > del) {  {
         del=fabs(fptt-(*fret));    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
         ibig=i;    double **m;
       }  
 #ifdef DEBUG    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       printf("%d %.12e",i,(*fret));    if (!m) nrerror("allocation failure 1 in matrix()");
       for (j=1;j<=n;j++) {    m += NR_END;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    m -= nrl;
         printf(" x(%d)=%.12e",j,xit[j]);  
       }    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()");
         printf(" p=%.12e",p[j]);    m[nrl] += NR_END;
       printf("\n");    m[nrl] -= ncl;
 #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 m;
 #ifdef DEBUG    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       int k[2],l;     */
       k[0]=1;  }
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  /*************************free matrix ************************/
       for (j=1;j<=n;j++)  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
         printf(" %.12e",p[j]);  {
       printf("\n");    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       for(l=0;l<=1;l++) {    free((FREE_ARG)(m+nrl-NR_END));
         for (j=1;j<=n;j++) {  }
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  /******************* ma3x *******************************/
         }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  {
       }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
 #endif    double ***m;
   
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       free_vector(xit,1,n);    if (!m) nrerror("allocation failure 1 in matrix()");
       free_vector(xits,1,n);    m += NR_END;
       free_vector(ptt,1,n);    m -= nrl;
       free_vector(pt,1,n);  
       return;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    m[nrl] += NR_END;
     for (j=1;j<=n;j++) {    m[nrl] -= ncl;
       ptt[j]=2.0*p[j]-pt[j];  
       xit[j]=p[j]-pt[j];    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       pt[j]=p[j];  
     }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     fptt=(*func)(ptt);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     if (fptt < fp) {    m[nrl][ncl] += NR_END;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    m[nrl][ncl] -= nll;
       if (t < 0.0) {    for (j=ncl+1; j<=nch; j++) 
         linmin(p,xit,n,fret,func);      m[nrl][j]=m[nrl][j-1]+nlay;
         for (j=1;j<=n;j++) {    
           xi[j][ibig]=xi[j][n];    for (i=nrl+1; i<=nrh; i++) {
           xi[j][n]=xit[j];      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         }      for (j=ncl+1; j<=nch; j++) 
 #ifdef DEBUG        m[i][j]=m[i][j-1]+nlay;
         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++)    return m; 
           printf(" %.12e",xit[j]);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
         printf("\n");             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 #endif    */
       }  }
     }  
   }  /*************************free ma3x ************************/
 }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   {
 /**** Prevalence limit ****************/    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    free((FREE_ARG)(m+nrl-NR_END));
 {  }
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  
      matrix by transitions matrix until convergence is reached */  /*************** function subdirf ***********/
   char *subdirf(char fileres[])
   int i, ii,j,k;  {
   double min, max, maxmin, maxmax,sumnew=0.;    /* Caution optionfilefiname is hidden */
   double **matprod2();    strcpy(tmpout,optionfilefiname);
   double **out, cov[NCOVMAX], **pmij();    strcat(tmpout,"/"); /* Add to the right */
   double **newm;    strcat(tmpout,fileres);
   double agefin, delaymax=50 ; /* Max number of years to converge */    return tmpout;
   }
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){  /*************** function subdirf2 ***********/
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  char *subdirf2(char fileres[], char *preop)
     }  {
     
    cov[1]=1.;    /* Caution optionfilefiname is hidden */
      strcpy(tmpout,optionfilefiname);
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    strcat(tmpout,"/");
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    strcat(tmpout,preop);
     newm=savm;    strcat(tmpout,fileres);
     /* Covariates have to be included here again */    return tmpout;
      cov[2]=agefin;  }
    
       for (k=1; k<=cptcovn;k++) {  /*************** function subdirf3 ***********/
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  char *subdirf3(char fileres[], char *preop, char *preop2)
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  {
       }    
       for (k=1; k<=cptcovage;k++)    /* Caution optionfilefiname is hidden */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    strcpy(tmpout,optionfilefiname);
       for (k=1; k<=cptcovprod;k++)    strcat(tmpout,"/");
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    strcat(tmpout,preop);
     strcat(tmpout,preop2);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    strcat(tmpout,fileres);
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    return tmpout;
   }
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  
   /***************** f1dim *************************/
     savm=oldm;  extern int ncom; 
     oldm=newm;  extern double *pcom,*xicom;
     maxmax=0.;  extern double (*nrfunc)(double []); 
     for(j=1;j<=nlstate;j++){   
       min=1.;  double f1dim(double x) 
       max=0.;  { 
       for(i=1; i<=nlstate; i++) {    int j; 
         sumnew=0;    double f;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    double *xt; 
         prlim[i][j]= newm[i][j]/(1-sumnew);   
         max=FMAX(max,prlim[i][j]);    xt=vector(1,ncom); 
         min=FMIN(min,prlim[i][j]);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       }    f=(*nrfunc)(xt); 
       maxmin=max-min;    free_vector(xt,1,ncom); 
       maxmax=FMAX(maxmax,maxmin);    return f; 
     }  } 
     if(maxmax < ftolpl){  
       return prlim;  /*****************brent *************************/
     }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   }  { 
 }    int iter; 
     double a,b,d,etemp;
 /*************** transition probabilities ***************/    double fu,fv,fw,fx;
     double ftemp;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    double p,q,r,tol1,tol2,u,v,w,x,xm; 
 {    double e=0.0; 
   double s1, s2;   
   /*double t34;*/    a=(ax < cx ? ax : cx); 
   int i,j,j1, nc, ii, jj;    b=(ax > cx ? ax : cx); 
     x=w=v=bx; 
     for(i=1; i<= nlstate; i++){    fw=fv=fx=(*f)(x); 
     for(j=1; j<i;j++){    for (iter=1;iter<=ITMAX;iter++) { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      xm=0.5*(a+b); 
         /*s2 += param[i][j][nc]*cov[nc];*/      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      printf(".");fflush(stdout);
       }      fprintf(ficlog,".");fflush(ficlog);
       ps[i][j]=s2;  #ifdef DEBUG
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      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);
     for(j=i+1; j<=nlstate+ndeath;j++){      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #endif
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        *xmin=x; 
       }        return fx; 
       ps[i][j]=s2;      } 
     }      ftemp=fu;
   }      if (fabs(e) > tol1) { 
     /*ps[3][2]=1;*/        r=(x-w)*(fx-fv); 
         q=(x-v)*(fx-fw); 
   for(i=1; i<= nlstate; i++){        p=(x-v)*q-(x-w)*r; 
      s1=0;        q=2.0*(q-r); 
     for(j=1; j<i; j++)        if (q > 0.0) p = -p; 
       s1+=exp(ps[i][j]);        q=fabs(q); 
     for(j=i+1; j<=nlstate+ndeath; j++)        etemp=e; 
       s1+=exp(ps[i][j]);        e=d; 
     ps[i][i]=1./(s1+1.);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     for(j=1; j<i; j++)          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        else { 
     for(j=i+1; j<=nlstate+ndeath; j++)          d=p/q; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];          u=x+d; 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */          if (u-a < tol2 || b-u < tol2) 
   } /* end i */            d=SIGN(tol1,xm-x); 
         } 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      } else { 
     for(jj=1; jj<= nlstate+ndeath; jj++){        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       ps[ii][jj]=0;      } 
       ps[ii][ii]=1;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     }      fu=(*f)(u); 
   }      if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
         SHFT(v,w,x,u) 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){          SHFT(fv,fw,fx,fu) 
     for(jj=1; jj<= nlstate+ndeath; jj++){          } else { 
      printf("%lf ",ps[ii][jj]);            if (u < x) a=u; else b=u; 
    }            if (fu <= fw || w == x) { 
     printf("\n ");              v=w; 
     }              w=u; 
     printf("\n ");printf("%lf ",cov[2]);*/              fv=fw; 
 /*              fw=fu; 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);            } else if (fu <= fv || v == x || v == w) { 
   goto end;*/              v=u; 
     return ps;              fv=fu; 
 }            } 
           } 
 /**************** Product of 2 matrices ******************/    } 
     nrerror("Too many iterations in brent"); 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    *xmin=x; 
 {    return fx; 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  } 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized  /****************** mnbrak ***********************/
      before: only the contents of out is modified. The function returns  
      a pointer to pointers identical to out */  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   long i, j, k;              double (*func)(double)) 
   for(i=nrl; i<= nrh; i++)  { 
     for(k=ncolol; k<=ncoloh; k++)    double ulim,u,r,q, dum;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    double fu; 
         out[i][k] +=in[i][j]*b[j][k];   
     *fa=(*func)(*ax); 
   return out;    *fb=(*func)(*bx); 
 }    if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
         SHFT(dum,*fb,*fa,dum) 
 /************* Higher Matrix Product ***************/        } 
     *cx=(*bx)+GOLD*(*bx-*ax); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    *fc=(*func)(*cx); 
 {    while (*fb > *fc) { 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      r=(*bx-*ax)*(*fb-*fc); 
      duration (i.e. until      q=(*bx-*cx)*(*fb-*fa); 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
      (typically every 2 years instead of every month which is too big).      ulim=(*bx)+GLIMIT*(*cx-*bx); 
      Model is determined by parameters x and covariates have to be      if ((*bx-u)*(u-*cx) > 0.0) { 
      included manually here.        fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { 
      */        fu=(*func)(u); 
         if (fu < *fc) { 
   int i, j, d, h, k;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double **out, cov[NCOVMAX];            SHFT(*fb,*fc,fu,(*func)(u)) 
   double **newm;            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   /* Hstepm could be zero and should return the unit matrix */        u=ulim; 
   for (i=1;i<=nlstate+ndeath;i++)        fu=(*func)(u); 
     for (j=1;j<=nlstate+ndeath;j++){      } else { 
       oldm[i][j]=(i==j ? 1.0 : 0.0);        u=(*cx)+GOLD*(*cx-*bx); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);        fu=(*func)(u); 
     }      } 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      SHFT(*ax,*bx,*cx,u) 
   for(h=1; h <=nhstepm; h++){        SHFT(*fa,*fb,*fc,fu) 
     for(d=1; d <=hstepm; d++){        } 
       newm=savm;  } 
       /* Covariates have to be included here again */  
       cov[1]=1.;  /*************** linmin ************************/
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  int ncom; 
       for (k=1; k<=cptcovage;k++)  double *pcom,*xicom;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  double (*nrfunc)(double []); 
       for (k=1; k<=cptcovprod;k++)   
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   { 
     double brent(double ax, double bx, double cx, 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/                 double (*f)(double), double tol, double *xmin); 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    double f1dim(double x); 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));                double *fc, double (*func)(double)); 
       savm=oldm;    int j; 
       oldm=newm;    double xx,xmin,bx,ax; 
     }    double fx,fb,fa;
     for(i=1; i<=nlstate+ndeath; i++)   
       for(j=1;j<=nlstate+ndeath;j++) {    ncom=n; 
         po[i][j][h]=newm[i][j];    pcom=vector(1,n); 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    xicom=vector(1,n); 
          */    nrfunc=func; 
       }    for (j=1;j<=n;j++) { 
   } /* end h */      pcom[j]=p[j]; 
   return po;      xicom[j]=xi[j]; 
 }    } 
     ax=0.0; 
     xx=1.0; 
 /*************** log-likelihood *************/    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
 double func( double *x)    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 {  #ifdef DEBUG
   int i, ii, j, k, mi, d, kk;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   double **out;  #endif
   double sw; /* Sum of weights */    for (j=1;j<=n;j++) { 
   double lli; /* Individual log likelihood */      xi[j] *= xmin; 
   long ipmx;      p[j] += xi[j]; 
   /*extern weight */    } 
   /* We are differentiating ll according to initial status */    free_vector(xicom,1,n); 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    free_vector(pcom,1,n); 
   /*for(i=1;i<imx;i++)  } 
     printf(" %d\n",s[4][i]);  
   */  char *asc_diff_time(long time_sec, char ascdiff[])
   cov[1]=1.;  {
     long sec_left, days, hours, minutes;
   for(k=1; k<=nlstate; k++) ll[k]=0.;    days = (time_sec) / (60*60*24);
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    sec_left = (time_sec) % (60*60*24);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    hours = (sec_left) / (60*60) ;
     for(mi=1; mi<= wav[i]-1; mi++){    sec_left = (sec_left) %(60*60);
       for (ii=1;ii<=nlstate+ndeath;ii++)    minutes = (sec_left) /60;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    sec_left = (sec_left) % (60);
       for(d=0; d<dh[mi][i]; d++){    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
         newm=savm;    return ascdiff;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  }
         for (kk=1; kk<=cptcovage;kk++) {  
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  /*************** powell ************************/
         }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
                      double (*func)(double [])) 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  { 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    void linmin(double p[], double xi[], int n, double *fret, 
         savm=oldm;                double (*func)(double [])); 
         oldm=newm;    int i,ibig,j; 
            double del,t,*pt,*ptt,*xit;
            double fp,fptt;
       } /* end mult */    double *xits;
          int niterf, itmp;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    pt=vector(1,n); 
       ipmx +=1;    ptt=vector(1,n); 
       sw += weight[i];    xit=vector(1,n); 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    xits=vector(1,n); 
     } /* end of wave */    *fret=(*func)(p); 
   } /* end of individual */    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      fp=(*fret); 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      ibig=0; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      del=0.0; 
   return -l;      last_time=curr_time;
 }      (void) gettimeofday(&curr_time,&tzp);
       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);
       /*    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);
 /*********** Maximum Likelihood Estimation ***************/      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))     for (i=1;i<=n;i++) {
 {        printf(" %d %.12f",i, p[i]);
   int i,j, iter;        fprintf(ficlog," %d %.12lf",i, p[i]);
   double **xi,*delti;        fprintf(ficrespow," %.12lf", p[i]);
   double fret;      }
   xi=matrix(1,npar,1,npar);      printf("\n");
   for (i=1;i<=npar;i++)      fprintf(ficlog,"\n");
     for (j=1;j<=npar;j++)      fprintf(ficrespow,"\n");fflush(ficrespow);
       xi[i][j]=(i==j ? 1.0 : 0.0);      if(*iter <=3){
   printf("Powell\n");        tm = *localtime(&curr_time.tv_sec);
   powell(p,xi,npar,ftol,&iter,&fret,func);        strcpy(strcurr,asctime(&tm));
   /*       asctime_r(&tm,strcurr); */
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        forecast_time=curr_time; 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        itmp = strlen(strcurr);
         if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
 }          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);
 /**** Computes Hessian and covariance matrix ***/        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        for(niterf=10;niterf<=30;niterf+=10){
 {          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   double  **a,**y,*x,pd;          tmf = *localtime(&forecast_time.tv_sec);
   double **hess;  /*      asctime_r(&tmf,strfor); */
   int i, j,jk;          strcpy(strfor,asctime(&tmf));
   int *indx;          itmp = strlen(strfor);
           if(strfor[itmp-1]=='\n')
   double hessii(double p[], double delta, int theta, double delti[]);          strfor[itmp-1]='\0';
   double hessij(double p[], double delti[], int i, int j);          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);
   void lubksb(double **a, int npar, int *indx, double b[]) ;          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
   void ludcmp(double **a, int npar, int *indx, double *d) ;        }
       }
   hess=matrix(1,npar,1,npar);      for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   printf("\nCalculation of the hessian matrix. Wait...\n");        fptt=(*fret); 
   for (i=1;i<=npar;i++){  #ifdef DEBUG
     printf("%d",i);fflush(stdout);        printf("fret=%lf \n",*fret);
     hess[i][i]=hessii(p,ftolhess,i,delti);        fprintf(ficlog,"fret=%lf \n",*fret);
     /*printf(" %f ",p[i]);*/  #endif
     /*printf(" %lf ",hess[i][i]);*/        printf("%d",i);fflush(stdout);
   }        fprintf(ficlog,"%d",i);fflush(ficlog);
          linmin(p,xit,n,fret,func); 
   for (i=1;i<=npar;i++) {        if (fabs(fptt-(*fret)) > del) { 
     for (j=1;j<=npar;j++)  {          del=fabs(fptt-(*fret)); 
       if (j>i) {          ibig=i; 
         printf(".%d%d",i,j);fflush(stdout);        } 
         hess[i][j]=hessij(p,delti,i,j);  #ifdef DEBUG
         hess[j][i]=hess[i][j];            printf("%d %.12e",i,(*fret));
         /*printf(" %lf ",hess[i][j]);*/        fprintf(ficlog,"%d %.12e",i,(*fret));
       }        for (j=1;j<=n;j++) {
     }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   }          printf(" x(%d)=%.12e",j,xit[j]);
   printf("\n");          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         }
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        for(j=1;j<=n;j++) {
            printf(" p=%.12e",p[j]);
   a=matrix(1,npar,1,npar);          fprintf(ficlog," p=%.12e",p[j]);
   y=matrix(1,npar,1,npar);        }
   x=vector(1,npar);        printf("\n");
   indx=ivector(1,npar);        fprintf(ficlog,"\n");
   for (i=1;i<=npar;i++)  #endif
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];      } 
   ludcmp(a,npar,indx,&pd);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   #ifdef DEBUG
   for (j=1;j<=npar;j++) {        int k[2],l;
     for (i=1;i<=npar;i++) x[i]=0;        k[0]=1;
     x[j]=1;        k[1]=-1;
     lubksb(a,npar,indx,x);        printf("Max: %.12e",(*func)(p));
     for (i=1;i<=npar;i++){        fprintf(ficlog,"Max: %.12e",(*func)(p));
       matcov[i][j]=x[i];        for (j=1;j<=n;j++) {
     }          printf(" %.12e",p[j]);
   }          fprintf(ficlog," %.12e",p[j]);
         }
   printf("\n#Hessian matrix#\n");        printf("\n");
   for (i=1;i<=npar;i++) {        fprintf(ficlog,"\n");
     for (j=1;j<=npar;j++) {        for(l=0;l<=1;l++) {
       printf("%.3e ",hess[i][j]);          for (j=1;j<=n;j++) {
     }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     printf("\n");            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
   /* Recompute Inverse */          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   for (i=1;i<=npar;i++)          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        }
   ludcmp(a,npar,indx,&pd);  #endif
   
   /*  printf("\n#Hessian matrix recomputed#\n");  
         free_vector(xit,1,n); 
   for (j=1;j<=npar;j++) {        free_vector(xits,1,n); 
     for (i=1;i<=npar;i++) x[i]=0;        free_vector(ptt,1,n); 
     x[j]=1;        free_vector(pt,1,n); 
     lubksb(a,npar,indx,x);        return; 
     for (i=1;i<=npar;i++){      } 
       y[i][j]=x[i];      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       printf("%.3e ",y[i][j]);      for (j=1;j<=n;j++) { 
     }        ptt[j]=2.0*p[j]-pt[j]; 
     printf("\n");        xit[j]=p[j]-pt[j]; 
   }        pt[j]=p[j]; 
   */      } 
       fptt=(*func)(ptt); 
   free_matrix(a,1,npar,1,npar);      if (fptt < fp) { 
   free_matrix(y,1,npar,1,npar);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   free_vector(x,1,npar);        if (t < 0.0) { 
   free_ivector(indx,1,npar);          linmin(p,xit,n,fret,func); 
   free_matrix(hess,1,npar,1,npar);          for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; 
             xi[j][n]=xit[j]; 
 }          }
   #ifdef DEBUG
 /*************** hessian matrix ****************/          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 double hessii( double x[], double delta, int theta, double delti[])          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++){
   int i;            printf(" %.12e",xit[j]);
   int l=1, lmax=20;            fprintf(ficlog," %.12e",xit[j]);
   double k1,k2;          }
   double p2[NPARMAX+1];          printf("\n");
   double res;          fprintf(ficlog,"\n");
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  #endif
   double fx;        }
   int k=0,kmax=10;      } 
   double l1;    } 
   } 
   fx=func(x);  
   for (i=1;i<=npar;i++) p2[i]=x[i];  /**** Prevalence limit (stable prevalence)  ****************/
   for(l=0 ; l <=lmax; l++){  
     l1=pow(10,l);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     delts=delt;  {
     for(k=1 ; k <kmax; k=k+1){    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       delt = delta*(l1*k);       matrix by transitions matrix until convergence is reached */
       p2[theta]=x[theta] +delt;  
       k1=func(p2)-fx;    int i, ii,j,k;
       p2[theta]=x[theta]-delt;    double min, max, maxmin, maxmax,sumnew=0.;
       k2=func(p2)-fx;    double **matprod2();
       /*res= (k1-2.0*fx+k2)/delt/delt; */    double **out, cov[NCOVMAX], **pmij();
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    double **newm;
          double agefin, delaymax=50 ; /* Max number of years to converge */
 #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);    for (ii=1;ii<=nlstate+ndeath;ii++)
 #endif      for (j=1;j<=nlstate+ndeath;j++){
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      }
         k=kmax;  
       }     cov[1]=1.;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */   
         k=kmax; l=lmax*10.;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       }    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      newm=savm;
         delts=delt;      /* Covariates have to be included here again */
       }       cov[2]=agefin;
     }    
   }        for (k=1; k<=cptcovn;k++) {
   delti[theta]=delts;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   return res;          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
          }
 }        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
 double hessij( double x[], double delti[], int thetai,int thetaj)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 {  
   int i;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   int l=1, l1, lmax=20;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   double k1,k2,k3,k4,res,fx;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   double p2[NPARMAX+1];      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   int k;  
       savm=oldm;
   fx=func(x);      oldm=newm;
   for (k=1; k<=2; k++) {      maxmax=0.;
     for (i=1;i<=npar;i++) p2[i]=x[i];      for(j=1;j<=nlstate;j++){
     p2[thetai]=x[thetai]+delti[thetai]/k;        min=1.;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        max=0.;
     k1=func(p2)-fx;        for(i=1; i<=nlstate; i++) {
            sumnew=0;
     p2[thetai]=x[thetai]+delti[thetai]/k;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          prlim[i][j]= newm[i][j]/(1-sumnew);
     k2=func(p2)-fx;          max=FMAX(max,prlim[i][j]);
            min=FMIN(min,prlim[i][j]);
     p2[thetai]=x[thetai]-delti[thetai]/k;        }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        maxmin=max-min;
     k3=func(p2)-fx;        maxmax=FMAX(maxmax,maxmin);
        }
     p2[thetai]=x[thetai]-delti[thetai]/k;      if(maxmax < ftolpl){
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        return prlim;
     k4=func(p2)-fx;      }
     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);  
 #endif  /*************** transition probabilities ***************/ 
   }  
   return res;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 }  {
     double s1, s2;
 /************** Inverse of matrix **************/    /*double t34;*/
 void ludcmp(double **a, int n, int *indx, double *d)    int i,j,j1, nc, ii, jj;
 {  
   int i,imax,j,k;      for(i=1; i<= nlstate; i++){
   double big,dum,sum,temp;        for(j=1; j<i;j++){
   double *vv;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
              /*s2 += param[i][j][nc]*cov[nc];*/
   vv=vector(1,n);            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   *d=1.0;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
   for (i=1;i<=n;i++) {          }
     big=0.0;          ps[i][j]=s2;
     for (j=1;j<=n;j++)  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
       if ((temp=fabs(a[i][j])) > big) big=temp;        }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        for(j=i+1; j<=nlstate+ndeath;j++){
     vv[i]=1.0/big;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   }            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   for (j=1;j<=n;j++) {  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     for (i=1;i<j;i++) {          }
       sum=a[i][j];          ps[i][j]=s2;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        }
       a[i][j]=sum;      }
     }      /*ps[3][2]=1;*/
     big=0.0;      
     for (i=j;i<=n;i++) {      for(i=1; i<= nlstate; i++){
       sum=a[i][j];        s1=0;
       for (k=1;k<j;k++)        for(j=1; j<i; j++)
         sum -= a[i][k]*a[k][j];          s1+=exp(ps[i][j]);
       a[i][j]=sum;        for(j=i+1; j<=nlstate+ndeath; j++)
       if ( (dum=vv[i]*fabs(sum)) >= big) {          s1+=exp(ps[i][j]);
         big=dum;        ps[i][i]=1./(s1+1.);
         imax=i;        for(j=1; j<i; j++)
       }          ps[i][j]= exp(ps[i][j])*ps[i][i];
     }        for(j=i+1; j<=nlstate+ndeath; j++)
     if (j != imax) {          ps[i][j]= exp(ps[i][j])*ps[i][i];
       for (k=1;k<=n;k++) {        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         dum=a[imax][k];      } /* end i */
         a[imax][k]=a[j][k];      
         a[j][k]=dum;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       }        for(jj=1; jj<= nlstate+ndeath; jj++){
       *d = -(*d);          ps[ii][jj]=0;
       vv[imax]=vv[j];          ps[ii][ii]=1;
     }        }
     indx[j]=imax;      }
     if (a[j][j] == 0.0) a[j][j]=TINY;      
     if (j != n) {  
       dum=1.0/(a[j][j]);  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
     }  /*         printf("ddd %lf ",ps[ii][jj]); */
   }  /*       } */
   free_vector(vv,1,n);  /* Doesn't work */  /*       printf("\n "); */
 ;  /*        } */
 }  /*        printf("\n ");printf("%lf ",cov[2]); */
          /*
 void lubksb(double **a, int n, int *indx, double b[])        for(i=1; i<= npar; i++) printf("%f ",x[i]);
 {        goto end;*/
   int i,ii=0,ip,j;      return ps;
   double sum;  }
    
   for (i=1;i<=n;i++) {  /**************** Product of 2 matrices ******************/
     ip=indx[i];  
     sum=b[ip];  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     b[ip]=b[i];  {
     if (ii)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     else if (sum) ii=i;    /* in, b, out are matrice of pointers which should have been initialized 
     b[i]=sum;       before: only the contents of out is modified. The function returns
   }       a pointer to pointers identical to out */
   for (i=n;i>=1;i--) {    long i, j, k;
     sum=b[i];    for(i=nrl; i<= nrh; i++)
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      for(k=ncolol; k<=ncoloh; k++)
     b[i]=sum/a[i][i];        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   }          out[i][k] +=in[i][j]*b[j][k];
 }  
     return out;
 /************ Frequencies ********************/  }
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)  
 {  /* Some frequencies */  
    /************* Higher Matrix Product ***************/
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   double *pp;  {
   double pos, k2, dateintsum=0,k2cpt=0;    /* Computes the transition matrix starting at age 'age' over 
   FILE *ficresp;       'nhstepm*hstepm*stepm' months (i.e. until
   char fileresp[FILENAMELENGTH];       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         nhstepm*hstepm matrices. 
   pp=vector(1,nlstate);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);       (typically every 2 years instead of every month which is too big 
   strcpy(fileresp,"p");       for the memory).
   strcat(fileresp,fileres);       Model is determined by parameters x and covariates have to be 
   if((ficresp=fopen(fileresp,"w"))==NULL) {       included manually here. 
     printf("Problem with prevalence resultfile: %s\n", fileresp);  
     exit(0);       */
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    int i, j, d, h, k;
   j1=0;    double **out, cov[NCOVMAX];
     double **newm;
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
   for(k1=1; k1<=j;k1++){      for (j=1;j<=nlstate+ndeath;j++){
    for(i1=1; i1<=ncodemax[k1];i1++){        oldm[i][j]=(i==j ? 1.0 : 0.0);
        j1++;        po[i][j][0]=(i==j ? 1.0 : 0.0);
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      }
          scanf("%d", i);*/    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         for (i=-1; i<=nlstate+ndeath; i++)      for(h=1; h <=nhstepm; h++){
          for (jk=-1; jk<=nlstate+ndeath; jk++)        for(d=1; d <=hstepm; d++){
            for(m=agemin; m <= agemax+3; m++)        newm=savm;
              freq[i][jk][m]=0;        /* Covariates have to be included here again */
         cov[1]=1.;
         dateintsum=0;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         k2cpt=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
        for (i=1; i<=imx; i++) {        for (k=1; k<=cptcovage;k++)
          bool=1;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
          if  (cptcovn>0) {        for (k=1; k<=cptcovprod;k++)
            for (z1=1; z1<=cptcoveff; z1++)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
                bool=0;  
          }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
          if (bool==1) {        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
            for(m=firstpass; m<=lastpass; m++){        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
              k2=anint[m][i]+(mint[m][i]/12.);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
              if ((k2>=dateprev1) && (k2<=dateprev2)) {        savm=oldm;
                if(agev[m][i]==0) agev[m][i]=agemax+1;        oldm=newm;
                if(agev[m][i]==1) agev[m][i]=agemax+2;      }
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      for(i=1; i<=nlstate+ndeath; i++)
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        for(j=1;j<=nlstate+ndeath;j++) {
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          po[i][j][h]=newm[i][j];
                  dateintsum=dateintsum+k2;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
                  k2cpt++;           */
                }        }
     } /* end h */
              }    return po;
            }  }
          }  
        }  
          /*************** log-likelihood *************/
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  double func( double *x)
   {
         if  (cptcovn>0) {    int i, ii, j, k, mi, d, kk;
          fprintf(ficresp, "\n#********** Variable ");    double l, ll[NLSTATEMAX], cov[NCOVMAX];
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double **out;
        fprintf(ficresp, "**********\n#");    double sw; /* Sum of weights */
         }    double lli; /* Individual log likelihood */
        for(i=1; i<=nlstate;i++)    int s1, s2;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    double bbh, survp;
        fprintf(ficresp, "\n");    long ipmx;
            /*extern weight */
   for(i=(int)agemin; i <= (int)agemax+3; i++){    /* We are differentiating ll according to initial status */
     if(i==(int)agemax+3)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       printf("Total");    /*for(i=1;i<imx;i++) 
     else      printf(" %d\n",s[4][i]);
       printf("Age %d", i);    */
     for(jk=1; jk <=nlstate ; jk++){    cov[1]=1.;
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  
         pp[jk] += freq[jk][m][i];    for(k=1; k<=nlstate; k++) ll[k]=0.;
     }  
     for(jk=1; jk <=nlstate ; jk++){    if(mle==1){
       for(m=-1, pos=0; m <=0 ; m++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         pos += freq[jk][m][i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       if(pp[jk]>=1.e-10)        for(mi=1; mi<= wav[i]-1; mi++){
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          for (ii=1;ii<=nlstate+ndeath;ii++)
       else            for (j=1;j<=nlstate+ndeath;j++){
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
      for(jk=1; jk <=nlstate ; jk++){          for(d=0; d<dh[mi][i]; d++){
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            newm=savm;
         pp[jk] += freq[jk][m][i];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(jk=1,pos=0; jk <=nlstate ; jk++)            }
       pos += pp[jk];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for(jk=1; jk <=nlstate ; jk++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       if(pos>=1.e-5)            savm=oldm;
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            oldm=newm;
       else          } /* end mult */
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        
       if( i <= (int) agemax){          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         if(pos>=1.e-5){          /* But now since version 0.9 we anticipate for bias at large stepm.
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
           probs[i][jk][j1]= pp[jk]/pos;           * (in months) between two waves is not a multiple of stepm, we rounded to 
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/           * 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
       else           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);           * 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
     }           * -stepm/2 to stepm/2 .
     for(jk=-1; jk <=nlstate+ndeath; jk++)           * For stepm=1 the results are the same as for previous versions of Imach.
       for(m=-1; m <=nlstate+ndeath; m++)           * For stepm > 1 the results are less biased than in previous versions. 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);           */
     if(i <= (int) agemax)          s1=s[mw[mi][i]][i];
       fprintf(ficresp,"\n");          s2=s[mw[mi+1][i]][i];
     printf("\n");          bbh=(double)bh[mi][i]/(double)stepm; 
     }          /* bias bh is positive if real duration
     }           * is higher than the multiple of stepm and negative otherwise.
  }           */
   dateintmean=dateintsum/k2cpt;          /* 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){ 
   fclose(ficresp);            /* i.e. if s2 is a death state and if the date of death is known 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);               then the contribution to the likelihood is the probability to 
   free_vector(pp,1,nlstate);               die between last step unit time and current  step unit time, 
                which is also equal to probability to die before dh 
   /* End of Freq */               minus probability to die before dh-stepm . 
 }               In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
 /************ Prevalence ********************/          health state: the date of the interview describes the actual state
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)          and not the date of a change in health state. The former idea was
 {  /* Some frequencies */          to consider that at each interview the state was recorded
            (healthy, disable or death) and IMaCh was corrected; but when we
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          introduced the exact date of death then we should have modified
   double ***freq; /* Frequencies */          the contribution of an exact death to the likelihood. This new
   double *pp;          contribution is smaller and very dependent of the step unit
   double pos, k2;          stepm. It is no more the probability to die between last interview
           and month of death but the probability to survive from last
   pp=vector(1,nlstate);          interview up to one month before death multiplied by the
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          probability to die within a month. Thanks to Chris
            Jackson for correcting this bug.  Former versions increased
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          mortality artificially. The bad side is that we add another loop
   j1=0;          which slows down the processing. The difference can be up to 10%
            lower mortality.
   j=cptcoveff;            */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            lli=log(out[s1][s2] - savm[s1][s2]);
    
  for(k1=1; k1<=j;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){          } else if  (s2==-2) {
       j1++;            for (j=1,survp=0. ; j<=nlstate; j++) 
                survp += out[s1][j];
       for (i=-1; i<=nlstate+ndeath; i++)              lli= survp;
         for (jk=-1; jk<=nlstate+ndeath; jk++)            }
           for(m=agemin; m <= agemax+3; m++)          
             freq[i][jk][m]=0;          else if  (s2==-4) {
                  for (j=3,survp=0. ; j<=nlstate; j++) 
       for (i=1; i<=imx; i++) {              survp += out[s1][j];
         bool=1;            lli= survp;
         if  (cptcovn>0) {          }
           for (z1=1; z1<=cptcoveff; z1++)          
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          else if  (s2==-5) {
               bool=0;            for (j=1,survp=0. ; j<=2; j++) 
         }              survp += out[s1][j];
         if (bool==1) {            lli= survp;
           for(m=firstpass; m<=lastpass; m++){          }
             k2=anint[m][i]+(mint[m][i]/12.);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  
               if(agev[m][i]==0) agev[m][i]=agemax+1;          else{
               if(agev[m][i]==1) agev[m][i]=agemax+2;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */          } 
             }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           }          /*if(lli ==000.0)*/
         }          /*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;
         for(i=(int)agemin; i <= (int)agemax+3; i++){          sw += weight[i];
           for(jk=1; jk <=nlstate ; jk++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        } /* end of wave */
               pp[jk] += freq[jk][m][i];      } /* end of individual */
           }    }  else if(mle==2){
           for(jk=1; jk <=nlstate ; jk++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             for(m=-1, pos=0; m <=0 ; m++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             pos += freq[jk][m][i];        for(mi=1; mi<= wav[i]-1; mi++){
         }          for (ii=1;ii<=nlstate+ndeath;ii++)
                    for (j=1;j<=nlstate+ndeath;j++){
          for(jk=1; jk <=nlstate ; jk++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              pp[jk] += freq[jk][m][i];            }
          }          for(d=0; d<=dh[mi][i]; d++){
                      newm=savm;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
          for(jk=1; jk <=nlstate ; jk++){                        cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
            if( i <= (int) agemax){            }
              if(pos>=1.e-5){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                probs[i][jk][j1]= pp[jk]/pos;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              }            savm=oldm;
            }            oldm=newm;
          }          } /* end mult */
                  
         }          s1=s[mw[mi][i]][i];
     }          s2=s[mw[mi+1][i]][i];
   }          bbh=(double)bh[mi][i]/(double)stepm; 
            lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
            ipmx +=1;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          sw += weight[i];
   free_vector(pp,1,nlstate);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
 }  /* End of Freq */      } /* end of individual */
     }  else if(mle==3){  /* exponential inter-extrapolation */
 /************* Waves Concatenation ***************/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        for(mi=1; mi<= wav[i]-1; mi++){
 {          for (ii=1;ii<=nlstate+ndeath;ii++)
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.            for (j=1;j<=nlstate+ndeath;j++){
      Death is a valid wave (if date is known).              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i              savm[ii][j]=(ii==j ? 1.0 : 0.0);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            }
      and mw[mi+1][i]. dh depends on stepm.          for(d=0; d<dh[mi][i]; d++){
      */            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int i, mi, m;            for (kk=1; kk<=cptcovage;kk++) {
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      double sum=0., jmean=0.;*/            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int j, k=0,jk, ju, jl;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double sum=0.;            savm=oldm;
   jmin=1e+5;            oldm=newm;
   jmax=-1;          } /* end mult */
   jmean=0.;        
   for(i=1; i<=imx; i++){          s1=s[mw[mi][i]][i];
     mi=0;          s2=s[mw[mi+1][i]][i];
     m=firstpass;          bbh=(double)bh[mi][i]/(double)stepm; 
     while(s[m][i] <= nlstate){          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 */
       if(s[m][i]>=1)          ipmx +=1;
         mw[++mi][i]=m;          sw += weight[i];
       if(m >=lastpass)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         break;        } /* end of wave */
       else      } /* end of individual */
         m++;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     }/* end while */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     if (s[m][i] > nlstate){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       mi++;     /* Death is another wave */        for(mi=1; mi<= wav[i]-1; mi++){
       /* if(mi==0)  never been interviewed correctly before death */          for (ii=1;ii<=nlstate+ndeath;ii++)
          /* Only death is a correct wave */            for (j=1;j<=nlstate+ndeath;j++){
       mw[mi][i]=m;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
     wav[i]=mi;          for(d=0; d<dh[mi][i]; d++){
     if(mi==0)            newm=savm;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for(i=1; i<=imx; i++){            }
     for(mi=1; mi<wav[i];mi++){          
       if (stepm <=0)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         dh[mi][i]=1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       else{            savm=oldm;
         if (s[mw[mi+1][i]][i] > nlstate) {            oldm=newm;
           if (agedc[i] < 2*AGESUP) {          } /* end mult */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        
           if(j==0) j=1;  /* Survives at least one month after exam */          s1=s[mw[mi][i]][i];
           k=k+1;          s2=s[mw[mi+1][i]][i];
           if (j >= jmax) jmax=j;          if( s2 > nlstate){ 
           if (j <= jmin) jmin=j;            lli=log(out[s1][s2] - savm[s1][s2]);
           sum=sum+j;          }else{
           /*if (j<0) printf("j=%d num=%d \n",j,i); */            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }          }
         }          ipmx +=1;
         else{          sw += weight[i];
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           k=k+1;  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
           if (j >= jmax) jmax=j;        } /* end of wave */
           else if (j <= jmin)jmin=j;      } /* end of individual */
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
           sum=sum+j;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         jk= j/stepm;        for(mi=1; mi<= wav[i]-1; mi++){
         jl= j -jk*stepm;          for (ii=1;ii<=nlstate+ndeath;ii++)
         ju= j -(jk+1)*stepm;            for (j=1;j<=nlstate+ndeath;j++){
         if(jl <= -ju)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           dh[mi][i]=jk;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         else            }
           dh[mi][i]=jk+1;          for(d=0; d<dh[mi][i]; d++){
         if(dh[mi][i]==0)            newm=savm;
           dh[mi][i]=1; /* At least one step */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
   jmean=sum/k;          
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
  }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 /*********** Tricode ****************************/            savm=oldm;
 void tricode(int *Tvar, int **nbcode, int imx)            oldm=newm;
 {          } /* end mult */
   int Ndum[20],ij=1, k, j, i;        
   int cptcode=0;          s1=s[mw[mi][i]][i];
   cptcoveff=0;          s2=s[mw[mi+1][i]][i];
            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   for (k=0; k<19; k++) Ndum[k]=0;          ipmx +=1;
   for (k=1; k<=7; k++) ncodemax[k]=0;          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
     for (i=1; i<=imx; i++) {        } /* end of wave */
       ij=(int)(covar[Tvar[j]][i]);      } /* end of individual */
       Ndum[ij]++;    } /* End of if */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       if (ij > cptcode) cptcode=ij;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     return -l;
     for (i=0; i<=cptcode; i++) {  }
       if(Ndum[i]!=0) ncodemax[j]++;  
     }  /*************** log-likelihood *************/
     ij=1;  double funcone( double *x)
   {
     /* Same as likeli but slower because of a lot of printf and if */
     for (i=1; i<=ncodemax[j]; i++) {    int i, ii, j, k, mi, d, kk;
       for (k=0; k<=19; k++) {    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         if (Ndum[k] != 0) {    double **out;
           nbcode[Tvar[j]][ij]=k;    double lli; /* Individual log likelihood */
           ij++;    double llt;
         }    int s1, s2;
         if (ij > ncodemax[j]) break;    double bbh, survp;
       }      /*extern weight */
     }    /* We are differentiating ll according to initial status */
   }      /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
  for (k=0; k<19; k++) Ndum[k]=0;      printf(" %d\n",s[4][i]);
     */
  for (i=1; i<=ncovmodel-2; i++) {    cov[1]=1.;
       ij=Tvar[i];  
       Ndum[ij]++;    for(k=1; k<=nlstate; k++) ll[k]=0.;
     }  
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
  ij=1;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
  for (i=1; i<=10; i++) {      for(mi=1; mi<= wav[i]-1; mi++){
    if((Ndum[i]!=0) && (i<=ncov)){        for (ii=1;ii<=nlstate+ndeath;ii++)
      Tvaraff[ij]=i;          for (j=1;j<=nlstate+ndeath;j++){
      ij++;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
    }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
  }          }
          for(d=0; d<dh[mi][i]; d++){
     cptcoveff=ij-1;          newm=savm;
 }          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {
 /*********** Health Expectancies ****************/            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           }
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 {                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /* Health expectancies */          savm=oldm;
   int i, j, nhstepm, hstepm, h, nstepm, k;          oldm=newm;
   double age, agelim,hf;        } /* end mult */
   double ***p3mat;        
          s1=s[mw[mi][i]][i];
   fprintf(ficreseij,"# Health expectancies\n");        s2=s[mw[mi+1][i]][i];
   fprintf(ficreseij,"# Age");        bbh=(double)bh[mi][i]/(double)stepm; 
   for(i=1; i<=nlstate;i++)        /* bias is positive if real duration
     for(j=1; j<=nlstate;j++)         * is higher than the multiple of stepm and negative otherwise.
       fprintf(ficreseij," %1d-%1d",i,j);         */
   fprintf(ficreseij,"\n");        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
   k=1;             /* For example stepm=6 months */        } else if (mle==1){
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */        } else if(mle==2){
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
      nhstepm is the number of hstepm from age to agelim        } else if(mle==3){  /* exponential inter-extrapolation */
      nstepm is the number of stepm from age to agelin.          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 */
      Look at hpijx to understand the reason of that which relies in memory size        } else if (mle==4){  /* mle=4 no inter-extrapolation */
      and note for a fixed period like k years */          lli=log(out[s1][s2]); /* Original formula */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
      survival function given by stepm (the optimization length). Unfortunately it          lli=log(out[s1][s2]); /* Original formula */
      means that if the survival funtion is printed only each two years of age and if        } /* End of if */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        ipmx +=1;
      results. So we changed our mind and took the option of the best precision.        sw += weight[i];
   */        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         if(globpr){
   agelim=AGESUP;          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */   %10.6f %10.6f %10.6f ", \
     /* nhstepm age range expressed in number of stepm */                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     nstepm=(int) rint((agelim-age)*YEARM/stepm);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     if (stepm >= YEARM) hstepm=1;            llt +=ll[k]*gipmx/gsw;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          fprintf(ficresilk," %10.6f\n", -llt);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        }
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        } /* end of wave */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    } /* end of individual */
     for(i=1; i<=nlstate;i++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       for(j=1; j<=nlstate;j++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    if(globpr==0){ /* First time we count the contributions and weights */
           /* 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]);*/      gipmx=ipmx;
         }      gsw=sw;
     fprintf(ficreseij,"%3.0f",age );    }
     for(i=1; i<=nlstate;i++)    return -l;
       for(j=1; j<=nlstate;j++){  }
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);  
       }  
     fprintf(ficreseij,"\n");  /*************** function likelione ***********/
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   }  {
 }    /* This routine should help understanding what is done with 
        the selection of individuals/waves and
 /************ Variance ******************/       to check the exact contribution to the likelihood.
 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)       Plotting could be done.
 {     */
   /* Variance of health expectancies */    int k;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;    if(*globpri !=0){ /* Just counts and sums, no printings */
   double **dnewm,**doldm;      strcpy(fileresilk,"ilk"); 
   int i, j, nhstepm, hstepm, h;      strcat(fileresilk,fileres);
   int k, cptcode;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   double *xp;        printf("Problem with resultfile: %s\n", fileresilk);
   double **gp, **gm;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   double ***gradg, ***trgradg;      }
   double ***p3mat;      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
   double age,agelim;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   int theta;      /*  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(k=1; k<=nlstate; k++) 
    fprintf(ficresvij,"# Covariances of life expectancies\n");        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   fprintf(ficresvij,"# Age");      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   for(i=1; i<=nlstate;i++)    }
     for(j=1; j<=nlstate;j++)  
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    *fretone=(*funcone)(p);
   fprintf(ficresvij,"\n");    if(*globpri !=0){
       fclose(ficresilk);
   xp=vector(1,npar);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   dnewm=matrix(1,nlstate,1,npar);      fflush(fichtm); 
   doldm=matrix(1,nlstate,1,nlstate);    } 
      return;
   hstepm=1*YEARM; /* Every year of age */  }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  /*********** Maximum Likelihood Estimation ***************/
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
     if (stepm >= YEARM) hstepm=1;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int i,j, iter;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    double **xi;
     gp=matrix(0,nhstepm,1,nlstate);    double fret;
     gm=matrix(0,nhstepm,1,nlstate);    double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
     for(theta=1; theta <=npar; theta++){    xi=matrix(1,npar,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++)
       }        xi[i][j]=(i==j ? 1.0 : 0.0);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      printf("Powell\n");  fprintf(ficlog,"Powell\n");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    strcpy(filerespow,"pow"); 
     strcat(filerespow,fileres);
       if (popbased==1) {    if((ficrespow=fopen(filerespow,"w"))==NULL) {
         for(i=1; i<=nlstate;i++)      printf("Problem with resultfile: %s\n", filerespow);
           prlim[i][i]=probs[(int)age][i][ij];      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }    }
      fprintf(ficrespow,"# Powell\n# iter -2*LL");
       for(j=1; j<= nlstate; j++){    for (i=1;i<=nlstate;i++)
         for(h=0; h<=nhstepm; h++){      for(j=1;j<=nlstate+ndeath;j++)
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    fprintf(ficrespow,"\n");
         }  
       }    powell(p,xi,npar,ftol,&iter,&fret,func);
      
       for(i=1; i<=npar; i++) /* Computes gradient */    fclose(ficrespow);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
    
       if (popbased==1) {  }
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];  /**** Computes Hessian and covariance matrix ***/
       }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   {
       for(j=1; j<= nlstate; j++){    double  **a,**y,*x,pd;
         for(h=0; h<=nhstepm; h++){    double **hess;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    int i, j,jk;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    int *indx;
         }  
       }    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);
       for(j=1; j<= nlstate; j++)    void lubksb(double **a, int npar, int *indx, double b[]) ;
         for(h=0; h<=nhstepm; h++){    void ludcmp(double **a, int npar, int *indx, double *d) ;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    double gompertz(double p[]);
         }    hess=matrix(1,npar,1,npar);
     } /* End theta */  
     printf("\nCalculation of the hessian matrix. Wait...\n");
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
     for(h=0; h<=nhstepm; h++)      printf("%d",i);fflush(stdout);
       for(j=1; j<=nlstate;j++)      fprintf(ficlog,"%d",i);fflush(ficlog);
         for(theta=1; theta <=npar; theta++)     
           trgradg[h][j][theta]=gradg[h][theta][j];       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       
     for(i=1;i<=nlstate;i++)      /*  printf(" %f ",p[i]);
       for(j=1;j<=nlstate;j++)          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
         vareij[i][j][(int)age] =0.;    }
     for(h=0;h<=nhstepm;h++){    
       for(k=0;k<=nhstepm;k++){    for (i=1;i<=npar;i++) {
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      for (j=1;j<=npar;j++)  {
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        if (j>i) { 
         for(i=1;i<=nlstate;i++)          printf(".%d%d",i,j);fflush(stdout);
           for(j=1;j<=nlstate;j++)          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
             vareij[i][j][(int)age] += doldm[i][j];          hess[i][j]=hessij(p,delti,i,j,func,npar);
       }          
     }          hess[j][i]=hess[i][j];    
     h=1;          /*printf(" %lf ",hess[i][j]);*/
     if (stepm >= YEARM) h=stepm/YEARM;        }
     fprintf(ficresvij,"%.0f ",age );      }
     for(i=1; i<=nlstate;i++)    }
       for(j=1; j<=nlstate;j++){    printf("\n");
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    fprintf(ficlog,"\n");
       }  
     fprintf(ficresvij,"\n");    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     free_matrix(gp,0,nhstepm,1,nlstate);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     free_matrix(gm,0,nhstepm,1,nlstate);    
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    a=matrix(1,npar,1,npar);
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    y=matrix(1,npar,1,npar);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    x=vector(1,npar);
   } /* End age */    indx=ivector(1,npar);
      for (i=1;i<=npar;i++)
   free_vector(xp,1,npar);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   free_matrix(doldm,1,nlstate,1,npar);    ludcmp(a,npar,indx,&pd);
   free_matrix(dnewm,1,nlstate,1,nlstate);  
     for (j=1;j<=npar;j++) {
 }      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
 /************ Variance of prevlim ******************/      lubksb(a,npar,indx,x);
 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)      for (i=1;i<=npar;i++){ 
 {        matcov[i][j]=x[i];
   /* Variance of prevalence limit */      }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    }
   double **newm;  
   double **dnewm,**doldm;    printf("\n#Hessian matrix#\n");
   int i, j, nhstepm, hstepm;    fprintf(ficlog,"\n#Hessian matrix#\n");
   int k, cptcode;    for (i=1;i<=npar;i++) { 
   double *xp;      for (j=1;j<=npar;j++) { 
   double *gp, *gm;        printf("%.3e ",hess[i][j]);
   double **gradg, **trgradg;        fprintf(ficlog,"%.3e ",hess[i][j]);
   double age,agelim;      }
   int theta;      printf("\n");
          fprintf(ficlog,"\n");
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    }
   fprintf(ficresvpl,"# Age");  
   for(i=1; i<=nlstate;i++)    /* Recompute Inverse */
       fprintf(ficresvpl," %1d-%1d",i,i);    for (i=1;i<=npar;i++)
   fprintf(ficresvpl,"\n");      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);    /*  printf("\n#Hessian matrix recomputed#\n");
   doldm=matrix(1,nlstate,1,nlstate);  
      for (j=1;j<=npar;j++) {
   hstepm=1*YEARM; /* Every year of age */      for (i=1;i<=npar;i++) x[i]=0;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      x[j]=1;
   agelim = AGESUP;      lubksb(a,npar,indx,x);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for (i=1;i<=npar;i++){ 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        y[i][j]=x[i];
     if (stepm >= YEARM) hstepm=1;        printf("%.3e ",y[i][j]);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        fprintf(ficlog,"%.3e ",y[i][j]);
     gradg=matrix(1,npar,1,nlstate);      }
     gp=vector(1,nlstate);      printf("\n");
     gm=vector(1,nlstate);      fprintf(ficlog,"\n");
     }
     for(theta=1; theta <=npar; theta++){    */
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    free_matrix(a,1,npar,1,npar);
       }    free_matrix(y,1,npar,1,npar);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    free_vector(x,1,npar);
       for(i=1;i<=nlstate;i++)    free_ivector(indx,1,npar);
         gp[i] = prlim[i][i];    free_matrix(hess,1,npar,1,npar);
      
       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);  
       for(i=1;i<=nlstate;i++)  /*************** hessian matrix ****************/
         gm[i] = prlim[i][i];  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   {
       for(i=1;i<=nlstate;i++)    int i;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    int l=1, lmax=20;
     } /* End theta */    double k1,k2;
     double p2[NPARMAX+1];
     trgradg =matrix(1,nlstate,1,npar);    double res;
     double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     for(j=1; j<=nlstate;j++)    double fx;
       for(theta=1; theta <=npar; theta++)    int k=0,kmax=10;
         trgradg[j][theta]=gradg[theta][j];    double l1;
   
     for(i=1;i<=nlstate;i++)    fx=func(x);
       varpl[i][(int)age] =0.;    for (i=1;i<=npar;i++) p2[i]=x[i];
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    for(l=0 ; l <=lmax; l++){
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      l1=pow(10,l);
     for(i=1;i<=nlstate;i++)      delts=delt;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      for(k=1 ; k <kmax; k=k+1){
         delt = delta*(l1*k);
     fprintf(ficresvpl,"%.0f ",age );        p2[theta]=x[theta] +delt;
     for(i=1; i<=nlstate;i++)        k1=func(p2)-fx;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        p2[theta]=x[theta]-delt;
     fprintf(ficresvpl,"\n");        k2=func(p2)-fx;
     free_vector(gp,1,nlstate);        /*res= (k1-2.0*fx+k2)/delt/delt; */
     free_vector(gm,1,nlstate);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     free_matrix(gradg,1,npar,1,nlstate);        
     free_matrix(trgradg,1,nlstate,1,npar);  #ifdef DEBUG
   } /* End age */        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   free_vector(xp,1,npar);  #endif
   free_matrix(doldm,1,nlstate,1,npar);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   free_matrix(dnewm,1,nlstate,1,nlstate);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k=kmax;
 }        }
         else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
 /************ Variance of one-step probabilities  ******************/          k=kmax; l=lmax*10.;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        }
 {        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   int i, j;          delts=delt;
   int k=0, cptcode;        }
   double **dnewm,**doldm;      }
   double *xp;    }
   double *gp, *gm;    delti[theta]=delts;
   double **gradg, **trgradg;    return res; 
   double age,agelim, cov[NCOVMAX];    
   int theta;  }
   char fileresprob[FILENAMELENGTH];  
   double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   strcpy(fileresprob,"prob");  {
   strcat(fileresprob,fileres);    int i;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    int l=1, l1, lmax=20;
     printf("Problem with resultfile: %s\n", fileresprob);    double k1,k2,k3,k4,res,fx;
   }    double p2[NPARMAX+1];
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    int k;
    
     fx=func(x);
   xp=vector(1,npar);    for (k=1; k<=2; k++) {
   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));      p2[thetai]=x[thetai]+delti[thetai]/k;
        p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   cov[1]=1;      k1=func(p2)-fx;
   for (age=bage; age<=fage; age ++){    
     cov[2]=age;      p2[thetai]=x[thetai]+delti[thetai]/k;
     gradg=matrix(1,npar,1,9);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     trgradg=matrix(1,9,1,npar);      k2=func(p2)-fx;
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      p2[thetai]=x[thetai]-delti[thetai]/k;
          p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     for(theta=1; theta <=npar; theta++){      k3=func(p2)-fx;
       for(i=1; i<=npar; i++)    
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      p2[thetai]=x[thetai]-delti[thetai]/k;
            p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      k4=func(p2)-fx;
          res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       k=0;  #ifdef DEBUG
       for(i=1; i<= (nlstate+ndeath); i++){      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         for(j=1; j<=(nlstate+ndeath);j++){      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
            k=k+1;  #endif
           gp[k]=pmmij[i][j];    }
         }    return res;
       }  }
   
       for(i=1; i<=npar; i++)  /************** Inverse of matrix **************/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  void ludcmp(double **a, int n, int *indx, double *d) 
      { 
     int i,imax,j,k; 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    double big,dum,sum,temp; 
       k=0;    double *vv; 
       for(i=1; i<=(nlstate+ndeath); i++){   
         for(j=1; j<=(nlstate+ndeath);j++){    vv=vector(1,n); 
           k=k+1;    *d=1.0; 
           gm[k]=pmmij[i][j];    for (i=1;i<=n;i++) { 
         }      big=0.0; 
       }      for (j=1;j<=n;j++) 
              if ((temp=fabs(a[i][j])) > big) big=temp; 
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        vv[i]=1.0/big; 
     }    } 
     for (j=1;j<=n;j++) { 
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)      for (i=1;i<j;i++) { 
       for(theta=1; theta <=npar; theta++)        sum=a[i][j]; 
       trgradg[j][theta]=gradg[theta][j];        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
          a[i][j]=sum; 
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      } 
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);      big=0.0; 
       for (i=j;i<=n;i++) { 
      pmij(pmmij,cov,ncovmodel,x,nlstate);        sum=a[i][j]; 
         for (k=1;k<j;k++) 
      k=0;          sum -= a[i][k]*a[k][j]; 
      for(i=1; i<=(nlstate+ndeath); i++){        a[i][j]=sum; 
        for(j=1; j<=(nlstate+ndeath);j++){        if ( (dum=vv[i]*fabs(sum)) >= big) { 
          k=k+1;          big=dum; 
          gm[k]=pmmij[i][j];          imax=i; 
         }        } 
      }      } 
            if (j != imax) { 
      /*printf("\n%d ",(int)age);        for (k=1;k<=n;k++) { 
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          dum=a[imax][k]; 
                  a[imax][k]=a[j][k]; 
           a[j][k]=dum; 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        } 
      }*/        *d = -(*d); 
         vv[imax]=vv[j]; 
   fprintf(ficresprob,"\n%d ",(int)age);      } 
       indx[j]=imax; 
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      if (a[j][j] == 0.0) a[j][j]=TINY; 
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      if (j != n) { 
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        dum=1.0/(a[j][j]); 
   }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       } 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    } 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    free_vector(vv,1,n);  /* Doesn't work */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  ;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  } 
 }  
  free_vector(xp,1,npar);  void lubksb(double **a, int n, int *indx, double b[]) 
 fclose(ficresprob);  { 
     int i,ii=0,ip,j; 
 }    double sum; 
    
 /******************* Printing html file ***********/    for (i=1;i<=n;i++) { 
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){      ip=indx[i]; 
   int jj1, k1, i1, cpt;      sum=b[ip]; 
   FILE *fichtm;      b[ip]=b[i]; 
   /*char optionfilehtm[FILENAMELENGTH];*/      if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   strcpy(optionfilehtm,optionfile);      else if (sum) ii=i; 
   strcat(optionfilehtm,".htm");      b[i]=sum; 
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    } 
     printf("Problem with %s \n",optionfilehtm), exit(0);    for (i=n;i>=1;i--) { 
   }      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71c </font> <hr size=\"2\" color=\"#EC5E5E\">      b[i]=sum/a[i][i]; 
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    } 
   } 
 Total number of observations=%d <br>  
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>  /************ Frequencies ********************/
 <hr  size=\"2\" color=\"#EC5E5E\">  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[])
 <li>Outputs files<br><br>\n  {  /* Some frequencies */
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    int first;
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    double ***freq; /* Frequencies */
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    double *pp, **prop;
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    double pos,posprop, k2, dateintsum=0,k2cpt=0;
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    FILE *ficresp;
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    char fileresp[FILENAMELENGTH];
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>    
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>    pp=vector(1,nlstate);
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>    prop=matrix(1,nlstate,iagemin,iagemax+3);
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    strcpy(fileresp,"p");
      strcat(fileresp,fileres);
 fprintf(fichtm," <li>Graphs</li><p>");    if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
  m=cptcoveff;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      exit(0);
     }
  jj1=0;    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
  for(k1=1; k1<=m;k1++){    j1=0;
    for(i1=1; i1<=ncodemax[k1];i1++){    
        jj1++;    j=cptcoveff;
        if (cptcovn > 0) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  
          for (cpt=1; cpt<=cptcoveff;cpt++)    first=1;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);  
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    for(k1=1; k1<=j;k1++){
        }      for(i1=1; i1<=ncodemax[k1];i1++){
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>        j1++;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
        for(cpt=1; cpt<nlstate;cpt++){          scanf("%d", i);*/
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>        for (i=-5; i<=nlstate+ndeath; i++)  
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
        }            for(m=iagemin; m <= iagemax+3; m++)
     for(cpt=1; cpt<=nlstate;cpt++) {              freq[i][jk][m]=0;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  
 interval) in state (%d): v%s%d%d.gif <br>      for (i=1; i<=nlstate; i++)  
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          for(m=iagemin; m <= iagemax+3; m++)
      }          prop[i][m]=0;
      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>        dateintsum=0;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        k2cpt=0;
      }        for (i=1; i<=imx; i++) {
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          bool=1;
 health expectancies in states (1) and (2): e%s%d.gif<br>          if  (cptcovn>0) {
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            for (z1=1; z1<=cptcoveff; z1++) 
 fprintf(fichtm,"\n</body>");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
    }                bool=0;
    }          }
 fclose(fichtm);          if (bool==1){
 }            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
 /******************* Gnuplot file **************/              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                 if (m<lastpass) {
   strcpy(optionfilegnuplot,optionfilefiname);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   strcat(optionfilegnuplot,".plt");                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {                }
     printf("Problem with file %s",optionfilegnuplot);                
   }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
 #ifdef windows                  k2cpt++;
     fprintf(ficgp,"cd \"%s\" \n",pathc);                }
 #endif                /*}*/
 m=pow(2,cptcoveff);            }
            }
  /* 1eme*/        }
   for (cpt=1; cpt<= nlstate ; cpt ++) {         
    for (k1=1; k1<= m ; k1 ++) {        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   fprintf(ficresp, "#Local time at start: %s", strstart);
 #ifdef windows        if  (cptcovn>0) {
     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);          fprintf(ficresp, "\n#********** Variable "); 
 #endif          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 #ifdef unix          fprintf(ficresp, "**********\n#");
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);        }
 #endif        for(i=1; i<=nlstate;i++) 
           fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 for (i=1; i<= nlstate ; i ++) {        fprintf(ficresp, "\n");
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(i=iagemin; i <= iagemax+3; i++){
 }          if(i==iagemax+3){
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);            fprintf(ficlog,"Total");
     for (i=1; i<= nlstate ; i ++) {          }else{
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            if(first==1){
   else fprintf(ficgp," \%%*lf (\%%*lf)");              first=0;
 }              printf("See log file for details...\n");
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);            }
      for (i=1; i<= nlstate ; i ++) {            fprintf(ficlog,"Age %d", i);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(jk=1; jk <=nlstate ; jk++){
 }              for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));              pp[jk] += freq[jk][m][i]; 
 #ifdef unix          }
 fprintf(ficgp,"\nset ter gif small size 400,300");          for(jk=1; jk <=nlstate ; jk++){
 #endif            for(m=-1, pos=0; m <=0 ; m++)
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              pos += freq[jk][m][i];
    }            if(pp[jk]>=1.e-10){
   }              if(first==1){
   /*2 eme*/              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               }
   for (k1=1; k1<= m ; k1 ++) {              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);            }else{
                  if(first==1)
     for (i=1; i<= nlstate+1 ; i ++) {                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       k=2*i;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);            }
       for (j=1; j<= nlstate+1 ; j ++) {          }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(jk=1; jk <=nlstate ; jk++){
 }              for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");              pp[jk] += freq[jk][m][i];
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          }       
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       for (j=1; j<= nlstate+1 ; j ++) {            pos += pp[jk];
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            posprop += prop[jk][i];
         else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }            for(jk=1; jk <=nlstate ; jk++){
       fprintf(ficgp,"\" t\"\" w l 0,");            if(pos>=1.e-5){
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);              if(first==1)
       for (j=1; j<= nlstate+1 ; j ++) {                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   else fprintf(ficgp," \%%*lf (\%%*lf)");            }else{
 }                if(first==1)
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       else fprintf(ficgp,"\" t\"\" w l 0,");              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     }            }
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);            if( i <= iagemax){
   }              if(pos>=1.e-5){
                  fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   /*3eme*/                /*probs[i][jk][j1]= pp[jk]/pos;*/
                 /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   for (k1=1; k1<= m ; k1 ++) {              }
     for (cpt=1; cpt<= nlstate ; cpt ++) {              else
       k=2+nlstate*(cpt-1);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);            }
       for (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);          
       }          for(jk=-1; jk <=nlstate+ndeath; jk++)
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            for(m=-1; m <=nlstate+ndeath; m++)
     }              if(freq[jk][m][i] !=0 ) {
     }              if(first==1)
                  printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   /* CV preval stat */                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     for (k1=1; k1<= m ; k1 ++) {              }
     for (cpt=1; cpt<nlstate ; cpt ++) {          if(i <= iagemax)
       k=3;            fprintf(ficresp,"\n");
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);          if(first==1)
             printf("Others in log...\n");
       for (i=1; i< nlstate ; i ++)          fprintf(ficlog,"\n");
         fprintf(ficgp,"+$%d",k+i+1);        }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      }
          }
       l=3+(nlstate+ndeath)*cpt;    dateintmean=dateintsum/k2cpt; 
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);   
       for (i=1; i< nlstate ; i ++) {    fclose(ficresp);
         l=3+(nlstate+ndeath)*cpt;    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
         fprintf(ficgp,"+$%d",l+i+1);    free_vector(pp,1,nlstate);
       }    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      /* End of Freq */
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  }
     }  
   }    /************ 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)
   /* proba elementaires */  {  
    for(i=1,jk=1; i <=nlstate; i++){    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     for(k=1; k <=(nlstate+ndeath); k++){       in each health status at the date of interview (if between dateprev1 and dateprev2).
       if (k != i) {       We still use firstpass and lastpass as another selection.
         for(j=1; j <=ncovmodel; j++){    */
           
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
           jk++;    double ***freq; /* Frequencies */
           fprintf(ficgp,"\n");    double *pp, **prop;
         }    double pos,posprop; 
       }    double  y2; /* in fractional years */
     }    int iagemin, iagemax;
     }  
     iagemin= (int) agemin;
     for(jk=1; jk <=m; jk++) {    iagemax= (int) agemax;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);    /*pp=vector(1,nlstate);*/
    i=1;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
    for(k2=1; k2<=nlstate; k2++) {    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
      k3=i;    j1=0;
      for(k=1; k<=(nlstate+ndeath); k++) {    
        if (k != k2){    j=cptcoveff;
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
 ij=1;    
         for(j=3; j <=ncovmodel; j++) {    for(k1=1; k1<=j;k1++){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      for(i1=1; i1<=ncodemax[k1];i1++){
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        j1++;
             ij++;        
           }        for (i=1; i<=nlstate; i++)  
           else          for(m=iagemin; m <= iagemax+3; m++)
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            prop[i][m]=0.0;
         }       
           fprintf(ficgp,")/(1");        for (i=1; i<=imx; i++) { /* Each individual */
                  bool=1;
         for(k1=1; k1 <=nlstate; k1++){            if  (cptcovn>0) {
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);            for (z1=1; z1<=cptcoveff; z1++) 
 ij=1;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           for(j=3; j <=ncovmodel; j++){                bool=0;
           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]]]);          if (bool==1) { 
             ij++;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
           }              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
           else              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           fprintf(ficgp,")");                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) { 
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);                  /*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]]);*/
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
         i=i+ncovmodel;                  prop[s[m][i]][iagemax+3] += weight[i]; 
        }                } 
      }              }
    }            } /* end selection of waves */
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);          }
    }        }
            for(i=iagemin; i <= iagemax+3; i++){  
   fclose(ficgp);          
 }  /* end gnuplot */          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
           } 
 /*************** Moving average **************/  
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){          for(jk=1; jk <=nlstate ; jk++){     
             if( i <=  iagemax){ 
   int i, cpt, cptcod;              if(posprop>=1.e-5){ 
     for (agedeb=agemin; agedeb<=fage; agedeb++)                probs[i][jk][j1]= prop[jk][i]/posprop;
       for (i=1; i<=nlstate;i++)              } 
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)            } 
           mobaverage[(int)agedeb][i][cptcod]=0.;          }/* end jk */ 
            }/* end i */ 
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){      } /* end i1 */
       for (i=1; i<=nlstate;i++){    } /* end k1 */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    
           for (cpt=0;cpt<=4;cpt++){    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    /*free_vector(pp,1,nlstate);*/
           }    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  }  /* End of prevalence */
         }  
       }  /************* Waves Concatenation ***************/
     }  
      void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
 }  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        Death is a valid wave (if date is known).
 /************** Forecasting ******************/       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         and mw[mi+1][i]. dh depends on stepm.
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;       */
   int *popage;  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    int i, mi, m;
   double *popeffectif,*popcount;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   double ***p3mat;       double sum=0., jmean=0.;*/
   char fileresf[FILENAMELENGTH];    int first;
     int j, k=0,jk, ju, jl;
  agelim=AGESUP;    double sum=0.;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    first=0;
     jmin=1e+5;
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    jmax=-1;
      jmean=0.;
      for(i=1; i<=imx; i++){
   strcpy(fileresf,"f");      mi=0;
   strcat(fileresf,fileres);      m=firstpass;
   if((ficresf=fopen(fileresf,"w"))==NULL) {      while(s[m][i] <= nlstate){
     printf("Problem with forecast resultfile: %s\n", fileresf);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   }          mw[++mi][i]=m;
   printf("Computing forecasting: result on file '%s' \n", fileresf);        if(m >=lastpass)
           break;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        else
           m++;
   if (mobilav==1) {      }/* end while */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      if (s[m][i] > nlstate){
     movingaverage(agedeb, fage, agemin, mobaverage);        mi++;     /* Death is another wave */
   }        /* if(mi==0)  never been interviewed correctly before death */
            /* Only death is a correct wave */
   stepsize=(int) (stepm+YEARM-1)/YEARM;        mw[mi][i]=m;
   if (stepm<=12) stepsize=1;      }
    
   agelim=AGESUP;      wav[i]=mi;
        if(mi==0){
   hstepm=1;        nbwarn++;
   hstepm=hstepm/stepm;        if(first==0){
   yp1=modf(dateintmean,&yp);          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   anprojmean=yp;          first=1;
   yp2=modf((yp1*12),&yp);        }
   mprojmean=yp;        if(first==1){
   yp1=modf((yp2*30.5),&yp);          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
   jprojmean=yp;        }
   if(jprojmean==0) jprojmean=1;      } /* end mi==0 */
   if(mprojmean==0) jprojmean=1;    } /* End individuals */
    
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    for(i=1; i<=imx; i++){
        for(mi=1; mi<wav[i];mi++){
   for(cptcov=1;cptcov<=i2;cptcov++){        if (stepm <=0)
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          dh[mi][i]=1;
       k=k+1;        else{
       fprintf(ficresf,"\n#******");          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       for(j=1;j<=cptcoveff;j++) {            if (agedc[i] < 2*AGESUP) {
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       }              if(j==0) j=1;  /* Survives at least one month after exam */
       fprintf(ficresf,"******\n");              else if(j<0){
       fprintf(ficresf,"# StartingAge FinalAge");                nberr++;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                      j=1; /* Temporary Dangerous patch */
                      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);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
         fprintf(ficresf,"\n");                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);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);                }
               k=k+1;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){              if (j >= jmax) jmax=j;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              if (j <= jmin) jmin=j;
           nhstepm = nhstepm/hstepm;              sum=sum+j;
                        /*if (j<0) printf("j=%d num=%d \n",j,i);*/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           oldm=oldms;savm=savms;            }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            }
                  else{
           for (h=0; h<=nhstepm; h++){            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
             if (h==(int) (calagedate+YEARM*cpt)) {  /*        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]); */
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);  
             }            k=k+1;
             for(j=1; j<=nlstate+ndeath;j++) {            if (j >= jmax) jmax=j;
               kk1=0.;kk2=0;            else if (j <= jmin)jmin=j;
               for(i=1; i<=nlstate;i++) {                          /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
                 if (mobilav==1)            /*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]);*/
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            if(j<0){
                 else {              nberr++;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 }              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                            }
               }            sum=sum+j;
               if (h==(int)(calagedate+12*cpt)){          }
                 fprintf(ficresf," %.3f", kk1);          jk= j/stepm;
                                  jl= j -jk*stepm;
               }          ju= j -(jk+1)*stepm;
             }          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           }            if(jl==0){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              dh[mi][i]=jk;
         }              bh[mi][i]=0;
       }            }else{ /* We want a negative bias in order to only have interpolation ie
     }                    * at the price of an extra matrix product in likelihood */
   }              dh[mi][i]=jk+1;
                      bh[mi][i]=ju;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            }
           }else{
   fclose(ficresf);            if(jl <= -ju){
 }              dh[mi][i]=jk;
 /************** Forecasting ******************/              bh[mi][i]=jl;       /* bias is positive if real duration
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){                                   * is higher than the multiple of stepm and negative otherwise.
                                     */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            }
   int *popage;            else{
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;              dh[mi][i]=jk+1;
   double *popeffectif,*popcount;              bh[mi][i]=ju;
   double ***p3mat,***tabpop,***tabpopprev;            }
   char filerespop[FILENAMELENGTH];            if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              bh[mi][i]=ju; /* At least one step */
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              /*  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);*/
   agelim=AGESUP;            }
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          } /* end if mle */
          }
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      } /* end wave */
      }
      jmean=sum/k;
   strcpy(filerespop,"pop");    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   strcat(filerespop,fileres);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {   }
     printf("Problem with forecast resultfile: %s\n", filerespop);  
   }  /*********** Tricode ****************************/
   printf("Computing forecasting: result on file '%s' \n", filerespop);  void tricode(int *Tvar, int **nbcode, int imx)
   {
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    
     int Ndum[20],ij=1, k, j, i, maxncov=19;
   if (mobilav==1) {    int cptcode=0;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    cptcoveff=0; 
     movingaverage(agedeb, fage, agemin, mobaverage);   
   }    for (k=0; k<maxncov; k++) Ndum[k]=0;
     for (k=1; k<=7; k++) ncodemax[k]=0;
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   if (stepm<=12) stepsize=1;    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
        for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   agelim=AGESUP;                                 modality*/ 
          ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   hstepm=1;        Ndum[ij]++; /*store the modality */
   hstepm=hstepm/stepm;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
          if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   if (popforecast==1) {                                         Tvar[j]. If V=sex and male is 0 and 
     if((ficpop=fopen(popfile,"r"))==NULL) {                                         female is 1, then  cptcode=1.*/
       printf("Problem with population file : %s\n",popfile);exit(0);      }
     }  
     popage=ivector(0,AGESUP);      for (i=0; i<=cptcode; i++) {
     popeffectif=vector(0,AGESUP);        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 */
     popcount=vector(0,AGESUP);      }
      
     i=1;        ij=1; 
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;      for (i=1; i<=ncodemax[j]; i++) {
            for (k=0; k<= maxncov; k++) {
     imx=i;          if (Ndum[k] != 0) {
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];            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; */
             
   for(cptcov=1;cptcov<=i2;cptcov++){            ij++;
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          }
       k=k+1;          if (ij > ncodemax[j]) break; 
       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");   for (k=0; k< maxncov; k++) Ndum[k]=0;
       fprintf(ficrespop,"# Age");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);   for (i=1; i<=ncovmodel-2; i++) { 
       if (popforecast==1)  fprintf(ficrespop," [Population]");     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
           ij=Tvar[i];
       for (cpt=0; cpt<=0;cpt++) {     Ndum[ij]++;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);     }
          
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){   ij=1;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);   for (i=1; i<= maxncov; i++) {
           nhstepm = nhstepm/hstepm;     if((Ndum[i]!=0) && (i<=ncovcol)){
                 Tvaraff[ij]=i; /*For printing */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       ij++;
           oldm=oldms;savm=savms;     }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);     }
           
           for (h=0; h<=nhstepm; h++){   cptcoveff=ij-1; /*Number of simple covariates*/
             if (h==(int) (calagedate+YEARM*cpt)) {  }
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  
             }  /*********** Health Expectancies ****************/
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;  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; i<=nlstate;i++) {                
                 if (mobilav==1)  {
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    /* Health expectancies */
                 else {    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    double age, agelim, hf;
                 }    double ***p3mat,***varhe;
               }    double **dnewm,**doldm;
               if (h==(int)(calagedate+12*cpt)){    double *xp;
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    double **gp, **gm;
                   /*fprintf(ficrespop," %.3f", kk1);    double ***gradg, ***trgradg;
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    int theta;
               }  
             }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
             for(i=1; i<=nlstate;i++){    xp=vector(1,npar);
               kk1=0.;    dnewm=matrix(1,nlstate*nlstate,1,npar);
                 for(j=1; j<=nlstate;j++){    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    
                 }    fprintf(ficreseij,"# Local time at start: %s", strstart);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    fprintf(ficreseij,"# Health expectancies\n");
             }    fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++)
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      for(j=1; j<=nlstate;j++)
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
           }    fprintf(ficreseij,"\n");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }    if(estepm < stepm){
       }      printf ("Problem %d lower than %d\n",estepm, stepm);
      }
   /******/    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {     * This is mainly to measure the difference between two models: for example
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);       * if stepm=24 months pijx are given only every 2 years and by summing them
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){     * we are calculating an estimate of the Life Expectancy assuming a linear 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);     * progression in between and thus overestimating or underestimating according
           nhstepm = nhstepm/hstepm;     * 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
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     * to compare the new estimate of Life expectancy with the same linear 
           oldm=oldms;savm=savms;     * hypothesis. A more precise result, taking into account a more precise
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       * curvature will be obtained if estepm is as small as stepm. */
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {    /* For example we decided to compute the life expectancy with the smallest unit */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
             }       nhstepm is the number of hstepm from age to agelim 
             for(j=1; j<=nlstate+ndeath;j++) {       nstepm is the number of stepm from age to agelin. 
               kk1=0.;kk2=0;       Look at hpijx to understand the reason of that which relies in memory size
               for(i=1; i<=nlstate;i++) {                     and note for a fixed period like estepm months */
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        /* We decided (b) to get a life expectancy respecting the most precise curvature of the
               }       survival function given by stepm (the optimization length). Unfortunately it
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);       means that if the survival funtion is printed only each two years of age and if
             }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           }       results. So we changed our mind and took the option of the best precision.
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    */
         }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       }  
    }    agelim=AGESUP;
   }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        /* nhstepm age range expressed in number of stepm */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   if (popforecast==1) {      /* if (stepm >= YEARM) hstepm=1;*/
     free_ivector(popage,0,AGESUP);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     free_vector(popeffectif,0,AGESUP);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_vector(popcount,0,AGESUP);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   }      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   fclose(ficrespop);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
 }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
 /***********************************************/   
 /**************** Main Program *****************/  
 /***********************************************/      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
 int main(int argc, char *argv[])      /* Computing  Variances of health expectancies */
 {  
        for(theta=1; theta <=npar; theta++){
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        for(i=1; i<=npar; i++){ 
   double agedeb, agefin,hf;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   double fret;    
   double **xi,tmp,delta;        cptj=0;
         for(j=1; j<= nlstate; j++){
   double dum; /* Dummy variable */          for(i=1; i<=nlstate; i++){
   double ***p3mat;            cptj=cptj+1;
   int *indx;            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   char line[MAXLINE], linepar[MAXLINE];              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   char title[MAXLINE];            }
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          }
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];        }
         
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];       
         for(i=1; i<=npar; i++) 
   char filerest[FILENAMELENGTH];          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   char fileregp[FILENAMELENGTH];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   char popfile[FILENAMELENGTH];        
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        cptj=0;
   int firstobs=1, lastobs=10;        for(j=1; j<= nlstate; j++){
   int sdeb, sfin; /* Status at beginning and end */          for(i=1;i<=nlstate;i++){
   int c,  h , cpt,l;            cptj=cptj+1;
   int ju,jl, mi;            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   int mobilav=0,popforecast=0;            }
   int hstepm, nhstepm;          }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;        }
         for(j=1; j<= nlstate*nlstate; j++)
   double bage, fage, age, agelim, agebase;          for(h=0; h<=nhstepm-1; h++){
   double ftolpl=FTOL;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   double **prlim;          }
   double *severity;       } 
   double ***param; /* Matrix of parameters */     
   double  *p;  /* End theta */
   double **matcov; /* Matrix of covariance */  
   double ***delti3; /* Scale */       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   double *delti; /* Scale */  
   double ***eij, ***vareij;       for(h=0; h<=nhstepm-1; h++)
   double **varpl; /* Variances of prevalence limits by age */        for(j=1; j<=nlstate*nlstate;j++)
   double *epj, vepp;          for(theta=1; theta <=npar; theta++)
   double kk1, kk2;            trgradg[h][j][theta]=gradg[h][theta][j];
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;       
    
        for(i=1;i<=nlstate*nlstate;i++)
   char version[80]="Imach version 0.71c, March 2002, INED-EUROREVES ";        for(j=1;j<=nlstate*nlstate;j++)
   char *alph[]={"a","a","b","c","d","e"}, str[4];          varhe[i][j][(int)age] =0.;
   
        printf("%d|",(int)age);fflush(stdout);
   char z[1]="c", occ;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 #include <sys/time.h>       for(h=0;h<=nhstepm-1;h++){
 #include <time.h>        for(k=0;k<=nhstepm-1;k++){
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   /* long total_usecs;          for(i=1;i<=nlstate*nlstate;i++)
   struct timeval start_time, end_time;            for(j=1;j<=nlstate*nlstate;j++)
                varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        }
       }
       /* Computing expectancies */
   printf("\n%s",version);      for(i=1; i<=nlstate;i++)
   if(argc <=1){        for(j=1; j<=nlstate;j++)
     printf("\nEnter the parameter file name: ");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     scanf("%s",pathtot);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   }            
   else{  /* 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]);*/
     strcpy(pathtot,argv[1]);  
   }          }
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/  
   /*cygwin_split_path(pathtot,path,optionfile);      fprintf(ficreseij,"%3.0f",age );
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      cptj=0;
   /* cutv(path,optionfile,pathtot,'\\');*/      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);          cptj++;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   chdir(path);        }
   replace(pathc,path);      fprintf(ficreseij,"\n");
      
 /*-------- arguments in the command line --------*/      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   strcpy(fileres,"r");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   strcat(fileres, optionfilefiname);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   strcat(fileres,".txt");    /* Other files have txt extension */      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }
   /*---------arguments file --------*/    printf("\n");
     fprintf(ficlog,"\n");
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  
     printf("Problem with optionfile %s\n",optionfile);    free_vector(xp,1,npar);
     goto end;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   strcpy(filereso,"o");  }
   strcat(filereso,fileres);  
   if((ficparo=fopen(filereso,"w"))==NULL) {  /************ Variance ******************/
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  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[])
   }  {
     /* Variance of health expectancies */
   /* Reads comments: lines beginning with '#' */    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   while((c=getc(ficpar))=='#' && c!= EOF){    /* double **newm;*/
     ungetc(c,ficpar);    double **dnewm,**doldm;
     fgets(line, MAXLINE, ficpar);    double **dnewmp,**doldmp;
     puts(line);    int i, j, nhstepm, hstepm, h, nstepm ;
     fputs(line,ficparo);    int k, cptcode;
   }    double *xp;
   ungetc(c,ficpar);    double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    double **gradgp, **trgradgp; /* for var p point j */
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    double *gpp, *gmp; /* for var p point j */
   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);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
 while((c=getc(ficpar))=='#' && c!= EOF){    double ***p3mat;
     ungetc(c,ficpar);    double age,agelim, hf;
     fgets(line, MAXLINE, ficpar);    double ***mobaverage;
     puts(line);    int theta;
     fputs(line,ficparo);    char digit[4];
   }    char digitp[25];
   ungetc(c,ficpar);  
      char fileresprobmorprev[FILENAMELENGTH];
      
   covar=matrix(0,NCOVMAX,1,n);    if(popbased==1){
   cptcovn=0;      if(mobilav!=0)
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;        strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
   ncovmodel=2+cptcovn;    }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    else 
        strcpy(digitp,"-stablbased-");
   /* Read guess parameters */  
   /* Reads comments: lines beginning with '#' */    if (mobilav!=0) {
   while((c=getc(ficpar))=='#' && c!= EOF){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     ungetc(c,ficpar);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     fgets(line, MAXLINE, ficpar);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     puts(line);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     fputs(line,ficparo);      }
   }    }
   ungetc(c,ficpar);  
      strcpy(fileresprobmorprev,"prmorprev"); 
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    sprintf(digit,"%-d",ij);
     for(i=1; i <=nlstate; i++)    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     for(j=1; j <=nlstate+ndeath-1; j++){    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       fscanf(ficpar,"%1d%1d",&i1,&j1);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
       fprintf(ficparo,"%1d%1d",i1,j1);    strcat(fileresprobmorprev,fileres);
       printf("%1d%1d",i,j);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       for(k=1; k<=ncovmodel;k++){      printf("Problem with resultfile: %s\n", fileresprobmorprev);
         fscanf(ficpar," %lf",&param[i][j][k]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
         printf(" %lf",param[i][j][k]);    }
         fprintf(ficparo," %lf",param[i][j][k]);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       }   
       fscanf(ficpar,"\n");    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       printf("\n");    fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
       fprintf(ficparo,"\n");    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
   p=param[1][1];        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
      }  
   /* Reads comments: lines beginning with '#' */    fprintf(ficresprobmorprev,"\n");
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficgp,"\n# Routine varevsij");
     ungetc(c,ficpar);    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fgets(line, MAXLINE, ficpar);    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");
     puts(line);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     fputs(line,ficparo);  /*   } */
   }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   ungetc(c,ficpar);   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");
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    fprintf(ficresvij,"# Age");
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    for(i=1; i<=nlstate;i++)
   for(i=1; i <=nlstate; i++){      for(j=1; j<=nlstate;j++)
     for(j=1; j <=nlstate+ndeath-1; j++){        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    fprintf(ficresvij,"\n");
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);    xp=vector(1,npar);
       for(k=1; k<=ncovmodel;k++){    dnewm=matrix(1,nlstate,1,npar);
         fscanf(ficpar,"%le",&delti3[i][j][k]);    doldm=matrix(1,nlstate,1,nlstate);
         printf(" %le",delti3[i][j][k]);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
         fprintf(ficparo," %le",delti3[i][j][k]);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       }  
       fscanf(ficpar,"\n");    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       printf("\n");    gpp=vector(nlstate+1,nlstate+ndeath);
       fprintf(ficparo,"\n");    gmp=vector(nlstate+1,nlstate+ndeath);
     }    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   }    
   delti=delti3[1][1];    if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){    else  hstepm=estepm;   
     ungetc(c,ficpar);    /* For example we decided to compute the life expectancy with the smallest unit */
     fgets(line, MAXLINE, ficpar);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     puts(line);       nhstepm is the number of hstepm from age to agelim 
     fputs(line,ficparo);       nstepm is the number of stepm from age to agelin. 
   }       Look at hpijx to understand the reason of that which relies in memory size
   ungetc(c,ficpar);       and note for a fixed period like k years */
      /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   matcov=matrix(1,npar,1,npar);       survival function given by stepm (the optimization length). Unfortunately it
   for(i=1; i <=npar; i++){       means that if the survival funtion is printed every two years of age and if
     fscanf(ficpar,"%s",&str);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     printf("%s",str);       results. So we changed our mind and took the option of the best precision.
     fprintf(ficparo,"%s",str);    */
     for(j=1; j <=i; j++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       fscanf(ficpar," %le",&matcov[i][j]);    agelim = AGESUP;
       printf(" %.5le",matcov[i][j]);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       fprintf(ficparo," %.5le",matcov[i][j]);      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 */
     fscanf(ficpar,"\n");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     fprintf(ficparo,"\n");      gp=matrix(0,nhstepm,1,nlstate);
   }      gm=matrix(0,nhstepm,1,nlstate);
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)  
       matcov[i][j]=matcov[j][i];      for(theta=1; theta <=npar; theta++){
            for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   printf("\n");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     /*-------- Rewriting paramater file ----------*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      strcpy(rfileres,"r");    /* "Rparameterfile */  
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        if (popbased==1) {
      strcat(rfileres,".");    /* */          if(mobilav ==0){
      strcat(rfileres,optionfilext);    /* Other files have txt extension */            for(i=1; i<=nlstate;i++)
     if((ficres =fopen(rfileres,"w"))==NULL) {              prlim[i][i]=probs[(int)age][i][ij];
       printf("Problem writing new parameter file: %s\n", fileres);goto end;          }else{ /* mobilav */ 
     }            for(i=1; i<=nlstate;i++)
     fprintf(ficres,"#%s\n",version);              prlim[i][i]=mobaverage[(int)age][i][ij];
              }
     /*-------- data file ----------*/        }
     if((fic=fopen(datafile,"r"))==NULL)    {    
       printf("Problem with datafile: %s\n", datafile);goto end;        for(j=1; j<= nlstate; j++){
     }          for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     n= lastobs;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     severity = vector(1,maxwav);          }
     outcome=imatrix(1,maxwav+1,1,n);        }
     num=ivector(1,n);        /* This for computing probability of death (h=1 means
     moisnais=vector(1,n);           computed over hstepm matrices product = hstepm*stepm months) 
     annais=vector(1,n);           as a weighted average of prlim.
     moisdc=vector(1,n);        */
     andc=vector(1,n);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     agedc=vector(1,n);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     cod=ivector(1,n);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     weight=vector(1,n);        }    
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        /* end probability of death */
     mint=matrix(1,maxwav,1,n);  
     anint=matrix(1,maxwav,1,n);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     s=imatrix(1,maxwav+1,1,n);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     adl=imatrix(1,maxwav+1,1,n);            hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     tab=ivector(1,NCOVMAX);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     ncodemax=ivector(1,8);   
         if (popbased==1) {
     i=1;          if(mobilav ==0){
     while (fgets(line, MAXLINE, fic) != NULL)    {            for(i=1; i<=nlstate;i++)
       if ((i >= firstobs) && (i <=lastobs)) {              prlim[i][i]=probs[(int)age][i][ij];
                  }else{ /* mobilav */ 
         for (j=maxwav;j>=1;j--){            for(i=1; i<=nlstate;i++)
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);              prlim[i][i]=mobaverage[(int)age][i][ij];
           strcpy(line,stra);          }
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        }
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }        for(j=1; j<= nlstate; j++){
                  for(h=0; h<=nhstepm; h++){
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        }
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);           as a weighted average of prlim.
         for (j=ncov;j>=1;j--){        */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
         }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
         num[i]=atol(stra);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
                }    
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        /* end probability of death */
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/  
         for(j=1; j<= nlstate; j++) /* vareij */
         i=i+1;          for(h=0; h<=nhstepm; h++){
       }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     }          }
     /* printf("ii=%d", ij);  
        scanf("%d",i);*/        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   imx=i-1; /* Number of individuals */          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   /* for (i=1; i<=imx; i++){  
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      } /* End theta */
     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;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     }  
       for(h=0; h<=nhstepm; h++) /* veij */
     for (i=1; i<=imx; i++)        for(j=1; j<=nlstate;j++)
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   /* Calculation of the number of parameter from char model*/  
   Tvar=ivector(1,15);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   Tprod=ivector(1,15);        for(theta=1; theta <=npar; theta++)
   Tvaraff=ivector(1,15);          trgradgp[j][theta]=gradgp[theta][j];
   Tvard=imatrix(1,15,1,2);    
   Tage=ivector(1,15);        
          hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   if (strlen(model) >1){      for(i=1;i<=nlstate;i++)
     j=0, j1=0, k1=1, k2=1;        for(j=1;j<=nlstate;j++)
     j=nbocc(model,'+');          vareij[i][j][(int)age] =0.;
     j1=nbocc(model,'*');  
     cptcovn=j+1;      for(h=0;h<=nhstepm;h++){
     cptcovprod=j1;        for(k=0;k<=nhstepm;k++){
              matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
              matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
     strcpy(modelsav,model);          for(i=1;i<=nlstate;i++)
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){            for(j=1;j<=nlstate;j++)
       printf("Error. Non available option model=%s ",model);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       goto end;        }
     }      }
        
     for(i=(j+1); i>=1;i--){      /* pptj */
       cutv(stra,strb,modelsav,'+');      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      for(j=nlstate+1;j<=nlstate+ndeath;j++)
       /*scanf("%d",i);*/        for(i=nlstate+1;i<=nlstate+ndeath;i++)
       if (strchr(strb,'*')) {          varppt[j][i]=doldmp[j][i];
         cutv(strd,strc,strb,'*');      /* end ppptj */
         if (strcmp(strc,"age")==0) {      /*  x centered again */
           cptcovprod--;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
           cutv(strb,stre,strd,'V');      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
           Tvar[i]=atoi(stre);   
           cptcovage++;      if (popbased==1) {
             Tage[cptcovage]=i;        if(mobilav ==0){
             /*printf("stre=%s ", stre);*/          for(i=1; i<=nlstate;i++)
         }            prlim[i][i]=probs[(int)age][i][ij];
         else if (strcmp(strd,"age")==0) {        }else{ /* mobilav */ 
           cptcovprod--;          for(i=1; i<=nlstate;i++)
           cutv(strb,stre,strc,'V');            prlim[i][i]=mobaverage[(int)age][i][ij];
           Tvar[i]=atoi(stre);        }
           cptcovage++;      }
           Tage[cptcovage]=i;               
         }      /* This for computing probability of death (h=1 means
         else {         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           cutv(strb,stre,strc,'V');         as a weighted average of prlim.
           Tvar[i]=ncov+k1;      */
           cutv(strb,strc,strd,'V');      for(j=nlstate+1;j<=nlstate+ndeath;j++){
           Tprod[k1]=i;        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           Tvard[k1][1]=atoi(strc);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           Tvard[k1][2]=atoi(stre);      }    
           Tvar[cptcovn+k2]=Tvard[k1][1];      /* end probability of death */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  
           for (k=1; k<=lastobs;k++)      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           k1++;        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
           k2=k2+2;        for(i=1; i<=nlstate;i++){
         }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
       }        }
       else {      } 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      fprintf(ficresprobmorprev,"\n");
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');      fprintf(ficresvij,"%.0f ",age );
       Tvar[i]=atoi(strc);      for(i=1; i<=nlstate;i++)
       }        for(j=1; j<=nlstate;j++){
       strcpy(modelsav,stra);            fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        }
         scanf("%d",i);*/      fprintf(ficresvij,"\n");
     }      free_matrix(gp,0,nhstepm,1,nlstate);
 }      free_matrix(gm,0,nhstepm,1,nlstate);
        free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   printf("cptcovprod=%d ", cptcovprod);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   scanf("%d ",i);*/    } /* End age */
     fclose(fic);    free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     /*  if(mle==1){*/    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     if (weightopt != 1) { /* Maximisation without weights*/    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       for(i=1;i<=n;i++) weight[i]=1.0;    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     }    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     /*-calculation of age at interview from date of interview and age at death -*/    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     agev=matrix(1,maxwav,1,imx);  /*   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 (i=1; i<=imx; i++)  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
      for(m=2; (m<= maxwav); m++)    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
          anint[m][i]=9999;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
          s[m][i]=-1;    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
        }    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
        /*  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<=imx; i++)  {  */
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
       for(m=1; (m<= maxwav); m++){    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
         if(s[m][i] >0){  
           if (s[m][i] == nlstate+1) {    free_vector(xp,1,npar);
             if(agedc[i]>0)    free_matrix(doldm,1,nlstate,1,nlstate);
               if(moisdc[i]!=99 && andc[i]!=9999)    free_matrix(dnewm,1,nlstate,1,npar);
               agev[m][i]=agedc[i];    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             else {    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
               if (andc[i]!=9999){    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
               agev[m][i]=-1;    fclose(ficresprobmorprev);
               }    fflush(ficgp);
             }    fflush(fichtm); 
           }  }  /* end varevsij */
           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]);  /************ Variance of prevlim ******************/
             if(mint[m][i]==99 || anint[m][i]==9999)  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[])
               agev[m][i]=1;  {
             else if(agev[m][i] <agemin){    /* Variance of prevalence limit */
               agemin=agev[m][i];    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    double **newm;
             }    double **dnewm,**doldm;
             else if(agev[m][i] >agemax){    int i, j, nhstepm, hstepm;
               agemax=agev[m][i];    int k, cptcode;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    double *xp;
             }    double *gp, *gm;
             /*agev[m][i]=anint[m][i]-annais[i];*/    double **gradg, **trgradg;
             /*   agev[m][i] = age[i]+2*m;*/    double age,agelim;
           }    int theta;
           else { /* =9 */    fprintf(ficresvpl, "#Local time at start: %s", strstart); 
             agev[m][i]=1;    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
             s[m][i]=-1;    fprintf(ficresvpl,"# Age");
           }    for(i=1; i<=nlstate;i++)
         }        fprintf(ficresvpl," %1d-%1d",i,i);
         else /*= 0 Unknown */    fprintf(ficresvpl,"\n");
           agev[m][i]=1;  
       }    xp=vector(1,npar);
        dnewm=matrix(1,nlstate,1,npar);
     }    doldm=matrix(1,nlstate,1,nlstate);
     for (i=1; i<=imx; i++)  {    
       for(m=1; (m<= maxwav); m++){    hstepm=1*YEARM; /* Every year of age */
         if (s[m][i] > (nlstate+ndeath)) {    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
           printf("Error: Wrong value in nlstate or ndeath\n");      agelim = AGESUP;
           goto end;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         }      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       }      if (stepm >= YEARM) hstepm=1;
     }      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      gp=vector(1,nlstate);
       gm=vector(1,nlstate);
     free_vector(severity,1,maxwav);  
     free_imatrix(outcome,1,maxwav+1,1,n);      for(theta=1; theta <=npar; theta++){
     free_vector(moisnais,1,n);        for(i=1; i<=npar; i++){ /* Computes gradient */
     free_vector(annais,1,n);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     /* free_matrix(mint,1,maxwav,1,n);        }
        free_matrix(anint,1,maxwav,1,n);*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     free_vector(moisdc,1,n);        for(i=1;i<=nlstate;i++)
     free_vector(andc,1,n);          gp[i] = prlim[i][i];
       
            for(i=1; i<=npar; i++) /* Computes gradient */
     wav=ivector(1,imx);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        for(i=1;i<=nlstate;i++)
              gm[i] = prlim[i][i];
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
       Tcode=ivector(1,100);  
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      trgradg =matrix(1,nlstate,1,npar);
       ncodemax[1]=1;  
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      for(j=1; j<=nlstate;j++)
              for(theta=1; theta <=npar; theta++)
    codtab=imatrix(1,100,1,10);          trgradg[j][theta]=gradg[theta][j];
    h=0;  
    m=pow(2,cptcoveff);      for(i=1;i<=nlstate;i++)
          varpl[i][(int)age] =0.;
    for(k=1;k<=cptcoveff; k++){      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
      for(i=1; i <=(m/pow(2,k));i++){      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
        for(j=1; j <= ncodemax[k]; j++){      for(i=1;i<=nlstate;i++)
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
            h++;  
            if (h>m) h=1;codtab[h][k]=j;      fprintf(ficresvpl,"%.0f ",age );
          }      for(i=1; i<=nlstate;i++)
        }        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
      }      fprintf(ficresvpl,"\n");
    }      free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
    /*for(i=1; i <=m ;i++){      free_matrix(trgradg,1,nlstate,1,npar);
      for(k=1; k <=cptcovn; k++){    } /* End age */
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);  
      }    free_vector(xp,1,npar);
      printf("\n");    free_matrix(doldm,1,nlstate,1,npar);
    }    free_matrix(dnewm,1,nlstate,1,nlstate);
    scanf("%d",i);*/  
      }
    /* Calculates basic frequencies. Computes observed prevalence at single age  
        and prints on file fileres'p'. */  /************ Variance of one-step probabilities  ******************/
   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[])
      {
        int i, j=0,  i1, k1, l1, t, tj;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int k2, l2, j1,  z1;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int k=0,l, cptcode;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int first=1, first1;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    double **dnewm,**doldm;
          double *xp;
     /* For Powell, parameters are in a vector p[] starting at p[1]    double *gp, *gm;
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    double **gradg, **trgradg;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    double **mu;
     double age,agelim, cov[NCOVMAX];
     if(mle==1){    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    int theta;
     }    char fileresprob[FILENAMELENGTH];
        char fileresprobcov[FILENAMELENGTH];
     /*--------- results files --------------*/    char fileresprobcor[FILENAMELENGTH];
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);  
      double ***varpij;
   
    jk=1;    strcpy(fileresprob,"prob"); 
    fprintf(ficres,"# Parameters\n");    strcat(fileresprob,fileres);
    printf("# Parameters\n");    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
    for(i=1,jk=1; i <=nlstate; i++){      printf("Problem with resultfile: %s\n", fileresprob);
      for(k=1; k <=(nlstate+ndeath); k++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
        if (k != i)    }
          {    strcpy(fileresprobcov,"probcov"); 
            printf("%d%d ",i,k);    strcat(fileresprobcov,fileres);
            fprintf(ficres,"%1d%1d ",i,k);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
            for(j=1; j <=ncovmodel; j++){      printf("Problem with resultfile: %s\n", fileresprobcov);
              printf("%f ",p[jk]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
              fprintf(ficres,"%f ",p[jk]);    }
              jk++;    strcpy(fileresprobcor,"probcor"); 
            }    strcat(fileresprobcor,fileres);
            printf("\n");    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
            fprintf(ficres,"\n");      printf("Problem with resultfile: %s\n", fileresprobcor);
          }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
      }    }
    }    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
  if(mle==1){    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     /* Computing hessian and covariance matrix */    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     ftolhess=ftol; /* Usually correct */    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     hesscov(matcov, p, npar, delti, ftolhess, func);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
  }    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficres,"# Scales\n");    fprintf(ficresprob, "#Local time at start: %s", strstart);
     printf("# Scales\n");    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
      for(i=1,jk=1; i <=nlstate; i++){    fprintf(ficresprob,"# Age");
       for(j=1; j <=nlstate+ndeath; j++){    fprintf(ficresprobcov, "#Local time at start: %s", strstart);
         if (j!=i) {    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
           fprintf(ficres,"%1d%1d",i,j);    fprintf(ficresprobcov,"# Age");
           printf("%1d%1d",i,j);    fprintf(ficresprobcor, "#Local time at start: %s", strstart);
           for(k=1; k<=ncovmodel;k++){    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
             printf(" %.5e",delti[jk]);    fprintf(ficresprobcov,"# Age");
             fprintf(ficres," %.5e",delti[jk]);  
             jk++;  
           }    for(i=1; i<=nlstate;i++)
           printf("\n");      for(j=1; j<=(nlstate+ndeath);j++){
           fprintf(ficres,"\n");        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
       }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
      }      }  
       /* fprintf(ficresprob,"\n");
     k=1;    fprintf(ficresprobcov,"\n");
     fprintf(ficres,"# Covariance\n");    fprintf(ficresprobcor,"\n");
     printf("# Covariance\n");   */
     for(i=1;i<=npar;i++){   xp=vector(1,npar);
       /*  if (k>nlstate) k=1;    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       i1=(i-1)/(ncovmodel*nlstate)+1;    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
       printf("%s%d%d",alph[k],i1,tab[i]);*/    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
       fprintf(ficres,"%3d",i);    first=1;
       printf("%3d",i);    fprintf(ficgp,"\n# Routine varprob");
       for(j=1; j<=i;j++){    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
         fprintf(ficres," %.5e",matcov[i][j]);    fprintf(fichtm,"\n");
         printf(" %.5e",matcov[i][j]);  
       }    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
       fprintf(ficres,"\n");    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
       printf("\n");    file %s<br>\n",optionfilehtmcov);
       k++;    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
     }  and drawn. It helps understanding how is the covariance between two incidences.\
       They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     while((c=getc(ficpar))=='#' && c!= EOF){    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. \
       ungetc(c,ficpar);  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
       fgets(line, MAXLINE, ficpar);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
       puts(line);  standard deviations wide on each axis. <br>\
       fputs(line,ficparo);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
     }   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
     ungetc(c,ficpar);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
    
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);    cov[1]=1;
        tj=cptcoveff;
     if (fage <= 2) {    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
       bage = agemin;    j1=0;
       fage = agemaxpar;    for(t=1; t<=tj;t++){
     }      for(i1=1; i1<=ncodemax[t];i1++){ 
            j1++;
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");        if  (cptcovn>0) {
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);          fprintf(ficresprob, "\n#********** Variable "); 
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresprob, "**********\n#\n");
     while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresprobcov, "\n#********** Variable "); 
     ungetc(c,ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fgets(line, MAXLINE, ficpar);          fprintf(ficresprobcov, "**********\n#\n");
     puts(line);          
     fputs(line,ficparo);          fprintf(ficgp, "\n#********** Variable "); 
   }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   ungetc(c,ficpar);          fprintf(ficgp, "**********\n#\n");
            
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);          
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   while((c=getc(ficpar))=='#' && c!= EOF){          
     ungetc(c,ficpar);          fprintf(ficresprobcor, "\n#********** Variable ");    
     fgets(line, MAXLINE, ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     puts(line);          fprintf(ficresprobcor, "**********\n#");    
     fputs(line,ficparo);        }
   }        
   ungetc(c,ficpar);        for (age=bage; age<=fage; age ++){ 
            cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
    dateprev1=anprev1+mprev1/12.+jprev1/365.;            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   fscanf(ficpar,"pop_based=%d\n",&popbased);          for (k=1; k<=cptcovprod;k++)
   fprintf(ficparo,"pop_based=%d\n",popbased);              cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   fprintf(ficres,"pop_based=%d\n",popbased);            
            gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   while((c=getc(ficpar))=='#' && c!= EOF){          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     ungetc(c,ficpar);          gp=vector(1,(nlstate)*(nlstate+ndeath));
     fgets(line, MAXLINE, ficpar);          gm=vector(1,(nlstate)*(nlstate+ndeath));
     puts(line);      
     fputs(line,ficparo);          for(theta=1; theta <=npar; theta++){
   }            for(i=1; i<=npar; i++)
   ungetc(c,ficpar);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);            
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);            k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
 while((c=getc(ficpar))=='#' && c!= EOF){                k=k+1;
     ungetc(c,ficpar);                gp[k]=pmmij[i][j];
     fgets(line, MAXLINE, ficpar);              }
     puts(line);            }
     fputs(line,ficparo);            
   }            for(i=1; i<=npar; i++)
   ungetc(c,ficpar);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);            k=0;
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);            for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                k=k+1;
                 gm[k]=pmmij[i][j];
 /*------------ gnuplot -------------*/              }
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);            }
         
 /*------------ free_vector  -------------*/            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
  chdir(path);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
            }
  free_ivector(wav,1,imx);  
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);              for(theta=1; theta <=npar; theta++)
  free_ivector(num,1,n);              trgradg[j][theta]=gradg[theta][j];
  free_vector(agedc,1,n);          
  /*free_matrix(covar,1,NCOVMAX,1,n);*/          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
  fclose(ficparo);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
  fclose(ficres);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
 /*--------- index.htm --------*/          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);  
           pmij(pmmij,cov,ncovmodel,x,nlstate);
            
   /*--------------- Prevalence limit --------------*/          k=0;
            for(i=1; i<=(nlstate); i++){
   strcpy(filerespl,"pl");            for(j=1; j<=(nlstate+ndeath);j++){
   strcat(filerespl,fileres);              k=k+1;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {              mu[k][(int) age]=pmmij[i][j];
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;            }
   }          }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   fprintf(ficrespl,"#Prevalence limit\n");            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   fprintf(ficrespl,"#Age ");              varpij[i][j][(int)age] = doldm[i][j];
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  
   fprintf(ficrespl,"\n");          /*printf("\n%d ",(int)age);
              for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   prlim=matrix(1,nlstate,1,nlstate);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   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 */          fprintf(ficresprob,"\n%d ",(int)age);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          fprintf(ficresprobcov,"\n%d ",(int)age);
   k=0;          fprintf(ficresprobcor,"\n%d ",(int)age);
   agebase=agemin;  
   agelim=agemaxpar;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   ftolpl=1.e-10;            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   i1=cptcoveff;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   if (cptcovn < 1){i1=1;}            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   for(cptcov=1;cptcov<=i1;cptcov++){          }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          i=0;
         k=k+1;          for (k=1; k<=(nlstate);k++){
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/            for (l=1; l<=(nlstate+ndeath);l++){ 
         fprintf(ficrespl,"\n#******");              i=i++;
         for(j=1;j<=cptcoveff;j++)              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
         fprintf(ficrespl,"******\n");              for (j=1; j<=i;j++){
                        fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
         for (age=agebase; age<=agelim; age++){                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);              }
           fprintf(ficrespl,"%.0f",age );            }
           for(i=1; i<=nlstate;i++)          }/* end of loop for state */
           fprintf(ficrespl," %.5f", prlim[i][i]);        } /* end of loop for age */
           fprintf(ficrespl,"\n");  
         }        /* Confidence intervalle of pij  */
       }        /*
     }          fprintf(ficgp,"\nset noparametric;unset label");
   fclose(ficrespl);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   /*------------- h Pij x at various ages ------------*/          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
            fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        */
   }  
   printf("Computing pij: result on file '%s' \n", filerespij);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
          first1=1;
   stepsize=(int) (stepm+YEARM-1)/YEARM;        for (k2=1; k2<=(nlstate);k2++){
   /*if (stepm<=24) stepsize=2;*/          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
   agelim=AGESUP;            j=(k2-1)*(nlstate+ndeath)+l2;
   hstepm=stepsize*YEARM; /* Every year of age */            for (k1=1; k1<=(nlstate);k1++){
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                  if(l1==k1) continue;
   k=0;                i=(k1-1)*(nlstate+ndeath)+l1;
   for(cptcov=1;cptcov<=i1;cptcov++){                if(i<=j) continue;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                for (age=bage; age<=fage; age ++){ 
       k=k+1;                  if ((int)age %5==0){
         fprintf(ficrespij,"\n#****** ");                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
         for(j=1;j<=cptcoveff;j++)                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
         fprintf(ficrespij,"******\n");                    mu1=mu[i][(int) age]/stepm*YEARM ;
                            mu2=mu[j][(int) age]/stepm*YEARM;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                    c12=cv12/sqrt(v1*v2);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                    /* Computing eigen value of matrix of covariance */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
           oldm=oldms;savm=savms;                    /* Eigen vectors */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                      v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
           fprintf(ficrespij,"# Age");                    /*v21=sqrt(1.-v11*v11); *//* error */
           for(i=1; i<=nlstate;i++)                    v21=(lc1-v1)/cv12*v11;
             for(j=1; j<=nlstate+ndeath;j++)                    v12=-v21;
               fprintf(ficrespij," %1d-%1d",i,j);                    v22=v11;
           fprintf(ficrespij,"\n");                    tnalp=v21/v11;
           for (h=0; h<=nhstepm; h++){                    if(first1==1){
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );                      first1=0;
             for(i=1; i<=nlstate;i++)                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
               for(j=1; j<=nlstate+ndeath;j++)                    }
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
             fprintf(ficrespij,"\n");                    /*printf(fignu*/
           }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
           fprintf(ficrespij,"\n");                    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");
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/                      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\">\
   fclose(ficrespij);  %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);
   /*---------- Forecasting ------------------*/                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   if((stepm == 1) && (strcmp(model,".")==0)){                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     free_matrix(mint,1,maxwav,1,n);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
     free_vector(weight,1,n);}                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   else{                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     erreur=108;                    }else{
     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);                      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);
   /*---------- Health expectancies and variances ------------*/                      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),\
   strcpy(filerest,"t");                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   strcat(filerest,fileres);                    }/* if first */
   if((ficrest=fopen(filerest,"w"))==NULL) {                  } /* age mod 5 */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                } /* end loop age */
   }                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                first=1;
               } /*l12 */
             } /* k12 */
   strcpy(filerese,"e");          } /*l1 */
   strcat(filerese,fileres);        }/* k1 */
   if((ficreseij=fopen(filerese,"w"))==NULL) {      } /* loop covariates */
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    }
   }    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
  strcpy(fileresv,"v");    fclose(ficresprob);
   strcat(fileresv,fileres);    fclose(ficresprobcov);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    fclose(ficresprobcor);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    fflush(ficgp);
   }    fflush(fichtmcov);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  }
   
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){  /******************* Printing html file ***********/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
       k=k+1;                    int lastpass, int stepm, int weightopt, char model[],\
       fprintf(ficrest,"\n#****** ");                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
       for(j=1;j<=cptcoveff;j++)                    int popforecast, int estepm ,\
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    double jprev1, double mprev1,double anprev1, \
       fprintf(ficrest,"******\n");                    double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
       fprintf(ficreseij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
       fprintf(ficreseij,"******\n");  </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
       fprintf(ficresvij,"\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 ",
       for(j=1;j<=cptcoveff;j++)             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);     fprintf(fichtm,"\
       fprintf(ficresvij,"******\n");   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);     fprintf(fichtm,"\
       oldm=oldms;savm=savms;   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);               subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);     fprintf(fichtm,"\
       oldm=oldms;savm=savms;   - Life expectancies by age and initial health status (estepm=%2d months): \
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);     <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>");
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);   m=cptcoveff;
       fprintf(ficrest,"\n");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
       hf=1;   jj1=0;
       if (stepm >= YEARM) hf=stepm/YEARM;   for(k1=1; k1<=m;k1++){
       epj=vector(1,nlstate+1);     for(i1=1; i1<=ncodemax[k1];i1++){
       for(age=bage; age <=fage ;age++){       jj1++;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);       if (cptcovn > 0) {
         if (popbased==1) {         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           for(i=1; i<=nlstate;i++)         for (cpt=1; cpt<=cptcoveff;cpt++) 
             prlim[i][i]=probs[(int)age][i][k];           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
         }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
               }
         fprintf(ficrest," %.0f",age);       /* Pij */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){       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> \
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];       /* Quasi-incidences */
           }       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
           epj[nlstate+1] +=epj[j];   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); 
         for(i=1, vepp=0.;i <=nlstate;i++)         /* Stable prevalence in each health state */
           for(j=1;j <=nlstate;j++)         for(cpt=1; cpt<nlstate;cpt++){
             vepp += vareij[i][j][(int)age];           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
         for(j=1;j <=nlstate;j++){         }
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));       for(cpt=1; cpt<=nlstate;cpt++) {
         }          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
         fprintf(ficrest,"\n");  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
       }       }
     }     } /* end i1 */
   }   }/* End k1 */
    fprintf(fichtm,"</ul>");
   fclose(ficreseij);  
   fclose(ficresvij);  
   fclose(ficrest);   fprintf(fichtm,"\
   fclose(ficpar);  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
   free_vector(epj,1,nlstate+1);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
    
   /*------- Variance limit prevalence------*/     fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
   strcpy(fileresvpl,"vpl");   fprintf(fichtm,"\
   strcat(fileresvpl,fileres);   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  
     exit(0);   fprintf(fichtm,"\
   }   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
   k=0;   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
   for(cptcov=1;cptcov<=i1;cptcov++){           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   fprintf(fichtm,"\
       k=k+1;   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
       fprintf(ficresvpl,"\n#****** ");           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
       for(j=1;j<=cptcoveff;j++)   fprintf(fichtm,"\
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
       fprintf(ficresvpl,"******\n");           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
        
       varpl=matrix(1,nlstate,(int) bage, (int) fage);  /*  if(popforecast==1) fprintf(fichtm,"\n */
       oldm=oldms;savm=savms;  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  /*  - 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); */
   fclose(ficresvpl);   fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);   m=cptcoveff;
     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);   jj1=0;
     for(k1=1; k1<=m;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);       jj1++;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);       if (cptcovn > 0) {
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);         for (cpt=1; cpt<=cptcoveff;cpt++) 
             fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   free_matrix(matcov,1,npar,1,npar);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   free_vector(delti,1,npar);       }
   free_matrix(agev,1,maxwav,1,imx);       for(cpt=1; cpt<=nlstate;cpt++) {
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   if(erreur >0)  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
     printf("End of Imach with error %d\n",erreur);       }
   else   printf("End of Imach\n");       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  health expectancies in states (1) and (2): %s%d.png<br>\
    <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
   /* 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);*/     } /* end i1 */
   /*printf("Total time was %d uSec.\n", total_usecs);*/   }/* End k1 */
   /*------ End -----------*/   fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
  end:  
 #ifdef windows  /******************* Gnuplot file **************/
   /* chdir(pathcd);*/  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
 #endif  
  /*system("wgnuplot graph.plt");*/    char dirfileres[132],optfileres[132];
  /*system("../gp37mgw/wgnuplot graph.plt");*/    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
  /*system("cd ../gp37mgw");*/    int ng;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
  strcpy(plotcmd,GNUPLOTPROGRAM);  /*     printf("Problem with file %s",optionfilegnuplot); */
  strcat(plotcmd," ");  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
  strcat(plotcmd,optionfilegnuplot);  /*   } */
  system(plotcmd);  
     /*#ifdef windows */
 #ifdef windows    fprintf(ficgp,"cd \"%s\" \n",pathc);
   while (z[0] != 'q') {      /*#endif */
     chdir(path);    m=pow(2,cptcoveff);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");  
     scanf("%s",z);    strcpy(dirfileres,optionfilefiname);
     if (z[0] == 'c') system("./imach");    strcpy(optfileres,"vpl");
     else if (z[0] == 'e') {   /* 1eme*/
       chdir(path);    for (cpt=1; cpt<= nlstate ; cpt ++) {
       system(optionfilehtm);     for (k1=1; k1<= m ; k1 ++) {
     }       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
     else if (z[0] == 'q') exit(0);       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
   }       fprintf(ficgp,"set xlabel \"Age\" \n\
 #endif  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) {
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
         for(j=0; line[j] != '\n';j++){  /* Untabifies line */
           if(line[j] == '\t')
             line[j] = ' ';
         }
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (j=1; j<=lastpass; j++)
           if (s[j][i]>nlstate) {
             dcwave[i]=j;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];agecens[i]=1.; 
           if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
           cens[i]=1;
           
           if (ageexmed[i]<1) cens[i]=-1;
           if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
   
       p[1]=0.1; p[2]=0.1;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow-mort"); 
     strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
     /*  for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     */
     fprintf(ficrespow,"\n");
   
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM,delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
   lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
      
        for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
      
         for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
   
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
   
    tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
          }
      
      
          printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
   
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
   
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
   
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficrespl, "#Local time at start: %s", strstart);
       fprintf(ficrespl,"#Stable prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       fprintf(ficrespij, "#Local time at start: %s", strstart);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /*---------- Health expectancies and variances ------------*/
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total LEs with variances: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficreseij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
           }
   
           fprintf(ficrest, "#Local time at start: %s", strstart);
           fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficreseij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of stable prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
   #ifndef UNIX
     /*  strcpy(plotcmd,"\""); */
   #endif
     strcpy(plotcmd,pathimach);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     strcat(plotcmd,GNUPLOTPROGRAM);
   #ifndef UNIX
     strcat(plotcmd,".exe");
     /*  strcat(plotcmd,"\"");*/
   #endif
     if(stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
     }
   
   #ifndef UNIX
     strcpy(plotcmd,"\"");
   #endif
     strcat(plotcmd,pathimach);
     strcat(plotcmd,GNUPLOTPROGRAM);
   #ifndef UNIX
     strcat(plotcmd,".exe");
     strcat(plotcmd,"\"");
   #endif
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",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.1.32  
changed lines
  Added in v.1.108


FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>