Diff for /imach/src/imach.c between versions 1.38 and 1.103

version 1.38, 2002/04/03 12:19:36 version 1.103, 2005/09/30 15:54:49
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.103  2005/09/30 15:54:49  lievre
      (Module): sump fixed, loop imx fixed, and simplifications.
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.102  2004/09/15 17:31:30  brouard
   first survey ("cross") where individuals from different ages are    Add the possibility to read data file including tab characters.
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.101  2004/09/15 10:38:38  brouard
   second wave of interviews ("longitudinal") which measure each change    Fix on curr_time
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.100  2004/07/12 18:29:06  brouard
   model. More health states you consider, more time is necessary to reach the    Add version for Mac OS X. Just define UNIX in Makefile
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.99  2004/06/05 08:57:40  brouard
   probabibility to be observed in state j at the second wave    *** empty log message ***
   conditional to be observed in state i at the first wave. Therefore  
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Revision 1.98  2004/05/16 15:05:56  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    New version 0.97 . First attempt to estimate force of mortality
   complex model than "constant and age", you should modify the program    directly from the data i.e. without the need of knowing the health
   where the markup *Covariates have to be included here again* invites    state at each age, but using a Gompertz model: log u =a + b*age .
   you to do it.  More covariates you add, slower the    This is the basic analysis of mortality and should be done before any
   convergence.    other analysis, in order to test if the mortality estimated from the
     cross-longitudinal survey is different from the mortality estimated
   The advantage of this computer programme, compared to a simple    from other sources like vital statistic data.
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    The same imach parameter file can be used but the option for mle should be -3.
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Agnès, who wrote this part of the code, tried to keep most of the
     former routines in order to include the new code within the former code.
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    The output is very simple: only an estimate of the intercept and of
   split into an exact number (nh*stepm) of unobserved intermediate    the slope with 95% confident intervals.
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Current limitations:
   matrix is simply the matrix product of nh*stepm elementary matrices    A) Even if you enter covariates, i.e. with the
   and the contribution of each individual to the likelihood is simply    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   hPijx.    B) There is no computation of Life Expectancy nor Life Table.
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.97  2004/02/20 13:25:42  lievre
   of the life expectancies. It also computes the prevalence limits.    Version 0.96d. Population forecasting command line is (temporarily)
      suppressed.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.96  2003/07/15 15:38:55  brouard
   This software have been partly granted by Euro-REVES, a concerted action    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   from the European Union.    rewritten within the same printf. Workaround: many printfs.
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.95  2003/07/08 07:54:34  brouard
   can be accessed at http://euroreves.ined.fr/imach .    * imach.c (Repository):
   **********************************************************************/    (Repository): Using imachwizard code to output a more meaningful covariance
      matrix (cov(a12,c31) instead of numbers.
 #include <math.h>  
 #include <stdio.h>    Revision 1.94  2003/06/27 13:00:02  brouard
 #include <stdlib.h>    Just cleaning
 #include <unistd.h>  
     Revision 1.93  2003/06/25 16:33:55  brouard
 #define MAXLINE 256    (Module): On windows (cygwin) function asctime_r doesn't
 #define GNUPLOTPROGRAM "wgnuplot"    exist so I changed back to asctime which exists.
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    (Module): Version 0.96b
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.92  2003/06/25 16:30:45  brouard
 #define windows    (Module): On windows (cygwin) function asctime_r doesn't
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    exist so I changed back to asctime which exists.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.91  2003/06/25 15:30:29  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    * imach.c (Repository): Duplicated warning errors corrected.
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
 #define NINTERVMAX 8    is stamped in powell.  We created a new html file for the graphs
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    concerning matrix of covariance. It has extension -cov.htm.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.90  2003/06/24 12:34:15  brouard
 #define MAXN 20000    (Module): Some bugs corrected for windows. Also, when
 #define YEARM 12. /* Number of months per year */    mle=-1 a template is output in file "or"mypar.txt with the design
 #define AGESUP 130    of the covariance matrix to be input.
 #define AGEBASE 40  
     Revision 1.89  2003/06/24 12:30:52  brouard
     (Module): Some bugs corrected for windows. Also, when
 int erreur; /* Error number */    mle=-1 a template is output in file "or"mypar.txt with the design
 int nvar;    of the covariance matrix to be input.
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.88  2003/06/23 17:54:56  brouard
 int nlstate=2; /* Number of live states */    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.87  2003/06/18 12:26:01  brouard
 int popbased=0;    Version 0.96
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.86  2003/06/17 20:04:08  brouard
 int maxwav; /* Maxim number of waves */    (Module): Change position of html and gnuplot routines and added
 int jmin, jmax; /* min, max spacing between 2 waves */    routine fileappend.
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.85  2003/06/17 13:12:43  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    * imach.c (Repository): Check when date of death was earlier that
 double jmean; /* Mean space between 2 waves */    current date of interview. It may happen when the death was just
 double **oldm, **newm, **savm; /* Working pointers to matrices */    prior to the death. In this case, dh was negative and likelihood
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    was wrong (infinity). We still send an "Error" but patch by
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    assuming that the date of death was just one stepm after the
 FILE *ficgp,*ficresprob,*ficpop;    interview.
 FILE *ficreseij;    (Repository): Because some people have very long ID (first column)
   char filerese[FILENAMELENGTH];    we changed int to long in num[] and we added a new lvector for
  FILE  *ficresvij;    memory allocation. But we also truncated to 8 characters (left
   char fileresv[FILENAMELENGTH];    truncation)
  FILE  *ficresvpl;    (Repository): No more line truncation errors.
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.84  2003/06/13 21:44:43  brouard
 #define NR_END 1    * imach.c (Repository): Replace "freqsummary" at a correct
 #define FREE_ARG char*    place. It differs from routine "prevalence" which may be called
 #define FTOL 1.0e-10    many times. Probs is memory consuming and must be used with
     parcimony.
 #define NRANSI    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #define ITMAX 200  
     Revision 1.83  2003/06/10 13:39:11  lievre
 #define TOL 2.0e-4    *** empty log message ***
   
 #define CGOLD 0.3819660    Revision 1.82  2003/06/05 15:57:20  brouard
 #define ZEPS 1.0e-10    Add log in  imach.c and  fullversion number is now printed.
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
   */
 #define GOLD 1.618034  /*
 #define GLIMIT 100.0     Interpolated Markov Chain
 #define TINY 1.0e-20  
     Short summary of the programme:
 static double maxarg1,maxarg2;    
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    This program computes Healthy Life Expectancies from
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
      first survey ("cross") where individuals from different ages are
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    interviewed on their health status or degree of disability (in the
 #define rint(a) floor(a+0.5)    case of a health survey which is our main interest) -2- at least a
     second wave of interviews ("longitudinal") which measure each change
 static double sqrarg;    (if any) in individual health status.  Health expectancies are
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    computed from the time spent in each health state according to a
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
 int imx;    simplest model is the multinomial logistic model where pij is the
 int stepm;    probability to be observed in state j at the second wave
 /* Stepm, step in month: minimum step interpolation*/    conditional to be observed in state i at the first wave. Therefore
     the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 int estepm;    'age' is age and 'sex' is a covariate. If you want to have a more
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
 int m,nb;    you to do it.  More covariates you add, slower the
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    convergence.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    The advantage of this computer programme, compared to a simple
 double dateintmean=0;    multinomial logistic model, is clear when the delay between waves is not
     identical for each individual. Also, if a individual missed an
 double *weight;    intermediate interview, the information is lost, but taken into
 int **s; /* Status */    account using an interpolation or extrapolation.  
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    hPijx is the probability to be observed in state i at age x+h
     conditional to the observed state i at age x. The delay 'h' can be
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    split into an exact number (nh*stepm) of unobserved intermediate
 double ftolhess; /* Tolerance for computing hessian */    states. This elementary transition (by month, quarter,
     semester or year) is modelled as a multinomial logistic.  The hPx
 /**************** split *************************/    matrix is simply the matrix product of nh*stepm elementary matrices
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    and the contribution of each individual to the likelihood is simply
 {    hPijx.
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the stable prevalence. 
    l1 = strlen( path );                 /* length of path */    
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #ifdef windows             Institut national d'études démographiques, Paris.
    s = strrchr( path, '\\' );           /* find last / */    This software have been partly granted by Euro-REVES, a concerted action
 #else    from the European Union.
    s = strrchr( path, '/' );            /* find last / */    It is copyrighted identically to a GNU software product, ie programme and
 #endif    software can be distributed freely for non commercial use. Latest version
    if ( s == NULL ) {                   /* no directory, so use current */    can be accessed at http://euroreves.ined.fr/imach .
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
       if ( getwd( dirc ) == NULL ) {    
 #else    **********************************************************************/
       extern char       *getcwd( );  /*
     main
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    read parameterfile
 #endif    read datafile
          return( GLOCK_ERROR_GETCWD );    concatwav
       }    freqsummary
       strcpy( name, path );             /* we've got it */    if (mle >= 1)
    } else {                             /* strip direcotry from path */      mlikeli
       s++;                              /* after this, the filename */    print results files
       l2 = strlen( s );                 /* length of filename */    if mle==1 
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );       computes hessian
       strcpy( name, s );                /* save file name */    read end of parameter file: agemin, agemax, bage, fage, estepm
       strncpy( dirc, path, l1 - l2 );   /* now the directory */        begin-prev-date,...
       dirc[l1-l2] = 0;                  /* add zero */    open gnuplot file
    }    open html file
    l1 = strlen( dirc );                 /* length of directory */    stable prevalence
 #ifdef windows     for age prevalim()
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    h Pij x
 #else    variance of p varprob
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    forecasting if prevfcast==1 prevforecast call prevalence()
 #endif    health expectancies
    s = strrchr( name, '.' );            /* find last / */    Variance-covariance of DFLE
    s++;    prevalence()
    strcpy(ext,s);                       /* save extension */     movingaverage()
    l1= strlen( name);    varevsij() 
    l2= strlen( s)+1;    if popbased==1 varevsij(,popbased)
    strncpy( finame, name, l1-l2);    total life expectancies
    finame[l1-l2]= 0;    Variance of stable prevalence
    return( 0 );                         /* we're done */   end
 }  */
   
   
 /******************************************/  
    
 void replace(char *s, char*t)  #include <math.h>
 {  #include <stdio.h>
   int i;  #include <stdlib.h>
   int lg=20;  #include <unistd.h>
   i=0;  
   lg=strlen(t);  /* #include <sys/time.h> */
   for(i=0; i<= lg; i++) {  #include <time.h>
     (s[i] = t[i]);  #include "timeval.h"
     if (t[i]== '\\') s[i]='/';  
   }  /* #include <libintl.h> */
 }  /* #define _(String) gettext (String) */
   
 int nbocc(char *s, char occ)  #define MAXLINE 256
 {  #define GNUPLOTPROGRAM "gnuplot"
   int i,j=0;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   int lg=20;  #define FILENAMELENGTH 132
   i=0;  /*#define DEBUG*/
   lg=strlen(s);  /*#define windows*/
   for(i=0; i<= lg; i++) {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   if  (s[i] == occ ) j++;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   }  
   return j;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 }  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 void cutv(char *u,char *v, char*t, char occ)  #define NINTERVMAX 8
 {  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   int i,lg,j,p=0;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   i=0;  #define NCOVMAX 8 /* Maximum number of covariates */
   for(j=0; j<=strlen(t)-1; j++) {  #define MAXN 20000
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  #define YEARM 12. /* Number of months per year */
   }  #define AGESUP 130
   #define AGEBASE 40
   lg=strlen(t);  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   for(j=0; j<p; j++) {  #ifdef UNIX
     (u[j] = t[j]);  #define DIRSEPARATOR '/'
   }  #define ODIRSEPARATOR '\\'
      u[p]='\0';  #else
   #define DIRSEPARATOR '\\'
    for(j=0; j<= lg; j++) {  #define ODIRSEPARATOR '/'
     if (j>=(p+1))(v[j-p-1] = t[j]);  #endif
   }  
 }  /* $Id$ */
   /* $State$ */
 /********************** nrerror ********************/  
   char version[]="Imach version 0.97c, September 2004, INED-EUROREVES ";
 void nrerror(char error_text[])  char fullversion[]="$Revision$ $Date$"; 
 {  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   fprintf(stderr,"ERREUR ...\n");  int nvar;
   fprintf(stderr,"%s\n",error_text);  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   exit(1);  int npar=NPARMAX;
 }  int nlstate=2; /* Number of live states */
 /*********************** vector *******************/  int ndeath=1; /* Number of dead states */
 double *vector(int nl, int nh)  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 {  int popbased=0;
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  int *wav; /* Number of waves for this individuual 0 is possible */
   if (!v) nrerror("allocation failure in vector");  int maxwav; /* Maxim number of waves */
   return v-nl+NR_END;  int jmin, jmax; /* min, max spacing between 2 waves */
 }  int gipmx, gsw; /* Global variables on the number of contributions 
                      to the likelihood and the sum of weights (done by funcone)*/
 /************************ free vector ******************/  int mle, weightopt;
 void free_vector(double*v, int nl, int nh)  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 {  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   free((FREE_ARG)(v+nl-NR_END));  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 }             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
 /************************ivector *******************************/  double **oldm, **newm, **savm; /* Working pointers to matrices */
 int *ivector(long nl,long nh)  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 {  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   int *v;  FILE *ficlog, *ficrespow;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  int globpr; /* Global variable for printing or not */
   if (!v) nrerror("allocation failure in ivector");  double fretone; /* Only one call to likelihood */
   return v-nl+NR_END;  long ipmx; /* Number of contributions */
 }  double sw; /* Sum of weights */
   char filerespow[FILENAMELENGTH];
 /******************free ivector **************************/  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 void free_ivector(int *v, long nl, long nh)  FILE *ficresilk;
 {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   free((FREE_ARG)(v+nl-NR_END));  FILE *ficresprobmorprev;
 }  FILE *fichtm, *fichtmcov; /* Html File */
   FILE *ficreseij;
 /******************* imatrix *******************************/  char filerese[FILENAMELENGTH];
 int **imatrix(long nrl, long nrh, long ncl, long nch)  FILE  *ficresvij;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  char fileresv[FILENAMELENGTH];
 {  FILE  *ficresvpl;
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  char fileresvpl[FILENAMELENGTH];
   int **m;  char title[MAXLINE];
    char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   /* allocate pointers to rows */  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  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];
    
   /* allocate rows and set pointers to them */  char filelog[FILENAMELENGTH]; /* Log file */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  char filerest[FILENAMELENGTH];
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  char fileregp[FILENAMELENGTH];
   m[nrl] += NR_END;  char popfile[FILENAMELENGTH];
   m[nrl] -= ncl;  
    char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   /* return pointer to array of pointers to rows */  struct timezone tzp;
   return m;  extern int gettimeofday();
 }  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   long time_value;
 /****************** free_imatrix *************************/  extern long time();
 void free_imatrix(m,nrl,nrh,ncl,nch)  char strcurr[80], strfor[80];
       int **m;  
       long nch,ncl,nrh,nrl;  #define NR_END 1
      /* free an int matrix allocated by imatrix() */  #define FREE_ARG char*
 {  #define FTOL 1.0e-10
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  #define NRANSI 
 }  #define ITMAX 200 
   
 /******************* matrix *******************************/  #define TOL 2.0e-4 
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {  #define CGOLD 0.3819660 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  #define ZEPS 1.0e-10 
   double **m;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define GOLD 1.618034 
   if (!m) nrerror("allocation failure 1 in matrix()");  #define GLIMIT 100.0 
   m += NR_END;  #define TINY 1.0e-20 
   m -= nrl;  
   static double maxarg1,maxarg2;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   m[nrl] += NR_END;    
   m[nrl] -= ncl;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;  static double sqrarg;
 }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 /*************************free matrix ************************/  int agegomp= AGEGOMP;
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {  int imx; 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int stepm=1;
   free((FREE_ARG)(m+nrl-NR_END));  /* Stepm, step in month: minimum step interpolation*/
 }  
   int estepm;
 /******************* ma3x *******************************/  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {  int m,nb;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  long *num;
   double ***m;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  double **pmmij, ***probs;
   if (!m) nrerror("allocation failure 1 in matrix()");  double *ageexmed,*agecens;
   m += NR_END;  double dateintmean=0;
   m -= nrl;  
   double *weight;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int **s; /* Status */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  double *agedc, **covar, idx;
   m[nrl] += NR_END;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   m[nrl] -= ncl;  
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  double ftolhess; /* Tolerance for computing hessian */
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  /**************** split *************************/
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   m[nrl][ncl] += NR_END;  {
   m[nrl][ncl] -= nll;    /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
   for (j=ncl+1; j<=nch; j++)       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     m[nrl][j]=m[nrl][j-1]+nlay;    */ 
      char  *ss;                            /* pointer */
   for (i=nrl+1; i<=nrh; i++) {    int   l1, l2;                         /* length counters */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)    l1 = strlen(path );                   /* length of path */
       m[i][j]=m[i][j-1]+nlay;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   return m;    if ( ss == NULL ) {                   /* no directory, so use current */
 }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 /*************************free ma3x ************************/      /* get current working directory */
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)      /*    extern  char* getcwd ( char *buf , int len);*/
 {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));        return( GLOCK_ERROR_GETCWD );
   free((FREE_ARG)(m[nrl]+ncl-NR_END));      }
   free((FREE_ARG)(m+nrl-NR_END));      strcpy( name, path );               /* we've got it */
 }    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
 /***************** f1dim *************************/      l2 = strlen( ss );                  /* length of filename */
 extern int ncom;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 extern double *pcom,*xicom;      strcpy( name, ss );         /* save file name */
 extern double (*nrfunc)(double []);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
        dirc[l1-l2] = 0;                    /* add zero */
 double f1dim(double x)    }
 {    l1 = strlen( dirc );                  /* length of directory */
   int j;    /*#ifdef windows
   double f;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   double *xt;  #else
      if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   xt=vector(1,ncom);  #endif
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    */
   f=(*nrfunc)(xt);    ss = strrchr( name, '.' );            /* find last / */
   free_vector(xt,1,ncom);    if (ss >0){
   return f;      ss++;
 }      strcpy(ext,ss);                     /* save extension */
       l1= strlen( name);
 /*****************brent *************************/      l2= strlen(ss)+1;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)      strncpy( finame, name, l1-l2);
 {      finame[l1-l2]= 0;
   int iter;    }
   double a,b,d,etemp;    return( 0 );                          /* we're done */
   double fu,fv,fw,fx;  }
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  /******************************************/
    
   a=(ax < cx ? ax : cx);  void replace_back_to_slash(char *s, char*t)
   b=(ax > cx ? ax : cx);  {
   x=w=v=bx;    int i;
   fw=fv=fx=(*f)(x);    int lg=0;
   for (iter=1;iter<=ITMAX;iter++) {    i=0;
     xm=0.5*(a+b);    lg=strlen(t);
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    for(i=0; i<= lg; i++) {
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/      (s[i] = t[i]);
     printf(".");fflush(stdout);      if (t[i]== '\\') s[i]='/';
 #ifdef DEBUG    }
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  }
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif  int nbocc(char *s, char occ)
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  {
       *xmin=x;    int i,j=0;
       return fx;    int lg=20;
     }    i=0;
     ftemp=fu;    lg=strlen(s);
     if (fabs(e) > tol1) {    for(i=0; i<= lg; i++) {
       r=(x-w)*(fx-fv);    if  (s[i] == occ ) j++;
       q=(x-v)*(fx-fw);    }
       p=(x-v)*q-(x-w)*r;    return j;
       q=2.0*(q-r);  }
       if (q > 0.0) p = -p;  
       q=fabs(q);  void cutv(char *u,char *v, char*t, char occ)
       etemp=e;  {
       e=d;    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
         d=CGOLD*(e=(x >= xm ? a-x : b-x));       gives u="abcedf" and v="ghi2j" */
       else {    int i,lg,j,p=0;
         d=p/q;    i=0;
         u=x+d;    for(j=0; j<=strlen(t)-1; j++) {
         if (u-a < tol2 || b-u < tol2)      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
           d=SIGN(tol1,xm-x);    }
       }  
     } else {    lg=strlen(t);
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    for(j=0; j<p; j++) {
     }      (u[j] = t[j]);
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    }
     fu=(*f)(u);       u[p]='\0';
     if (fu <= fx) {  
       if (u >= x) a=x; else b=x;     for(j=0; j<= lg; j++) {
       SHFT(v,w,x,u)      if (j>=(p+1))(v[j-p-1] = t[j]);
         SHFT(fv,fw,fx,fu)    }
         } else {  }
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  /********************** nrerror ********************/
             v=w;  
             w=u;  void nrerror(char error_text[])
             fv=fw;  {
             fw=fu;    fprintf(stderr,"ERREUR ...\n");
           } else if (fu <= fv || v == x || v == w) {    fprintf(stderr,"%s\n",error_text);
             v=u;    exit(EXIT_FAILURE);
             fv=fu;  }
           }  /*********************** vector *******************/
         }  double *vector(int nl, int nh)
   }  {
   nrerror("Too many iterations in brent");    double *v;
   *xmin=x;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   return fx;    if (!v) nrerror("allocation failure in vector");
 }    return v-nl+NR_END;
   }
 /****************** mnbrak ***********************/  
   /************************ free vector ******************/
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  void free_vector(double*v, int nl, int nh)
             double (*func)(double))  {
 {    free((FREE_ARG)(v+nl-NR_END));
   double ulim,u,r,q, dum;  }
   double fu;  
    /************************ivector *******************************/
   *fa=(*func)(*ax);  int *ivector(long nl,long nh)
   *fb=(*func)(*bx);  {
   if (*fb > *fa) {    int *v;
     SHFT(dum,*ax,*bx,dum)    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       SHFT(dum,*fb,*fa,dum)    if (!v) nrerror("allocation failure in ivector");
       }    return v-nl+NR_END;
   *cx=(*bx)+GOLD*(*bx-*ax);  }
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  /******************free ivector **************************/
     r=(*bx-*ax)*(*fb-*fc);  void free_ivector(int *v, long nl, long nh)
     q=(*bx-*cx)*(*fb-*fa);  {
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    free((FREE_ARG)(v+nl-NR_END));
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  }
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {  /************************lvector *******************************/
       fu=(*func)(u);  long *lvector(long nl,long nh)
     } else if ((*cx-u)*(u-ulim) > 0.0) {  {
       fu=(*func)(u);    long *v;
       if (fu < *fc) {    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    if (!v) nrerror("allocation failure in ivector");
           SHFT(*fb,*fc,fu,(*func)(u))    return v-nl+NR_END;
           }  }
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  /******************free lvector **************************/
       fu=(*func)(u);  void free_lvector(long *v, long nl, long nh)
     } else {  {
       u=(*cx)+GOLD*(*cx-*bx);    free((FREE_ARG)(v+nl-NR_END));
       fu=(*func)(u);  }
     }  
     SHFT(*ax,*bx,*cx,u)  /******************* imatrix *******************************/
       SHFT(*fa,*fb,*fc,fu)  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       }       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 }  { 
     long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 /*************** linmin ************************/    int **m; 
     
 int ncom;    /* allocate pointers to rows */ 
 double *pcom,*xicom;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 double (*nrfunc)(double []);    if (!m) nrerror("allocation failure 1 in matrix()"); 
      m += NR_END; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    m -= nrl; 
 {    
   double brent(double ax, double bx, double cx,    
                double (*f)(double), double tol, double *xmin);    /* allocate rows and set pointers to them */ 
   double f1dim(double x);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
               double *fc, double (*func)(double));    m[nrl] += NR_END; 
   int j;    m[nrl] -= ncl; 
   double xx,xmin,bx,ax;    
   double fx,fb,fa;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
      
   ncom=n;    /* return pointer to array of pointers to rows */ 
   pcom=vector(1,n);    return m; 
   xicom=vector(1,n);  } 
   nrfunc=func;  
   for (j=1;j<=n;j++) {  /****************** free_imatrix *************************/
     pcom[j]=p[j];  void free_imatrix(m,nrl,nrh,ncl,nch)
     xicom[j]=xi[j];        int **m;
   }        long nch,ncl,nrh,nrl; 
   ax=0.0;       /* free an int matrix allocated by imatrix() */ 
   xx=1.0;  { 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    free((FREE_ARG) (m+nrl-NR_END)); 
 #ifdef DEBUG  } 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif  /******************* matrix *******************************/
   for (j=1;j<=n;j++) {  double **matrix(long nrl, long nrh, long ncl, long nch)
     xi[j] *= xmin;  {
     p[j] += xi[j];    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   }    double **m;
   free_vector(xicom,1,n);  
   free_vector(pcom,1,n);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 }    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
 /*************** powell ************************/    m -= nrl;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  
             double (*func)(double []))    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   void linmin(double p[], double xi[], int n, double *fret,    m[nrl] += NR_END;
               double (*func)(double []));    m[nrl] -= ncl;
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double fp,fptt;    return m;
   double *xits;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   pt=vector(1,n);     */
   ptt=vector(1,n);  }
   xit=vector(1,n);  
   xits=vector(1,n);  /*************************free matrix ************************/
   *fret=(*func)(p);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   for (j=1;j<=n;j++) pt[j]=p[j];  {
   for (*iter=1;;++(*iter)) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     fp=(*fret);    free((FREE_ARG)(m+nrl-NR_END));
     ibig=0;  }
     del=0.0;  
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  /******************* ma3x *******************************/
     for (i=1;i<=n;i++)  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       printf(" %d %.12f",i, p[i]);  {
     printf("\n");    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     for (i=1;i<=n;i++) {    double ***m;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 #ifdef DEBUG    if (!m) nrerror("allocation failure 1 in matrix()");
       printf("fret=%lf \n",*fret);    m += NR_END;
 #endif    m -= nrl;
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       if (fabs(fptt-(*fret)) > del) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         del=fabs(fptt-(*fret));    m[nrl] += NR_END;
         ibig=i;    m[nrl] -= ncl;
       }  
 #ifdef DEBUG    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       printf("%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
         printf(" x(%d)=%.12e",j,xit[j]);    m[nrl][ncl] += NR_END;
       }    m[nrl][ncl] -= nll;
       for(j=1;j<=n;j++)    for (j=ncl+1; j<=nch; j++) 
         printf(" p=%.12e",p[j]);      m[nrl][j]=m[nrl][j-1]+nlay;
       printf("\n");    
 #endif    for (i=nrl+1; i<=nrh; i++) {
     }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      for (j=ncl+1; j<=nch; j++) 
 #ifdef DEBUG        m[i][j]=m[i][j-1]+nlay;
       int k[2],l;    }
       k[0]=1;    return m; 
       k[1]=-1;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       printf("Max: %.12e",(*func)(p));             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       for (j=1;j<=n;j++)    */
         printf(" %.12e",p[j]);  }
       printf("\n");  
       for(l=0;l<=1;l++) {  /*************************free ma3x ************************/
         for (j=1;j<=n;j++) {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
           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]);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
         }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    free((FREE_ARG)(m+nrl-NR_END));
       }  }
 #endif  
   /*************** function subdirf ***********/
   char *subdirf(char fileres[])
       free_vector(xit,1,n);  {
       free_vector(xits,1,n);    /* Caution optionfilefiname is hidden */
       free_vector(ptt,1,n);    strcpy(tmpout,optionfilefiname);
       free_vector(pt,1,n);    strcat(tmpout,"/"); /* Add to the right */
       return;    strcat(tmpout,fileres);
     }    return tmpout;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  }
     for (j=1;j<=n;j++) {  
       ptt[j]=2.0*p[j]-pt[j];  /*************** function subdirf2 ***********/
       xit[j]=p[j]-pt[j];  char *subdirf2(char fileres[], char *preop)
       pt[j]=p[j];  {
     }    
     fptt=(*func)(ptt);    /* Caution optionfilefiname is hidden */
     if (fptt < fp) {    strcpy(tmpout,optionfilefiname);
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    strcat(tmpout,"/");
       if (t < 0.0) {    strcat(tmpout,preop);
         linmin(p,xit,n,fret,func);    strcat(tmpout,fileres);
         for (j=1;j<=n;j++) {    return tmpout;
           xi[j][ibig]=xi[j][n];  }
           xi[j][n]=xit[j];  
         }  /*************** function subdirf3 ***********/
 #ifdef DEBUG  char *subdirf3(char fileres[], char *preop, char *preop2)
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  {
         for(j=1;j<=n;j++)    
           printf(" %.12e",xit[j]);    /* Caution optionfilefiname is hidden */
         printf("\n");    strcpy(tmpout,optionfilefiname);
 #endif    strcat(tmpout,"/");
       }    strcat(tmpout,preop);
     }    strcat(tmpout,preop2);
   }    strcat(tmpout,fileres);
 }    return tmpout;
   }
 /**** Prevalence limit ****************/  
   /***************** f1dim *************************/
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  extern int ncom; 
 {  extern double *pcom,*xicom;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  extern double (*nrfunc)(double []); 
      matrix by transitions matrix until convergence is reached */   
   double f1dim(double x) 
   int i, ii,j,k;  { 
   double min, max, maxmin, maxmax,sumnew=0.;    int j; 
   double **matprod2();    double f;
   double **out, cov[NCOVMAX], **pmij();    double *xt; 
   double **newm;   
   double agefin, delaymax=50 ; /* Max number of years to converge */    xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   for (ii=1;ii<=nlstate+ndeath;ii++)    f=(*nrfunc)(xt); 
     for (j=1;j<=nlstate+ndeath;j++){    free_vector(xt,1,ncom); 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    return f; 
     }  } 
   
    cov[1]=1.;  /*****************brent *************************/
    double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  { 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    int iter; 
     newm=savm;    double a,b,d,etemp;
     /* Covariates have to be included here again */    double fu,fv,fw,fx;
      cov[2]=agefin;    double ftemp;
      double p,q,r,tol1,tol2,u,v,w,x,xm; 
       for (k=1; k<=cptcovn;k++) {    double e=0.0; 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];   
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/    a=(ax < cx ? ax : cx); 
       }    b=(ax > cx ? ax : cx); 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    x=w=v=bx; 
       for (k=1; k<=cptcovprod;k++)    fw=fv=fx=(*f)(x); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    for (iter=1;iter<=ITMAX;iter++) { 
       xm=0.5*(a+b); 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      printf(".");fflush(stdout);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      fprintf(ficlog,".");fflush(ficlog);
   #ifdef DEBUG
     savm=oldm;      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);
     oldm=newm;      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);
     maxmax=0.;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     for(j=1;j<=nlstate;j++){  #endif
       min=1.;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       max=0.;        *xmin=x; 
       for(i=1; i<=nlstate; i++) {        return fx; 
         sumnew=0;      } 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      ftemp=fu;
         prlim[i][j]= newm[i][j]/(1-sumnew);      if (fabs(e) > tol1) { 
         max=FMAX(max,prlim[i][j]);        r=(x-w)*(fx-fv); 
         min=FMIN(min,prlim[i][j]);        q=(x-v)*(fx-fw); 
       }        p=(x-v)*q-(x-w)*r; 
       maxmin=max-min;        q=2.0*(q-r); 
       maxmax=FMAX(maxmax,maxmin);        if (q > 0.0) p = -p; 
     }        q=fabs(q); 
     if(maxmax < ftolpl){        etemp=e; 
       return prlim;        e=d; 
     }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   }          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 }        else { 
           d=p/q; 
 /*************** transition probabilities ***************/          u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )            d=SIGN(tol1,xm-x); 
 {        } 
   double s1, s2;      } else { 
   /*double t34;*/        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   int i,j,j1, nc, ii, jj;      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     for(i=1; i<= nlstate; i++){      fu=(*f)(u); 
     for(j=1; j<i;j++){      if (fu <= fx) { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        if (u >= x) a=x; else b=x; 
         /*s2 += param[i][j][nc]*cov[nc];*/        SHFT(v,w,x,u) 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          SHFT(fv,fw,fx,fu) 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/          } else { 
       }            if (u < x) a=u; else b=u; 
       ps[i][j]=s2;            if (fu <= fw || w == x) { 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/              v=w; 
     }              w=u; 
     for(j=i+1; j<=nlstate+ndeath;j++){              fv=fw; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){              fw=fu; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];            } else if (fu <= fv || v == x || v == w) { 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/              v=u; 
       }              fv=fu; 
       ps[i][j]=s2;            } 
     }          } 
   }    } 
     /*ps[3][2]=1;*/    nrerror("Too many iterations in brent"); 
     *xmin=x; 
   for(i=1; i<= nlstate; i++){    return fx; 
      s1=0;  } 
     for(j=1; j<i; j++)  
       s1+=exp(ps[i][j]);  /****************** mnbrak ***********************/
     for(j=i+1; j<=nlstate+ndeath; j++)  
       s1+=exp(ps[i][j]);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     ps[i][i]=1./(s1+1.);              double (*func)(double)) 
     for(j=1; j<i; j++)  { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    double ulim,u,r,q, dum;
     for(j=i+1; j<=nlstate+ndeath; j++)    double fu; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];   
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    *fa=(*func)(*ax); 
   } /* end i */    *fb=(*func)(*bx); 
     if (*fb > *fa) { 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      SHFT(dum,*ax,*bx,dum) 
     for(jj=1; jj<= nlstate+ndeath; jj++){        SHFT(dum,*fb,*fa,dum) 
       ps[ii][jj]=0;        } 
       ps[ii][ii]=1;    *cx=(*bx)+GOLD*(*bx-*ax); 
     }    *fc=(*func)(*cx); 
   }    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     for(jj=1; jj<= nlstate+ndeath; jj++){        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
      printf("%lf ",ps[ii][jj]);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
    }      if ((*bx-u)*(u-*cx) > 0.0) { 
     printf("\n ");        fu=(*func)(u); 
     }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     printf("\n ");printf("%lf ",cov[2]);*/        fu=(*func)(u); 
 /*        if (fu < *fc) { 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   goto end;*/            SHFT(*fb,*fc,fu,(*func)(u)) 
     return ps;            } 
 }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         u=ulim; 
 /**************** Product of 2 matrices ******************/        fu=(*func)(u); 
       } else { 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        u=(*cx)+GOLD*(*cx-*bx); 
 {        fu=(*func)(u); 
   /* 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(...) */      SHFT(*ax,*bx,*cx,u) 
   /* in, b, out are matrice of pointers which should have been initialized        SHFT(*fa,*fb,*fc,fu) 
      before: only the contents of out is modified. The function returns        } 
      a pointer to pointers identical to out */  } 
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)  /*************** linmin ************************/
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  int ncom; 
         out[i][k] +=in[i][j]*b[j][k];  double *pcom,*xicom;
   double (*nrfunc)(double []); 
   return out;   
 }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   { 
     double brent(double ax, double bx, double cx, 
 /************* Higher Matrix Product ***************/                 double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 {                double *fc, double (*func)(double)); 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    int j; 
      duration (i.e. until    double xx,xmin,bx,ax; 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    double fx,fb,fa;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step   
      (typically every 2 years instead of every month which is too big).    ncom=n; 
      Model is determined by parameters x and covariates have to be    pcom=vector(1,n); 
      included manually here.    xicom=vector(1,n); 
     nrfunc=func; 
      */    for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
   int i, j, d, h, k;      xicom[j]=xi[j]; 
   double **out, cov[NCOVMAX];    } 
   double **newm;    ax=0.0; 
     xx=1.0; 
   /* Hstepm could be zero and should return the unit matrix */    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   for (i=1;i<=nlstate+ndeath;i++)    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     for (j=1;j<=nlstate+ndeath;j++){  #ifdef DEBUG
       oldm[i][j]=(i==j ? 1.0 : 0.0);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       po[i][j][0]=(i==j ? 1.0 : 0.0);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     }  #endif
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    for (j=1;j<=n;j++) { 
   for(h=1; h <=nhstepm; h++){      xi[j] *= xmin; 
     for(d=1; d <=hstepm; d++){      p[j] += xi[j]; 
       newm=savm;    } 
       /* Covariates have to be included here again */    free_vector(xicom,1,n); 
       cov[1]=1.;    free_vector(pcom,1,n); 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  } 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
       for (k=1; k<=cptcovage;k++)  char *asc_diff_time(long time_sec, char ascdiff[])
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  {
       for (k=1; k<=cptcovprod;k++)    long sec_left, days, hours, minutes;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    sec_left = (sec_left) %(60*60);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    minutes = (sec_left) /60;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    sec_left = (sec_left) % (60);
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
       savm=oldm;    return ascdiff;
       oldm=newm;  }
     }  
     for(i=1; i<=nlstate+ndeath; i++)  /*************** powell ************************/
       for(j=1;j<=nlstate+ndeath;j++) {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         po[i][j][h]=newm[i][j];              double (*func)(double [])) 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  { 
          */    void linmin(double p[], double xi[], int n, double *fret, 
       }                double (*func)(double [])); 
   } /* end h */    int i,ibig,j; 
   return po;    double del,t,*pt,*ptt,*xit;
 }    double fp,fptt;
     double *xits;
     int niterf, itmp;
 /*************** log-likelihood *************/  
 double func( double *x)    pt=vector(1,n); 
 {    ptt=vector(1,n); 
   int i, ii, j, k, mi, d, kk;    xit=vector(1,n); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    xits=vector(1,n); 
   double **out;    *fret=(*func)(p); 
   double sw; /* Sum of weights */    for (j=1;j<=n;j++) pt[j]=p[j]; 
   double lli; /* Individual log likelihood */    for (*iter=1;;++(*iter)) { 
   long ipmx;      fp=(*fret); 
   /*extern weight */      ibig=0; 
   /* We are differentiating ll according to initial status */      del=0.0; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      last_time=curr_time;
   /*for(i=1;i<imx;i++)      (void) gettimeofday(&curr_time,&tzp);
     printf(" %d\n",s[4][i]);      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);
   cov[1]=1.;      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       */
   for(k=1; k<=nlstate; k++) ll[k]=0.;     for (i=1;i<=n;i++) {
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        printf(" %d %.12f",i, p[i]);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        fprintf(ficlog," %d %.12lf",i, p[i]);
     for(mi=1; mi<= wav[i]-1; mi++){        fprintf(ficrespow," %.12lf", p[i]);
       for (ii=1;ii<=nlstate+ndeath;ii++)      }
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      printf("\n");
       for(d=0; d<dh[mi][i]; d++){      fprintf(ficlog,"\n");
         newm=savm;      fprintf(ficrespow,"\n");fflush(ficrespow);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      if(*iter <=3){
         for (kk=1; kk<=cptcovage;kk++) {        tm = *localtime(&curr_time.tv_sec);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        strcpy(strcurr,asctime(&tm));
         }  /*       asctime_r(&tm,strcurr); */
                forecast_time=curr_time; 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        itmp = strlen(strcurr);
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         savm=oldm;          strcurr[itmp-1]='\0';
         oldm=newm;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
                fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
                for(niterf=10;niterf<=30;niterf+=10){
       } /* end mult */          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
                tmf = *localtime(&forecast_time.tv_sec);
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  /*      asctime_r(&tmf,strfor); */
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/          strcpy(strfor,asctime(&tmf));
       ipmx +=1;          itmp = strlen(strfor);
       sw += weight[i];          if(strfor[itmp-1]=='\n')
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          strfor[itmp-1]='\0';
     } /* end of wave */          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);
   } /* end of individual */          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
         }
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      }
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      for (i=1;i<=n;i++) { 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   return -l;        fptt=(*fret); 
 }  #ifdef DEBUG
         printf("fret=%lf \n",*fret);
         fprintf(ficlog,"fret=%lf \n",*fret);
 /*********** Maximum Likelihood Estimation ***************/  #endif
         printf("%d",i);fflush(stdout);
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        fprintf(ficlog,"%d",i);fflush(ficlog);
 {        linmin(p,xit,n,fret,func); 
   int i,j, iter;        if (fabs(fptt-(*fret)) > del) { 
   double **xi,*delti;          del=fabs(fptt-(*fret)); 
   double fret;          ibig=i; 
   xi=matrix(1,npar,1,npar);        } 
   for (i=1;i<=npar;i++)  #ifdef DEBUG
     for (j=1;j<=npar;j++)        printf("%d %.12e",i,(*fret));
       xi[i][j]=(i==j ? 1.0 : 0.0);        fprintf(ficlog,"%d %.12e",i,(*fret));
   printf("Powell\n");        for (j=1;j<=n;j++) {
   powell(p,xi,npar,ftol,&iter,&fret,func);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           printf(" x(%d)=%.12e",j,xit[j]);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        }
         for(j=1;j<=n;j++) {
 }          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
 /**** Computes Hessian and covariance matrix ***/        }
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        printf("\n");
 {        fprintf(ficlog,"\n");
   double  **a,**y,*x,pd;  #endif
   double **hess;      } 
   int i, j,jk;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   int *indx;  #ifdef DEBUG
         int k[2],l;
   double hessii(double p[], double delta, int theta, double delti[]);        k[0]=1;
   double hessij(double p[], double delti[], int i, int j);        k[1]=-1;
   void lubksb(double **a, int npar, int *indx, double b[]) ;        printf("Max: %.12e",(*func)(p));
   void ludcmp(double **a, int npar, int *indx, double *d) ;        fprintf(ficlog,"Max: %.12e",(*func)(p));
         for (j=1;j<=n;j++) {
   hess=matrix(1,npar,1,npar);          printf(" %.12e",p[j]);
           fprintf(ficlog," %.12e",p[j]);
   printf("\nCalculation of the hessian matrix. Wait...\n");        }
   for (i=1;i<=npar;i++){        printf("\n");
     printf("%d",i);fflush(stdout);        fprintf(ficlog,"\n");
     hess[i][i]=hessii(p,ftolhess,i,delti);        for(l=0;l<=1;l++) {
     /*printf(" %f ",p[i]);*/          for (j=1;j<=n;j++) {
     /*printf(" %lf ",hess[i][i]);*/            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   }            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
              fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   for (i=1;i<=npar;i++) {          }
     for (j=1;j<=npar;j++)  {          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       if (j>i) {          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         printf(".%d%d",i,j);fflush(stdout);        }
         hess[i][j]=hessij(p,delti,i,j);  #endif
         hess[j][i]=hess[i][j];      
         /*printf(" %lf ",hess[i][j]);*/  
       }        free_vector(xit,1,n); 
     }        free_vector(xits,1,n); 
   }        free_vector(ptt,1,n); 
   printf("\n");        free_vector(pt,1,n); 
         return; 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      } 
        if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   a=matrix(1,npar,1,npar);      for (j=1;j<=n;j++) { 
   y=matrix(1,npar,1,npar);        ptt[j]=2.0*p[j]-pt[j]; 
   x=vector(1,npar);        xit[j]=p[j]-pt[j]; 
   indx=ivector(1,npar);        pt[j]=p[j]; 
   for (i=1;i<=npar;i++)      } 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];      fptt=(*func)(ptt); 
   ludcmp(a,npar,indx,&pd);      if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   for (j=1;j<=npar;j++) {        if (t < 0.0) { 
     for (i=1;i<=npar;i++) x[i]=0;          linmin(p,xit,n,fret,func); 
     x[j]=1;          for (j=1;j<=n;j++) { 
     lubksb(a,npar,indx,x);            xi[j][ibig]=xi[j][n]; 
     for (i=1;i<=npar;i++){            xi[j][n]=xit[j]; 
       matcov[i][j]=x[i];          }
     }  #ifdef DEBUG
   }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   printf("\n#Hessian matrix#\n");          for(j=1;j<=n;j++){
   for (i=1;i<=npar;i++) {            printf(" %.12e",xit[j]);
     for (j=1;j<=npar;j++) {            fprintf(ficlog," %.12e",xit[j]);
       printf("%.3e ",hess[i][j]);          }
     }          printf("\n");
     printf("\n");          fprintf(ficlog,"\n");
   }  #endif
         }
   /* Recompute Inverse */      } 
   for (i=1;i<=npar;i++)    } 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  } 
   ludcmp(a,npar,indx,&pd);  
   /**** Prevalence limit (stable prevalence)  ****************/
   /*  printf("\n#Hessian matrix recomputed#\n");  
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   for (j=1;j<=npar;j++) {  {
     for (i=1;i<=npar;i++) x[i]=0;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     x[j]=1;       matrix by transitions matrix until convergence is reached */
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){    int i, ii,j,k;
       y[i][j]=x[i];    double min, max, maxmin, maxmax,sumnew=0.;
       printf("%.3e ",y[i][j]);    double **matprod2();
     }    double **out, cov[NCOVMAX], **pmij();
     printf("\n");    double **newm;
   }    double agefin, delaymax=50 ; /* Max number of years to converge */
   */  
     for (ii=1;ii<=nlstate+ndeath;ii++)
   free_matrix(a,1,npar,1,npar);      for (j=1;j<=nlstate+ndeath;j++){
   free_matrix(y,1,npar,1,npar);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(x,1,npar);      }
   free_ivector(indx,1,npar);  
   free_matrix(hess,1,npar,1,npar);     cov[1]=1.;
    
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 }    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       newm=savm;
 /*************** hessian matrix ****************/      /* Covariates have to be included here again */
 double hessii( double x[], double delta, int theta, double delti[])       cov[2]=agefin;
 {    
   int i;        for (k=1; k<=cptcovn;k++) {
   int l=1, lmax=20;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double k1,k2;          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
   double p2[NPARMAX+1];        }
   double res;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        for (k=1; k<=cptcovprod;k++)
   double fx;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   int k=0,kmax=10;  
   double l1;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   fx=func(x);        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   for (i=1;i<=npar;i++) p2[i]=x[i];      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   for(l=0 ; l <=lmax; l++){  
     l1=pow(10,l);      savm=oldm;
     delts=delt;      oldm=newm;
     for(k=1 ; k <kmax; k=k+1){      maxmax=0.;
       delt = delta*(l1*k);      for(j=1;j<=nlstate;j++){
       p2[theta]=x[theta] +delt;        min=1.;
       k1=func(p2)-fx;        max=0.;
       p2[theta]=x[theta]-delt;        for(i=1; i<=nlstate; i++) {
       k2=func(p2)-fx;          sumnew=0;
       /*res= (k1-2.0*fx+k2)/delt/delt; */          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          prlim[i][j]= newm[i][j]/(1-sumnew);
                max=FMAX(max,prlim[i][j]);
 #ifdef DEBUG          min=FMIN(min,prlim[i][j]);
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        }
 #endif        maxmin=max-min;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        maxmax=FMAX(maxmax,maxmin);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      }
         k=kmax;      if(maxmax < ftolpl){
       }        return prlim;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      }
         k=kmax; l=lmax*10.;    }
       }  }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  
         delts=delt;  /*************** transition probabilities ***************/ 
       }  
     }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   }  {
   delti[theta]=delts;    double s1, s2;
   return res;    /*double t34;*/
      int i,j,j1, nc, ii, jj;
 }  
       for(i=1; i<= nlstate; i++){
 double hessij( double x[], double delti[], int thetai,int thetaj)        for(j=1; j<i;j++){
 {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   int i;            /*s2 += param[i][j][nc]*cov[nc];*/
   int l=1, l1, lmax=20;            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   double k1,k2,k3,k4,res,fx;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
   double p2[NPARMAX+1];          }
   int k;          ps[i][j]=s2;
   /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
   fx=func(x);        }
   for (k=1; k<=2; k++) {        for(j=i+1; j<=nlstate+ndeath;j++){
     for (i=1;i<=npar;i++) p2[i]=x[i];          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     p2[thetai]=x[thetai]+delti[thetai]/k;            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     k1=func(p2)-fx;          }
            ps[i][j]=s2;
     p2[thetai]=x[thetai]+delti[thetai]/k;        }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      }
     k2=func(p2)-fx;      /*ps[3][2]=1;*/
        
     p2[thetai]=x[thetai]-delti[thetai]/k;      for(i=1; i<= nlstate; i++){
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        s1=0;
     k3=func(p2)-fx;        for(j=1; j<i; j++)
            s1+=exp(ps[i][j]);
     p2[thetai]=x[thetai]-delti[thetai]/k;        for(j=i+1; j<=nlstate+ndeath; j++)
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          s1+=exp(ps[i][j]);
     k4=func(p2)-fx;        ps[i][i]=1./(s1+1.);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        for(j=1; j<i; j++)
 #ifdef DEBUG          ps[i][j]= exp(ps[i][j])*ps[i][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=i+1; j<=nlstate+ndeath; j++)
 #endif          ps[i][j]= exp(ps[i][j])*ps[i][i];
   }        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   return res;      } /* end i */
 }      
       for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
 /************** Inverse of matrix **************/        for(jj=1; jj<= nlstate+ndeath; jj++){
 void ludcmp(double **a, int n, int *indx, double *d)          ps[ii][jj]=0;
 {          ps[ii][ii]=1;
   int i,imax,j,k;        }
   double big,dum,sum,temp;      }
   double *vv;      
    
   vv=vector(1,n);  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   *d=1.0;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   for (i=1;i<=n;i++) {  /*         printf("ddd %lf ",ps[ii][jj]); */
     big=0.0;  /*       } */
     for (j=1;j<=n;j++)  /*       printf("\n "); */
       if ((temp=fabs(a[i][j])) > big) big=temp;  /*        } */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  /*        printf("\n ");printf("%lf ",cov[2]); */
     vv[i]=1.0/big;         /*
   }        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   for (j=1;j<=n;j++) {        goto end;*/
     for (i=1;i<j;i++) {      return ps;
       sum=a[i][j];  }
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;  /**************** Product of 2 matrices ******************/
     }  
     big=0.0;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     for (i=j;i<=n;i++) {  {
       sum=a[i][j];    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       for (k=1;k<j;k++)       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         sum -= a[i][k]*a[k][j];    /* in, b, out are matrice of pointers which should have been initialized 
       a[i][j]=sum;       before: only the contents of out is modified. The function returns
       if ( (dum=vv[i]*fabs(sum)) >= big) {       a pointer to pointers identical to out */
         big=dum;    long i, j, k;
         imax=i;    for(i=nrl; i<= nrh; i++)
       }      for(k=ncolol; k<=ncoloh; k++)
     }        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     if (j != imax) {          out[i][k] +=in[i][j]*b[j][k];
       for (k=1;k<=n;k++) {  
         dum=a[imax][k];    return out;
         a[imax][k]=a[j][k];  }
         a[j][k]=dum;  
       }  
       *d = -(*d);  /************* Higher Matrix Product ***************/
       vv[imax]=vv[j];  
     }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     indx[j]=imax;  {
     if (a[j][j] == 0.0) a[j][j]=TINY;    /* Computes the transition matrix starting at age 'age' over 
     if (j != n) {       'nhstepm*hstepm*stepm' months (i.e. until
       dum=1.0/(a[j][j]);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;       nhstepm*hstepm matrices. 
     }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   }       (typically every 2 years instead of every month which is too big 
   free_vector(vv,1,n);  /* Doesn't work */       for the memory).
 ;       Model is determined by parameters x and covariates have to be 
 }       included manually here. 
   
 void lubksb(double **a, int n, int *indx, double b[])       */
 {  
   int i,ii=0,ip,j;    int i, j, d, h, k;
   double sum;    double **out, cov[NCOVMAX];
      double **newm;
   for (i=1;i<=n;i++) {  
     ip=indx[i];    /* Hstepm could be zero and should return the unit matrix */
     sum=b[ip];    for (i=1;i<=nlstate+ndeath;i++)
     b[ip]=b[i];      for (j=1;j<=nlstate+ndeath;j++){
     if (ii)        oldm[i][j]=(i==j ? 1.0 : 0.0);
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        po[i][j][0]=(i==j ? 1.0 : 0.0);
     else if (sum) ii=i;      }
     b[i]=sum;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   }    for(h=1; h <=nhstepm; h++){
   for (i=n;i>=1;i--) {      for(d=1; d <=hstepm; d++){
     sum=b[i];        newm=savm;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        /* Covariates have to be included here again */
     b[i]=sum/a[i][i];        cov[1]=1.;
   }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
 }        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
 /************ Frequencies ********************/          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)        for (k=1; k<=cptcovprod;k++)
 {  /* Some frequencies */          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
    
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   double *pp;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   double pos, k2, dateintsum=0,k2cpt=0;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   FILE *ficresp;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   char fileresp[FILENAMELENGTH];        savm=oldm;
          oldm=newm;
   pp=vector(1,nlstate);      }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      for(i=1; i<=nlstate+ndeath; i++)
   strcpy(fileresp,"p");        for(j=1;j<=nlstate+ndeath;j++) {
   strcat(fileresp,fileres);          po[i][j][h]=newm[i][j];
   if((ficresp=fopen(fileresp,"w"))==NULL) {          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     printf("Problem with prevalence resultfile: %s\n", fileresp);           */
     exit(0);        }
   }    } /* end h */
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    return po;
   j1=0;  }
    
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  /*************** log-likelihood *************/
    double func( double *x)
   for(k1=1; k1<=j;k1++){  {
     for(i1=1; i1<=ncodemax[k1];i1++){    int i, ii, j, k, mi, d, kk;
       j1++;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    double **out;
         scanf("%d", i);*/    double sw; /* Sum of weights */
       for (i=-1; i<=nlstate+ndeath; i++)      double lli; /* Individual log likelihood */
         for (jk=-1; jk<=nlstate+ndeath; jk++)      int s1, s2;
           for(m=agemin; m <= agemax+3; m++)    double bbh, survp;
             freq[i][jk][m]=0;    long ipmx;
          /*extern weight */
       dateintsum=0;    /* We are differentiating ll according to initial status */
       k2cpt=0;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       for (i=1; i<=imx; i++) {    /*for(i=1;i<imx;i++) 
         bool=1;      printf(" %d\n",s[4][i]);
         if  (cptcovn>0) {    */
           for (z1=1; z1<=cptcoveff; z1++)    cov[1]=1.;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
               bool=0;    for(k=1; k<=nlstate; k++) ll[k]=0.;
         }  
         if (bool==1) {    if(mle==1){
           for(m=firstpass; m<=lastpass; m++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             k2=anint[m][i]+(mint[m][i]/12.);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        for(mi=1; mi<= wav[i]-1; mi++){
               if(agev[m][i]==0) agev[m][i]=agemax+1;          for (ii=1;ii<=nlstate+ndeath;ii++)
               if(agev[m][i]==1) agev[m][i]=agemax+2;            for (j=1;j<=nlstate+ndeath;j++){
               if (m<lastpass) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];            }
               }          for(d=0; d<dh[mi][i]; d++){
                          newm=savm;
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                 dateintsum=dateintsum+k2;            for (kk=1; kk<=cptcovage;kk++) {
                 k2cpt++;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
               }            }
             }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
       }            oldm=newm;
                  } /* end mult */
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       if  (cptcovn>0) {          /* But now since version 0.9 we anticipate for bias at large stepm.
         fprintf(ficresp, "\n#********** Variable ");           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);           * (in months) between two waves is not a multiple of stepm, we rounded to 
         fprintf(ficresp, "**********\n#");           * 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
       for(i=1; i<=nlstate;i++)           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);           * probability in order to take into account the bias as a fraction of the way
       fprintf(ficresp, "\n");           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
                 * -stepm/2 to stepm/2 .
       for(i=(int)agemin; i <= (int)agemax+3; i++){           * For stepm=1 the results are the same as for previous versions of Imach.
         if(i==(int)agemax+3)           * For stepm > 1 the results are less biased than in previous versions. 
           printf("Total");           */
         else          s1=s[mw[mi][i]][i];
           printf("Age %d", i);          s2=s[mw[mi+1][i]][i];
         for(jk=1; jk <=nlstate ; jk++){          bbh=(double)bh[mi][i]/(double)stepm; 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          /* bias bh is positive if real duration
             pp[jk] += freq[jk][m][i];           * is higher than the multiple of stepm and negative otherwise.
         }           */
         for(jk=1; jk <=nlstate ; jk++){          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           for(m=-1, pos=0; m <=0 ; m++)          if( s2 > nlstate){ 
             pos += freq[jk][m][i];            /* i.e. if s2 is a death state and if the date of death is known then the contribution
           if(pp[jk]>=1.e-10)               to the likelihood is the probability to die between last step unit time and current 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);               step unit time, which is also equal to probability to die before dh 
           else               minus probability to die before dh-stepm . 
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);               In version up to 0.92 likelihood was computed
         }          as if date of death was unknown. Death was treated as any other
           health state: the date of the interview describes the actual state
         for(jk=1; jk <=nlstate ; jk++){          and not the date of a change in health state. The former idea was
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          to consider that at each interview the state was recorded
             pp[jk] += freq[jk][m][i];          (healthy, disable or death) and IMaCh was corrected; but when we
         }          introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
         for(jk=1,pos=0; jk <=nlstate ; jk++)          contribution is smaller and very dependent of the step unit
           pos += pp[jk];          stepm. It is no more the probability to die between last interview
         for(jk=1; jk <=nlstate ; jk++){          and month of death but the probability to survive from last
           if(pos>=1.e-5)          interview up to one month before death multiplied by the
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          probability to die within a month. Thanks to Chris
           else          Jackson for correcting this bug.  Former versions increased
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          mortality artificially. The bad side is that we add another loop
           if( i <= (int) agemax){          which slows down the processing. The difference can be up to 10%
             if(pos>=1.e-5){          lower mortality.
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            */
               probs[i][jk][j1]= pp[jk]/pos;            lli=log(out[s1][s2] - savm[s1][s2]);
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          }else{
             }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             else            /*  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 */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          } 
           }          /*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); */
         for(jk=-1; jk <=nlstate+ndeath; jk++)          ipmx +=1;
           for(m=-1; m <=nlstate+ndeath; m++)          sw += weight[i];
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         if(i <= (int) agemax)        } /* end of wave */
           fprintf(ficresp,"\n");      } /* end of individual */
         printf("\n");    }  else if(mle==2){
       }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   dateintmean=dateintsum/k2cpt;          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   fclose(ficresp);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(pp,1,nlstate);            }
            for(d=0; d<=dh[mi][i]; d++){
   /* End of Freq */            newm=savm;
 }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
 /************ Prevalence ********************/              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)            }
 {  /* Some frequencies */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;            savm=oldm;
   double ***freq; /* Frequencies */            oldm=newm;
   double *pp;          } /* end mult */
   double pos, k2;        
           s1=s[mw[mi][i]][i];
   pp=vector(1,nlstate);          s2=s[mw[mi+1][i]][i];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          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 */
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          ipmx +=1;
   j1=0;          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   j=cptcoveff;        } /* end of wave */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      } /* end of individual */
      }  else if(mle==3){  /* exponential inter-extrapolation */
  for(k1=1; k1<=j;k1++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(i1=1; i1<=ncodemax[k1];i1++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       j1++;        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
       for (i=-1; i<=nlstate+ndeath; i++)              for (j=1;j<=nlstate+ndeath;j++){
         for (jk=-1; jk<=nlstate+ndeath; jk++)                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(m=agemin; m <= agemax+3; m++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             freq[i][jk][m]=0;            }
                for(d=0; d<dh[mi][i]; d++){
       for (i=1; i<=imx; i++) {            newm=savm;
         bool=1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         if  (cptcovn>0) {            for (kk=1; kk<=cptcovage;kk++) {
           for (z1=1; z1<=cptcoveff; z1++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            }
               bool=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if (bool==1) {            savm=oldm;
           for(m=firstpass; m<=lastpass; m++){            oldm=newm;
             k2=anint[m][i]+(mint[m][i]/12.);          } /* end mult */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        
               if(agev[m][i]==0) agev[m][i]=agemax+1;          s1=s[mw[mi][i]][i];
               if(agev[m][i]==1) agev[m][i]=agemax+2;          s2=s[mw[mi+1][i]][i];
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          bbh=(double)bh[mi][i]/(double)stepm; 
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
             }          ipmx +=1;
           }          sw += weight[i];
         }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       }        } /* end of wave */
         for(i=(int)agemin; i <= (int)agemax+3; i++){      } /* end of individual */
           for(jk=1; jk <=nlstate ; jk++){    }else if (mle==4){  /* ml=4 no inter-extrapolation */
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
               pp[jk] += freq[jk][m][i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           }        for(mi=1; mi<= wav[i]-1; mi++){
           for(jk=1; jk <=nlstate ; jk++){          for (ii=1;ii<=nlstate+ndeath;ii++)
             for(m=-1, pos=0; m <=0 ; m++)            for (j=1;j<=nlstate+ndeath;j++){
             pos += freq[jk][m][i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }              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];            }
           
          for(jk=1; jk <=nlstate ; jk++){                      out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
            if( i <= (int) agemax){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              if(pos>=1.e-5){            savm=oldm;
                probs[i][jk][j1]= pp[jk]/pos;            oldm=newm;
              }          } /* end mult */
            }        
          }          s1=s[mw[mi][i]][i];
                    s2=s[mw[mi+1][i]][i];
         }          if( s2 > nlstate){ 
     }            lli=log(out[s1][s2] - savm[s1][s2]);
   }          }else{
              lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
            }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          ipmx +=1;
   free_vector(pp,1,nlstate);          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 }  /* End of Freq */  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         } /* end of wave */
 /************* Waves Concatenation ***************/      } /* end of individual */
     }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
 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 (i=1,ipmx=0, sw=0.; i<=imx; i++){
 {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        for(mi=1; mi<= wav[i]-1; mi++){
      Death is a valid wave (if date is known).          for (ii=1;ii<=nlstate+ndeath;ii++)
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i            for (j=1;j<=nlstate+ndeath;j++){
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      and mw[mi+1][i]. dh depends on stepm.              savm[ii][j]=(ii==j ? 1.0 : 0.0);
      */            }
           for(d=0; d<dh[mi][i]; d++){
   int i, mi, m;            newm=savm;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      double sum=0., jmean=0.;*/            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int j, k=0,jk, ju, jl;            }
   double sum=0.;          
   jmin=1e+5;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   jmax=-1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   jmean=0.;            savm=oldm;
   for(i=1; i<=imx; i++){            oldm=newm;
     mi=0;          } /* end mult */
     m=firstpass;        
     while(s[m][i] <= nlstate){          s1=s[mw[mi][i]][i];
       if(s[m][i]>=1)          s2=s[mw[mi+1][i]][i];
         mw[++mi][i]=m;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       if(m >=lastpass)          ipmx +=1;
         break;          sw += weight[i];
       else          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         m++;          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
     }/* end while */        } /* end of wave */
     if (s[m][i] > nlstate){      } /* end of individual */
       mi++;     /* Death is another wave */    } /* End of if */
       /* if(mi==0)  never been interviewed correctly before death */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
          /* Only death is a correct wave */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       mw[mi][i]=m;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     }    return -l;
   }
     wav[i]=mi;  
     if(mi==0)  /*************** log-likelihood *************/
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  double funcone( double *x)
   }  {
     /* Same as likeli but slower because of a lot of printf and if */
   for(i=1; i<=imx; i++){    int i, ii, j, k, mi, d, kk;
     for(mi=1; mi<wav[i];mi++){    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       if (stepm <=0)    double **out;
         dh[mi][i]=1;    double lli; /* Individual log likelihood */
       else{    double llt;
         if (s[mw[mi+1][i]][i] > nlstate) {    int s1, s2;
           if (agedc[i] < 2*AGESUP) {    double bbh, survp;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    /*extern weight */
           if(j==0) j=1;  /* Survives at least one month after exam */    /* We are differentiating ll according to initial status */
           k=k+1;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           if (j >= jmax) jmax=j;    /*for(i=1;i<imx;i++) 
           if (j <= jmin) jmin=j;      printf(" %d\n",s[4][i]);
           sum=sum+j;    */
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    cov[1]=1.;
           }  
         }    for(k=1; k<=nlstate; k++) ll[k]=0.;
         else{  
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           k=k+1;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           if (j >= jmax) jmax=j;      for(mi=1; mi<= wav[i]-1; mi++){
           else if (j <= jmin)jmin=j;        for (ii=1;ii<=nlstate+ndeath;ii++)
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          for (j=1;j<=nlstate+ndeath;j++){
           sum=sum+j;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
         jk= j/stepm;          }
         jl= j -jk*stepm;        for(d=0; d<dh[mi][i]; d++){
         ju= j -(jk+1)*stepm;          newm=savm;
         if(jl <= -ju)          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           dh[mi][i]=jk;          for (kk=1; kk<=cptcovage;kk++) {
         else            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           dh[mi][i]=jk+1;          }
         if(dh[mi][i]==0)          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           dh[mi][i]=1; /* At least one step */                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }          savm=oldm;
     }          oldm=newm;
   }        } /* end mult */
   jmean=sum/k;        
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        s1=s[mw[mi][i]][i];
  }        s2=s[mw[mi+1][i]][i];
 /*********** Tricode ****************************/        bbh=(double)bh[mi][i]/(double)stepm; 
 void tricode(int *Tvar, int **nbcode, int imx)        /* bias is positive if real duration
 {         * is higher than the multiple of stepm and negative otherwise.
   int Ndum[20],ij=1, k, j, i;         */
   int cptcode=0;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   cptcoveff=0;          lli=log(out[s1][s2] - savm[s1][s2]);
          } else if (mle==1){
   for (k=0; k<19; k++) Ndum[k]=0;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   for (k=1; k<=7; k++) ncodemax[k]=0;        } else if(mle==2){
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        } else if(mle==3){  /* exponential inter-extrapolation */
     for (i=1; i<=imx; i++) {          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 */
       ij=(int)(covar[Tvar[j]][i]);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       Ndum[ij]++;          lli=log(out[s1][s2]); /* Original formula */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
       if (ij > cptcode) cptcode=ij;          lli=log(out[s1][s2]); /* Original formula */
     }        } /* End of if */
         ipmx +=1;
     for (i=0; i<=cptcode; i++) {        sw += weight[i];
       if(Ndum[i]!=0) ncodemax[j]++;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     ij=1;        if(globpr){
           fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
    %10.6f %10.6f %10.6f ", \
     for (i=1; i<=ncodemax[j]; i++) {                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       for (k=0; k<=19; k++) {                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         if (Ndum[k] != 0) {          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
           nbcode[Tvar[j]][ij]=k;            llt +=ll[k]*gipmx/gsw;
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           ij++;          }
         }          fprintf(ficresilk," %10.6f\n", -llt);
         if (ij > ncodemax[j]) break;        }
       }        } /* end of wave */
     }    } /* end of individual */
   }      for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
  for (k=0; k<19; k++) Ndum[k]=0;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if(globpr==0){ /* First time we count the contributions and weights */
  for (i=1; i<=ncovmodel-2; i++) {      gipmx=ipmx;
       ij=Tvar[i];      gsw=sw;
       Ndum[ij]++;    }
     }    return -l;
   }
  ij=1;  
  for (i=1; i<=10; i++) {  
    if((Ndum[i]!=0) && (i<=ncovcol)){  /*************** function likelione ***********/
      Tvaraff[ij]=i;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
      ij++;  {
    }    /* This routine should help understanding what is done with 
  }       the selection of individuals/waves and
         to check the exact contribution to the likelihood.
     cptcoveff=ij-1;       Plotting could be done.
 }     */
     int k;
 /*********** Health Expectancies ****************/  
     if(*globpri !=0){ /* Just counts and sums, no printings */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)      strcpy(fileresilk,"ilk"); 
 {      strcat(fileresilk,fileres);
   /* Health expectancies */      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   int i, j, nhstepm, hstepm, h, nstepm;        printf("Problem with resultfile: %s\n", fileresilk);
   double age, agelim, hf;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   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");
   fprintf(ficreseij,"# Health expectancies\n");      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   fprintf(ficreseij,"# Age");      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   for(i=1; i<=nlstate;i++)      for(k=1; k<=nlstate; k++) 
     for(j=1; j<=nlstate;j++)        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficreseij," %1d-%1d",i,j);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   fprintf(ficreseij,"\n");    }
   
   if(estepm < stepm){    *fretone=(*funcone)(p);
     printf ("Problem %d lower than %d\n",estepm, stepm);    if(*globpri !=0){
   }      fclose(ficresilk);
   else  hstepm=estepm;        fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   /* We compute the life expectancy from trapezoids spaced every estepm months      fflush(fichtm); 
    * This is mainly to measure the difference between two models: for example    } 
    * if stepm=24 months pijx are given only every 2 years and by summing them    return;
    * we are calculating an estimate of the Life Expectancy assuming a linear  }
    * progression inbetween and thus overestimating or underestimating according  
    * 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  /*********** Maximum Likelihood Estimation ***************/
    * to compare the new estimate of Life expectancy with the same linear  
    * hypothesis. A more precise result, taking into account a more precise  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
    * curvature will be obtained if estepm is as small as stepm. */  {
     int i,j, iter;
   /* For example we decided to compute the life expectancy with the smallest unit */    double **xi;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    double fret;
      nhstepm is the number of hstepm from age to agelim    double fretone; /* Only one call to likelihood */
      nstepm is the number of stepm from age to agelin.    /*  char filerespow[FILENAMELENGTH];*/
      Look at hpijx to understand the reason of that which relies in memory size    xi=matrix(1,npar,1,npar);
      and note for a fixed period like estepm months */    for (i=1;i<=npar;i++)
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      for (j=1;j<=npar;j++)
      survival function given by stepm (the optimization length). Unfortunately it        xi[i][j]=(i==j ? 1.0 : 0.0);
      means that if the survival funtion is printed only each two years of age and if    printf("Powell\n");  fprintf(ficlog,"Powell\n");
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    strcpy(filerespow,"pow"); 
      results. So we changed our mind and took the option of the best precision.    strcat(filerespow,fileres);
   */    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   agelim=AGESUP;    }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     /* nhstepm age range expressed in number of stepm */    for (i=1;i<=nlstate;i++)
     nstepm=(int) rint((agelim-age)*YEARM/stepm);      for(j=1;j<=nlstate+ndeath;j++)
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     /* if (stepm >= YEARM) hstepm=1;*/    fprintf(ficrespow,"\n");
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    powell(p,xi,npar,ftol,&iter,&fret,func);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    fclose(ficrespow);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     for(i=1; i<=nlstate;i++)    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       for(j=1; j<=nlstate;j++)  
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){  }
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;  
           /* 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]);*/  /**** Computes Hessian and covariance matrix ***/
         }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     fprintf(ficreseij,"%3.0f",age );  {
     for(i=1; i<=nlstate;i++)    double  **a,**y,*x,pd;
       for(j=1; j<=nlstate;j++){    double **hess;
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);    int i, j,jk;
       }    int *indx;
     fprintf(ficreseij,"\n");  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   }    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
 }    void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
 /************ Variance ******************/    double gompertz(double p[]);
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)    hess=matrix(1,npar,1,npar);
 {  
   /* Variance of health expectancies */    printf("\nCalculation of the hessian matrix. Wait...\n");
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   double **newm;    for (i=1;i<=npar;i++){
   double **dnewm,**doldm;      printf("%d",i);fflush(stdout);
   int i, j, nhstepm, hstepm, h, nstepm ;      fprintf(ficlog,"%d",i);fflush(ficlog);
   int k, cptcode;     
   double *xp;       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   double **gp, **gm;      
   double ***gradg, ***trgradg;      /*  printf(" %f ",p[i]);
   double ***p3mat;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   double age,agelim, hf;    }
   int theta;    
     for (i=1;i<=npar;i++) {
    fprintf(ficresvij,"# Covariances of life expectancies\n");      for (j=1;j<=npar;j++)  {
   fprintf(ficresvij,"# Age");        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);
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          hess[i][j]=hessij(p,delti,i,j,func,npar);
   fprintf(ficresvij,"\n");          
           hess[j][i]=hess[i][j];    
   xp=vector(1,npar);          /*printf(" %lf ",hess[i][j]);*/
   dnewm=matrix(1,nlstate,1,npar);        }
   doldm=matrix(1,nlstate,1,nlstate);      }
      }
   if(estepm < stepm){    printf("\n");
     printf ("Problem %d lower than %d\n",estepm, stepm);    fprintf(ficlog,"\n");
   }  
   else  hstepm=estepm;      printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   /* For example we decided to compute the life expectancy with the smallest unit */    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   /* 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    a=matrix(1,npar,1,npar);
      nstepm is the number of stepm from age to agelin.    y=matrix(1,npar,1,npar);
      Look at hpijx to understand the reason of that which relies in memory size    x=vector(1,npar);
      and note for a fixed period like k years */    indx=ivector(1,npar);
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    for (i=1;i<=npar;i++)
      survival function given by stepm (the optimization length). Unfortunately it      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
      means that if the survival funtion is printed only each two years of age and if    ludcmp(a,npar,indx,&pd);
      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.    for (j=1;j<=npar;j++) {
   */      for (i=1;i<=npar;i++) x[i]=0;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 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++){ 
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        matcov[i][j]=x[i];
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  
     gp=matrix(0,nhstepm,1,nlstate);    printf("\n#Hessian matrix#\n");
     gm=matrix(0,nhstepm,1,nlstate);    fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
     for(theta=1; theta <=npar; theta++){      for (j=1;j<=npar;j++) { 
       for(i=1; i<=npar; i++){ /* Computes gradient */        printf("%.3e ",hess[i][j]);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        fprintf(ficlog,"%.3e ",hess[i][j]);
       }      }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        printf("\n");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      fprintf(ficlog,"\n");
     }
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)    /* Recompute Inverse */
           prlim[i][i]=probs[(int)age][i][ij];    for (i=1;i<=npar;i++)
       }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
      ludcmp(a,npar,indx,&pd);
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){    /*  printf("\n#Hessian matrix recomputed#\n");
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    for (j=1;j<=npar;j++) {
         }      for (i=1;i<=npar;i++) x[i]=0;
       }      x[j]=1;
          lubksb(a,npar,indx,x);
       for(i=1; i<=npar; i++) /* Computes gradient */      for (i=1;i<=npar;i++){ 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        y[i][j]=x[i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          printf("%.3e ",y[i][j]);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        fprintf(ficlog,"%.3e ",y[i][j]);
        }
       if (popbased==1) {      printf("\n");
         for(i=1; i<=nlstate;i++)      fprintf(ficlog,"\n");
           prlim[i][i]=probs[(int)age][i][ij];    }
       }    */
   
       for(j=1; j<= nlstate; j++){    free_matrix(a,1,npar,1,npar);
         for(h=0; h<=nhstepm; h++){    free_matrix(y,1,npar,1,npar);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    free_vector(x,1,npar);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    free_ivector(indx,1,npar);
         }    free_matrix(hess,1,npar,1,npar);
       }  
   
       for(j=1; j<= nlstate; j++)  }
         for(h=0; h<=nhstepm; h++){  
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  /*************** hessian matrix ****************/
         }  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     } /* End theta */  {
     int i;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    int l=1, lmax=20;
     double k1,k2;
     for(h=0; h<=nhstepm; h++)    double p2[NPARMAX+1];
       for(j=1; j<=nlstate;j++)    double res;
         for(theta=1; theta <=npar; theta++)    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           trgradg[h][j][theta]=gradg[h][theta][j];    double fx;
     int k=0,kmax=10;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    double l1;
     for(i=1;i<=nlstate;i++)  
       for(j=1;j<=nlstate;j++)    fx=func(x);
         vareij[i][j][(int)age] =0.;    for (i=1;i<=npar;i++) p2[i]=x[i];
     for(l=0 ; l <=lmax; l++){
     for(h=0;h<=nhstepm;h++){      l1=pow(10,l);
       for(k=0;k<=nhstepm;k++){      delts=delt;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      for(k=1 ; k <kmax; k=k+1){
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        delt = delta*(l1*k);
         for(i=1;i<=nlstate;i++)        p2[theta]=x[theta] +delt;
           for(j=1;j<=nlstate;j++)        k1=func(p2)-fx;
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;        p2[theta]=x[theta]-delt;
       }        k2=func(p2)-fx;
     }        /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     fprintf(ficresvij,"%.0f ",age );        
     for(i=1; i<=nlstate;i++)  #ifdef DEBUG
       for(j=1; j<=nlstate;j++){        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(ficresvij," %.4f", vareij[i][j][(int)age]);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       }  #endif
     fprintf(ficresvij,"\n");        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     free_matrix(gp,0,nhstepm,1,nlstate);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     free_matrix(gm,0,nhstepm,1,nlstate);          k=kmax;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        }
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          k=kmax; l=lmax*10.;
   } /* End age */        }
          else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   free_vector(xp,1,npar);          delts=delt;
   free_matrix(doldm,1,nlstate,1,npar);        }
   free_matrix(dnewm,1,nlstate,1,nlstate);      }
     }
 }    delti[theta]=delts;
     return res; 
 /************ Variance of prevlim ******************/    
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)  }
 {  
   /* Variance of prevalence limit */  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  {
   double **newm;    int i;
   double **dnewm,**doldm;    int l=1, l1, lmax=20;
   int i, j, nhstepm, hstepm;    double k1,k2,k3,k4,res,fx;
   int k, cptcode;    double p2[NPARMAX+1];
   double *xp;    int k;
   double *gp, *gm;  
   double **gradg, **trgradg;    fx=func(x);
   double age,agelim;    for (k=1; k<=2; k++) {
   int theta;      for (i=1;i<=npar;i++) p2[i]=x[i];
          p2[thetai]=x[thetai]+delti[thetai]/k;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   fprintf(ficresvpl,"# Age");      k1=func(p2)-fx;
   for(i=1; i<=nlstate;i++)    
       fprintf(ficresvpl," %1d-%1d",i,i);      p2[thetai]=x[thetai]+delti[thetai]/k;
   fprintf(ficresvpl,"\n");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
   xp=vector(1,npar);    
   dnewm=matrix(1,nlstate,1,npar);      p2[thetai]=x[thetai]-delti[thetai]/k;
   doldm=matrix(1,nlstate,1,nlstate);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
        k3=func(p2)-fx;
   hstepm=1*YEARM; /* Every year of age */    
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      p2[thetai]=x[thetai]-delti[thetai]/k;
   agelim = AGESUP;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      k4=func(p2)-fx;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     if (stepm >= YEARM) hstepm=1;  #ifdef DEBUG
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      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);
     gradg=matrix(1,npar,1,nlstate);      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     gp=vector(1,nlstate);  #endif
     gm=vector(1,nlstate);    }
     return res;
     for(theta=1; theta <=npar; theta++){  }
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  /************** Inverse of matrix **************/
       }  void ludcmp(double **a, int n, int *indx, double *d) 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  { 
       for(i=1;i<=nlstate;i++)    int i,imax,j,k; 
         gp[i] = prlim[i][i];    double big,dum,sum,temp; 
        double *vv; 
       for(i=1; i<=npar; i++) /* Computes gradient */   
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    vv=vector(1,n); 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    *d=1.0; 
       for(i=1;i<=nlstate;i++)    for (i=1;i<=n;i++) { 
         gm[i] = prlim[i][i];      big=0.0; 
       for (j=1;j<=n;j++) 
       for(i=1;i<=nlstate;i++)        if ((temp=fabs(a[i][j])) > big) big=temp; 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     } /* End theta */      vv[i]=1.0/big; 
     } 
     trgradg =matrix(1,nlstate,1,npar);    for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
     for(j=1; j<=nlstate;j++)        sum=a[i][j]; 
       for(theta=1; theta <=npar; theta++)        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         trgradg[j][theta]=gradg[theta][j];        a[i][j]=sum; 
       } 
     for(i=1;i<=nlstate;i++)      big=0.0; 
       varpl[i][(int)age] =0.;      for (i=j;i<=n;i++) { 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        sum=a[i][j]; 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        for (k=1;k<j;k++) 
     for(i=1;i<=nlstate;i++)          sum -= a[i][k]*a[k][j]; 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
     fprintf(ficresvpl,"%.0f ",age );          big=dum; 
     for(i=1; i<=nlstate;i++)          imax=i; 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        } 
     fprintf(ficresvpl,"\n");      } 
     free_vector(gp,1,nlstate);      if (j != imax) { 
     free_vector(gm,1,nlstate);        for (k=1;k<=n;k++) { 
     free_matrix(gradg,1,npar,1,nlstate);          dum=a[imax][k]; 
     free_matrix(trgradg,1,nlstate,1,npar);          a[imax][k]=a[j][k]; 
   } /* End age */          a[j][k]=dum; 
         } 
   free_vector(xp,1,npar);        *d = -(*d); 
   free_matrix(doldm,1,nlstate,1,npar);        vv[imax]=vv[j]; 
   free_matrix(dnewm,1,nlstate,1,nlstate);      } 
       indx[j]=imax; 
 }      if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
 /************ Variance of one-step probabilities  ******************/        dum=1.0/(a[j][j]); 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
 {      } 
   int i, j;    } 
   int k=0, cptcode;    free_vector(vv,1,n);  /* Doesn't work */
   double **dnewm,**doldm;  ;
   double *xp;  } 
   double *gp, *gm;  
   double **gradg, **trgradg;  void lubksb(double **a, int n, int *indx, double b[]) 
   double age,agelim, cov[NCOVMAX];  { 
   int theta;    int i,ii=0,ip,j; 
   char fileresprob[FILENAMELENGTH];    double sum; 
    
   strcpy(fileresprob,"prob");    for (i=1;i<=n;i++) { 
   strcat(fileresprob,fileres);      ip=indx[i]; 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      sum=b[ip]; 
     printf("Problem with resultfile: %s\n", fileresprob);      b[ip]=b[i]; 
   }      if (ii) 
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
        else if (sum) ii=i; 
       b[i]=sum; 
   xp=vector(1,npar);    } 
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    for (i=n;i>=1;i--) { 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      sum=b[i]; 
        for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   cov[1]=1;      b[i]=sum/a[i][i]; 
   for (age=bage; age<=fage; age ++){    } 
     cov[2]=age;  } 
     gradg=matrix(1,npar,1,9);  
     trgradg=matrix(1,9,1,npar);  /************ Frequencies ********************/
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  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)
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  {  /* Some frequencies */
        
     for(theta=1; theta <=npar; theta++){    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       for(i=1; i<=npar; i++)    int first;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double ***freq; /* Frequencies */
          double *pp, **prop;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
        FILE *ficresp;
       k=0;    char fileresp[FILENAMELENGTH];
       for(i=1; i<= (nlstate+ndeath); i++){    
         for(j=1; j<=(nlstate+ndeath);j++){    pp=vector(1,nlstate);
            k=k+1;    prop=matrix(1,nlstate,iagemin,iagemax+3);
           gp[k]=pmmij[i][j];    strcpy(fileresp,"p");
         }    strcat(fileresp,fileres);
       }    if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
       for(i=1; i<=npar; i++)      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      exit(0);
        }
     freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    j1=0;
       k=0;    
       for(i=1; i<=(nlstate+ndeath); i++){    j=cptcoveff;
         for(j=1; j<=(nlstate+ndeath);j++){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           k=k+1;  
           gm[k]=pmmij[i][j];    first=1;
         }  
       }    for(k1=1; k1<=j;k1++){
            for(i1=1; i1<=ncodemax[k1];i1++){
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        j1++;
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     }          scanf("%d", i);*/
         for (i=-1; i<=nlstate+ndeath; i++)  
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          for (jk=-1; jk<=nlstate+ndeath; jk++)  
       for(theta=1; theta <=npar; theta++)            for(m=iagemin; m <= iagemax+3; m++)
       trgradg[j][theta]=gradg[theta][j];              freq[i][jk][m]=0;
    
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      for (i=1; i<=nlstate; i++)  
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);        for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
      pmij(pmmij,cov,ncovmodel,x,nlstate);        
         dateintsum=0;
      k=0;        k2cpt=0;
      for(i=1; i<=(nlstate+ndeath); i++){        for (i=1; i<=imx; i++) {
        for(j=1; j<=(nlstate+ndeath);j++){          bool=1;
          k=k+1;          if  (cptcovn>0) {
          gm[k]=pmmij[i][j];            for (z1=1; z1<=cptcoveff; z1++) 
         }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
      }                bool=0;
                }
      /*printf("\n%d ",(int)age);          if (bool==1){
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){            for(m=firstpass; m<=lastpass; m++){
                      k2=anint[m][i]+(mint[m][i]/12.);
               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));                if(agev[m][i]==0) agev[m][i]=iagemax+1;
      }*/                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   fprintf(ficresprob,"\n%d ",(int)age);                if (m<lastpass) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);                }
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);                
   }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));                  k2cpt++;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));                }
     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);        }
 fclose(ficresprob);         
         /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
 }  
         if  (cptcovn>0) {
 /******************* Printing html file ***********/          fprintf(ficresp, "\n#********** Variable "); 
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  int lastpass, int stepm, int weightopt, char model[],\          fprintf(ficresp, "**********\n#");
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \        }
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\        for(i=1; i<=nlstate;i++) 
  char version[], int popforecast, int estepm ){          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   int jj1, k1, i1, cpt;        fprintf(ficresp, "\n");
   FILE *fichtm;        
   /*char optionfilehtm[FILENAMELENGTH];*/        for(i=iagemin; i <= iagemax+3; i++){
           if(i==iagemax+3){
   strcpy(optionfilehtm,optionfile);            fprintf(ficlog,"Total");
   strcat(optionfilehtm,".htm");          }else{
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {            if(first==1){
     printf("Problem with %s \n",optionfilehtm), exit(0);              first=0;
   }              printf("See log file for details...\n");
             }
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n            fprintf(ficlog,"Age %d", i);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n          }
 \n          for(jk=1; jk <=nlstate ; jk++){
 Total number of observations=%d <br>\n            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n              pp[jk] += freq[jk][m][i]; 
 <hr  size=\"2\" color=\"#EC5E5E\">          }
  <ul><li>Outputs files<br>\n          for(jk=1; jk <=nlstate ; jk++){
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n            for(m=-1, pos=0; m <=0 ; m++)
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n              pos += freq[jk][m][i];
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n            if(pp[jk]>=1.e-10){
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n              if(first==1){
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);              }
               fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
  fprintf(fichtm,"\n            }else{
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n              if(first==1)
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);            }
           }
  if(popforecast==1) fprintf(fichtm,"\n  
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n          for(jk=1; jk <=nlstate ; jk++){
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         <br>",fileres,fileres,fileres,fileres);              pp[jk] += freq[jk][m][i];
  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);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
 fprintf(fichtm," <li>Graphs</li><p>");            pos += pp[jk];
             posprop += prop[jk][i];
  m=cptcoveff;          }
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
  jj1=0;              if(first==1)
  for(k1=1; k1<=m;k1++){                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
    for(i1=1; i1<=ncodemax[k1];i1++){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
        jj1++;            }else{
        if (cptcovn > 0) {              if(first==1)
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
          for (cpt=1; cpt<=cptcoveff;cpt++)              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);            }
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");            if( i <= iagemax){
        }              if(pos>=1.e-5){
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                    /*probs[i][jk][j1]= pp[jk]/pos;*/
        for(cpt=1; cpt<nlstate;cpt++){                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>              }
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              else
        }                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     for(cpt=1; cpt<=nlstate;cpt++) {            }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          }
 interval) in state (%d): v%s%d%d.gif <br>          
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            for(jk=-1; jk <=nlstate+ndeath; jk++)
      }            for(m=-1; m <=nlstate+ndeath; m++)
      for(cpt=1; cpt<=nlstate;cpt++) {              if(freq[jk][m][i] !=0 ) {
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>              if(first==1)
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
      }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and              }
 health expectancies in states (1) and (2): e%s%d.gif<br>          if(i <= iagemax)
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            fprintf(ficresp,"\n");
 fprintf(fichtm,"\n</body>");          if(first==1)
    }            printf("Others in log...\n");
    }          fprintf(ficlog,"\n");
 fclose(fichtm);        }
 }      }
     }
 /******************* Gnuplot file **************/    dateintmean=dateintsum/k2cpt; 
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){   
     fclose(ficresp);
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
   strcpy(optionfilegnuplot,optionfilefiname);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   strcat(optionfilegnuplot,".gp.txt");    /* End of Freq */
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  }
     printf("Problem with file %s",optionfilegnuplot);  
   }  /************ 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)
 #ifdef windows  {  
     fprintf(ficgp,"cd \"%s\" \n",pathc);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
 #endif       in each health status at the date of interview (if between dateprev1 and dateprev2).
 m=pow(2,cptcoveff);       We still use firstpass and lastpass as another selection.
      */
  /* 1eme*/   
   for (cpt=1; cpt<= nlstate ; cpt ++) {    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
    for (k1=1; k1<= m ; k1 ++) {    double ***freq; /* Frequencies */
     double *pp, **prop;
 #ifdef windows    double pos,posprop; 
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);    double  y2; /* in fractional years */
 #endif    int iagemin, iagemax;
 #ifdef unix  
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    iagemin= (int) agemin;
 #endif    iagemax= (int) agemax;
     /*pp=vector(1,nlstate);*/
 for (i=1; i<= nlstate ; i ++) {    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");    j1=0;
 }    
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    j=cptcoveff;
     for (i=1; i<= nlstate ; i ++) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for(k1=1; k1<=j;k1++){
 }      for(i1=1; i1<=ncodemax[k1];i1++){
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        j1++;
      for (i=1; i<= nlstate ; i ++) {        
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for (i=1; i<=nlstate; i++)  
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(m=iagemin; m <= iagemax+3; m++)
 }              prop[i][m]=0.0;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));       
 #ifdef unix        for (i=1; i<=imx; i++) { /* Each individual */
 fprintf(ficgp,"\nset ter gif small size 400,300");          bool=1;
 #endif          if  (cptcovn>0) {
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            for (z1=1; z1<=cptcoveff; z1++) 
    }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   }                bool=0;
   /*2 eme*/          } 
           if (bool==1) { 
   for (k1=1; k1<= m ; k1 ++) {            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                  if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     for (i=1; i<= nlstate+1 ; i ++) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       k=2*i;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
       for (j=1; j<= nlstate+1 ; j ++) {                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                  /*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]]);*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
 }                    prop[s[m][i]][iagemax+3] += weight[i]; 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");                } 
       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);            } /* end selection of waves */
       for (j=1; j<= nlstate+1 ; j ++) {          }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        }
         else fprintf(ficgp," \%%*lf (\%%*lf)");        for(i=iagemin; i <= iagemax+3; i++){  
 }            
       fprintf(ficgp,"\" t\"\" w l 0,");          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);            posprop += prop[jk][i]; 
       for (j=1; j<= nlstate+1 ; j ++) {          } 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(jk=1; jk <=nlstate ; jk++){     
 }              if( i <=  iagemax){ 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");              if(posprop>=1.e-5){ 
       else fprintf(ficgp,"\" t\"\" w l 0,");                probs[i][jk][j1]= prop[jk][i]/posprop;
     }              } 
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);            } 
   }          }/* end jk */ 
          }/* end i */ 
   /*3eme*/      } /* end i1 */
     } /* end k1 */
   for (k1=1; k1<= m ; k1 ++) {    
     for (cpt=1; cpt<= nlstate ; cpt ++) {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
       k=2+nlstate*(cpt-1);    /*free_vector(pp,1,nlstate);*/
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       for (i=1; i< nlstate ; i ++) {  }  /* End of prevalence */
         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);  
       }  /************* Waves Concatenation ***************/
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }  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.
   /* CV preval stat */       Death is a valid wave (if date is known).
     for (k1=1; k1<= m ; k1 ++) {       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     for (cpt=1; cpt<nlstate ; cpt ++) {       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       k=3;       and mw[mi+1][i]. dh depends on stepm.
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);       */
   
       for (i=1; i< nlstate ; i ++)    int i, mi, m;
         fprintf(ficgp,"+$%d",k+i+1);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);       double sum=0., jmean=0.;*/
          int first;
       l=3+(nlstate+ndeath)*cpt;    int j, k=0,jk, ju, jl;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    double sum=0.;
       for (i=1; i< nlstate ; i ++) {    first=0;
         l=3+(nlstate+ndeath)*cpt;    jmin=1e+5;
         fprintf(ficgp,"+$%d",l+i+1);    jmax=-1;
       }    jmean=0.;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      for(i=1; i<=imx; i++){
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      mi=0;
     }      m=firstpass;
   }        while(s[m][i] <= nlstate){
          if(s[m][i]>=1)
   /* proba elementaires */          mw[++mi][i]=m;
    for(i=1,jk=1; i <=nlstate; i++){        if(m >=lastpass)
     for(k=1; k <=(nlstate+ndeath); k++){          break;
       if (k != i) {        else
         for(j=1; j <=ncovmodel; j++){          m++;
              }/* end while */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      if (s[m][i] > nlstate){
           jk++;        mi++;     /* Death is another wave */
           fprintf(ficgp,"\n");        /* if(mi==0)  never been interviewed correctly before death */
         }           /* Only death is a correct wave */
       }        mw[mi][i]=m;
     }      }
     }  
       wav[i]=mi;
     for(jk=1; jk <=m; jk++) {      if(mi==0){
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);        nbwarn++;
    i=1;        if(first==0){
    for(k2=1; k2<=nlstate; k2++) {          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
      k3=i;          first=1;
      for(k=1; k<=(nlstate+ndeath); k++) {        }
        if (k != k2){        if(first==1){
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
 ij=1;        }
         for(j=3; j <=ncovmodel; j++) {      } /* end mi==0 */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    } /* End individuals */
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;    for(i=1; i<=imx; i++){
           }      for(mi=1; mi<wav[i];mi++){
           else        if (stepm <=0)
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          dh[mi][i]=1;
         }        else{
           fprintf(ficgp,")/(1");          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                    if (agedc[i] < 2*AGESUP) {
         for(k1=1; k1 <=nlstate; k1++){                j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);              if(j==0) j=1;  /* Survives at least one month after exam */
 ij=1;              else if(j<0){
           for(j=3; j <=ncovmodel; j++){                nberr++;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                j=1; /* Temporary Dangerous patch */
             ij++;                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
           }                fprintf(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]);
           else                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              }
           }              k=k+1;
           fprintf(ficgp,")");              if (j >= jmax) jmax=j;
         }              if (j <= jmin) jmin=j;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);              sum=sum+j;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         i=i+ncovmodel;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
        }            }
      }          }
    }          else{
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
    }            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                k=k+1;
   fclose(ficgp);            if (j >= jmax) jmax=j;
 }  /* end gnuplot */            else if (j <= jmin)jmin=j;
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
 /*************** Moving average **************/            if(j<0){
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){              nberr++;
               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]);
   int i, cpt, cptcod;              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)            }
       for (i=1; i<=nlstate;i++)            sum=sum+j;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          }
           mobaverage[(int)agedeb][i][cptcod]=0.;          jk= j/stepm;
              jl= j -jk*stepm;
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          ju= j -(jk+1)*stepm;
       for (i=1; i<=nlstate;i++){          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            if(jl==0){
           for (cpt=0;cpt<=4;cpt++){              dh[mi][i]=jk;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];              bh[mi][i]=0;
           }            }else{ /* We want a negative bias in order to only have interpolation ie
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;                    * at the price of an extra matrix product in likelihood */
         }              dh[mi][i]=jk+1;
       }              bh[mi][i]=ju;
     }            }
              }else{
 }            if(jl <= -ju){
               dh[mi][i]=jk;
               bh[mi][i]=jl;       /* bias is positive if real duration
 /************** Forecasting ******************/                                   * is higher than the multiple of stepm and negative otherwise.
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){                                   */
              }
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            else{
   int *popage;              dh[mi][i]=jk+1;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;              bh[mi][i]=ju;
   double *popeffectif,*popcount;            }
   double ***p3mat;            if(dh[mi][i]==0){
   char fileresf[FILENAMELENGTH];              dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
  agelim=AGESUP;              /*  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);*/
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;            }
           } /* end if mle */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        }
        } /* end wave */
      }
   strcpy(fileresf,"f");    jmean=sum/k;
   strcat(fileresf,fileres);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     printf("Problem with forecast resultfile: %s\n", fileresf);   }
   }  
   printf("Computing forecasting: result on file '%s' \n", fileresf);  /*********** Tricode ****************************/
   void tricode(int *Tvar, int **nbcode, int imx)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  {
     
   if (mobilav==1) {    int Ndum[20],ij=1, k, j, i, maxncov=19;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int cptcode=0;
     movingaverage(agedeb, fage, ageminpar, mobaverage);    cptcoveff=0; 
   }   
     for (k=0; k<maxncov; k++) Ndum[k]=0;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    for (k=1; k<=7; k++) ncodemax[k]=0;
   if (stepm<=12) stepsize=1;  
      for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   agelim=AGESUP;      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                   modality*/ 
   hstepm=1;        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   hstepm=hstepm/stepm;        Ndum[ij]++; /*store the modality */
   yp1=modf(dateintmean,&yp);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   anprojmean=yp;        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   yp2=modf((yp1*12),&yp);                                         Tvar[j]. If V=sex and male is 0 and 
   mprojmean=yp;                                         female is 1, then  cptcode=1.*/
   yp1=modf((yp2*30.5),&yp);      }
   jprojmean=yp;  
   if(jprojmean==0) jprojmean=1;      for (i=0; i<=cptcode; i++) {
   if(mprojmean==0) jprojmean=1;        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
        }
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);  
        ij=1; 
   for(cptcov=1;cptcov<=i2;cptcov++){      for (i=1; i<=ncodemax[j]; i++) {
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        for (k=0; k<= maxncov; k++) {
       k=k+1;          if (Ndum[k] != 0) {
       fprintf(ficresf,"\n#******");            nbcode[Tvar[j]][ij]=k; 
       for(j=1;j<=cptcoveff;j++) {            /* 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; */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            
       }            ij++;
       fprintf(ficresf,"******\n");          }
       fprintf(ficresf,"# StartingAge FinalAge");          if (ij > ncodemax[j]) break; 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        }  
            } 
          }  
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {  
         fprintf(ficresf,"\n");   for (k=0; k< maxncov; k++) Ndum[k]=0;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    
    for (i=1; i<=ncovmodel-2; i++) { 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);     ij=Tvar[i];
           nhstepm = nhstepm/hstepm;     Ndum[ij]++;
             }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;   ij=1;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);     for (i=1; i<= maxncov; i++) {
             if((Ndum[i]!=0) && (i<=ncovcol)){
           for (h=0; h<=nhstepm; h++){       Tvaraff[ij]=i; /*For printing */
             if (h==(int) (calagedate+YEARM*cpt)) {       ij++;
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);     }
             }   }
             for(j=1; j<=nlstate+ndeath;j++) {   
               kk1=0.;kk2=0;   cptcoveff=ij-1; /*Number of simple covariates*/
               for(i=1; i<=nlstate;i++) {                }
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  /*********** Health Expectancies ****************/
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
                 }  
                  {
               }    /* Health expectancies */
               if (h==(int)(calagedate+12*cpt)){    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
                 fprintf(ficresf," %.3f", kk1);    double age, agelim, hf;
                            double ***p3mat,***varhe;
               }    double **dnewm,**doldm;
             }    double *xp;
           }    double **gp, **gm;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double ***gradg, ***trgradg;
         }    int theta;
       }  
     }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   }    xp=vector(1,npar);
            dnewm=matrix(1,nlstate*nlstate,1,npar);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
   fclose(ficresf);    fprintf(ficreseij,"# Health expectancies\n");
 }    fprintf(ficreseij,"# Age");
 /************** Forecasting ******************/    for(i=1; i<=nlstate;i++)
 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){      for(j=1; j<=nlstate;j++)
          fprintf(ficreseij," %1d-%1d (SE)",i,j);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    fprintf(ficreseij,"\n");
   int *popage;  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    if(estepm < stepm){
   double *popeffectif,*popcount;      printf ("Problem %d lower than %d\n",estepm, stepm);
   double ***p3mat,***tabpop,***tabpopprev;    }
   char filerespop[FILENAMELENGTH];    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * This is mainly to measure the difference between two models: for example
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * if stepm=24 months pijx are given only every 2 years and by summing them
   agelim=AGESUP;     * we are calculating an estimate of the Life Expectancy assuming a linear 
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;     * progression in between and thus overestimating or underestimating according
       * to the curvature of the survival function. If, for the same date, we 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       * to compare the new estimate of Life expectancy with the same linear 
       * hypothesis. A more precise result, taking into account a more precise
   strcpy(filerespop,"pop");     * curvature will be obtained if estepm is as small as stepm. */
   strcat(filerespop,fileres);  
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    /* For example we decided to compute the life expectancy with the smallest unit */
     printf("Problem with forecast resultfile: %s\n", filerespop);    /* 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 
   printf("Computing forecasting: result on file '%s' \n", filerespop);       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
   if (cptcoveff==0) ncodemax[cptcoveff]=1;       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   if (mobilav==1) {       survival function given by stepm (the optimization length). Unfortunately it
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       means that if the survival funtion is printed only each two years of age and if
     movingaverage(agedeb, fage, ageminpar, mobaverage);       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.
     */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   if (stepm<=12) stepsize=1;  
      agelim=AGESUP;
   agelim=AGESUP;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        /* nhstepm age range expressed in number of stepm */
   hstepm=1;      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   hstepm=hstepm/stepm;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        /* if (stepm >= YEARM) hstepm=1;*/
   if (popforecast==1) {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     if((ficpop=fopen(popfile,"r"))==NULL) {      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       printf("Problem with population file : %s\n",popfile);exit(0);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     }      gp=matrix(0,nhstepm,1,nlstate*nlstate);
     popage=ivector(0,AGESUP);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
     popeffectif=vector(0,AGESUP);  
     popcount=vector(0,AGESUP);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
             in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     i=1;        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;   
      
     imx=i;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];  
   }      /* Computing  Variances of health expectancies */
   
   for(cptcov=1;cptcov<=i2;cptcov++){       for(theta=1; theta <=npar; theta++){
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        for(i=1; i<=npar; i++){ 
       k=k+1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fprintf(ficrespop,"\n#******");        }
       for(j=1;j<=cptcoveff;j++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
       }        cptj=0;
       fprintf(ficrespop,"******\n");        for(j=1; j<= nlstate; j++){
       fprintf(ficrespop,"# Age");          for(i=1; i<=nlstate; i++){
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);            cptj=cptj+1;
       if (popforecast==1)  fprintf(ficrespop," [Population]");            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
                    gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       for (cpt=0; cpt<=0;cpt++) {            }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            }
                }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){       
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);       
           nhstepm = nhstepm/hstepm;        for(i=1; i<=npar; i++) 
                    xp[i] = x[i] - (i==theta ?delti[theta]:0);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           oldm=oldms;savm=savms;        
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          cptj=0;
                for(j=1; j<= nlstate; j++){
           for (h=0; h<=nhstepm; h++){          for(i=1;i<=nlstate;i++){
             if (h==(int) (calagedate+YEARM*cpt)) {            cptj=cptj+1;
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
             }  
             for(j=1; j<=nlstate+ndeath;j++) {              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
               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];        for(j=1; j<= nlstate*nlstate; j++)
                 else {          for(h=0; h<=nhstepm-1; h++){
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                 }          }
               }       } 
               if (h==(int)(calagedate+12*cpt)){     
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;  /* End theta */
                   /*fprintf(ficrespop," %.3f", kk1);  
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
               }  
             }       for(h=0; h<=nhstepm-1; h++)
             for(i=1; i<=nlstate;i++){        for(j=1; j<=nlstate*nlstate;j++)
               kk1=0.;          for(theta=1; theta <=npar; theta++)
                 for(j=1; j<=nlstate;j++){            trgradg[h][j][theta]=gradg[h][theta][j];
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];       
                 }  
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];       for(i=1;i<=nlstate*nlstate;i++)
             }        for(j=1;j<=nlstate*nlstate;j++)
           varhe[i][j][(int)age] =0.;
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)  
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);       printf("%d|",(int)age);fflush(stdout);
           }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       for(h=0;h<=nhstepm-1;h++){
         }        for(k=0;k<=nhstepm-1;k++){
       }          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   /******/          for(i=1;i<=nlstate*nlstate;i++)
             for(j=1;j<=nlstate*nlstate;j++)
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      /* Computing expectancies */
           nhstepm = nhstepm/hstepm;      for(i=1; i<=nlstate;i++)
                  for(j=1; j<=nlstate;j++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           oldm=oldms;savm=savms;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              
           for (h=0; h<=nhstepm; h++){  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          }
             }  
             for(j=1; j<=nlstate+ndeath;j++) {      fprintf(ficreseij,"%3.0f",age );
               kk1=0.;kk2=0;      cptj=0;
               for(i=1; i<=nlstate;i++) {                    for(i=1; i<=nlstate;i++)
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];            for(j=1; j<=nlstate;j++){
               }          cptj++;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
             }        }
           }      fprintf(ficreseij,"\n");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     
         }      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
    }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   }      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    }
     printf("\n");
   if (popforecast==1) {    fprintf(ficlog,"\n");
     free_ivector(popage,0,AGESUP);  
     free_vector(popeffectif,0,AGESUP);    free_vector(xp,1,npar);
     free_vector(popcount,0,AGESUP);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  }
   fclose(ficrespop);  
 }  /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
 /***********************************************/  {
 /**************** Main Program *****************/    /* Variance of health expectancies */
 /***********************************************/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
 int main(int argc, char *argv[])    double **dnewm,**doldm;
 {    double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    int k, cptcode;
   double agedeb, agefin,hf;    double *xp;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
   double fret;    double **gradgp, **trgradgp; /* for var p point j */
   double **xi,tmp,delta;    double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   double dum; /* Dummy variable */    double ***p3mat;
   double ***p3mat;    double age,agelim, hf;
   int *indx;    double ***mobaverage;
   char line[MAXLINE], linepar[MAXLINE];    int theta;
   char title[MAXLINE];    char digit[4];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    char digitp[25];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  
      char fileresprobmorprev[FILENAMELENGTH];
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  
     if(popbased==1){
   char filerest[FILENAMELENGTH];      if(mobilav!=0)
   char fileregp[FILENAMELENGTH];        strcpy(digitp,"-populbased-mobilav-");
   char popfile[FILENAMELENGTH];      else strcpy(digitp,"-populbased-nomobil-");
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    }
   int firstobs=1, lastobs=10;    else 
   int sdeb, sfin; /* Status at beginning and end */      strcpy(digitp,"-stablbased-");
   int c,  h , cpt,l;  
   int ju,jl, mi;    if (mobilav!=0) {
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   int mobilav=0,popforecast=0;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   int hstepm, nhstepm;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;      }
     }
   double bage, fage, age, agelim, agebase;  
   double ftolpl=FTOL;    strcpy(fileresprobmorprev,"prmorprev"); 
   double **prlim;    sprintf(digit,"%-d",ij);
   double *severity;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   double ***param; /* Matrix of parameters */    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   double  *p;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   double **matcov; /* Matrix of covariance */    strcat(fileresprobmorprev,fileres);
   double ***delti3; /* Scale */    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   double *delti; /* Scale */      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   double ***eij, ***vareij;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   double **varpl; /* Variances of prevalence limits by age */    }
   double *epj, vepp;    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   double kk1, kk2;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    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++){
   char version[80]="Imach version 0.8b, March 2002, INED-EUROREVES ";      fprintf(ficresprobmorprev," p.%-d SE",j);
   char *alph[]={"a","a","b","c","d","e"}, str[4];      for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
   char z[1]="c", occ;    fprintf(ficresprobmorprev,"\n");
 #include <sys/time.h>    fprintf(ficgp,"\n# Routine varevsij");
 #include <time.h>    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
    /*   } */
   /* long total_usecs;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   struct timeval start_time, end_time;  
      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");
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    fprintf(ficresvij,"# Age");
   getcwd(pathcd, size);    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
   printf("\n%s",version);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   if(argc <=1){    fprintf(ficresvij,"\n");
     printf("\nEnter the parameter file name: ");  
     scanf("%s",pathtot);    xp=vector(1,npar);
   }    dnewm=matrix(1,nlstate,1,npar);
   else{    doldm=matrix(1,nlstate,1,nlstate);
     strcpy(pathtot,argv[1]);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/  
   /*cygwin_split_path(pathtot,path,optionfile);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    gpp=vector(nlstate+1,nlstate+ndeath);
   /* cutv(path,optionfile,pathtot,'\\');*/    gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    if(estepm < stepm){
   chdir(path);      printf ("Problem %d lower than %d\n",estepm, stepm);
   replace(pathc,path);    }
     else  hstepm=estepm;   
 /*-------- arguments in the command line --------*/    /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   strcpy(fileres,"r");       nhstepm is the number of hstepm from age to agelim 
   strcat(fileres, optionfilefiname);       nstepm is the number of stepm from age to agelin. 
   strcat(fileres,".txt");    /* Other files have txt extension */       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
   /*---------arguments file --------*/    /* 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((ficpar=fopen(optionfile,"r"))==NULL)    {       means that if the survival funtion is printed every two years of age and if
     printf("Problem with optionfile %s\n",optionfile);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     goto end;       results. So we changed our mind and took the option of the best precision.
   }    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   strcpy(filereso,"o");    agelim = AGESUP;
   strcat(filereso,fileres);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   if((ficparo=fopen(filereso,"w"))==NULL) {      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   /* Reads comments: lines beginning with '#' */      gp=matrix(0,nhstepm,1,nlstate);
   while((c=getc(ficpar))=='#' && c!= EOF){      gm=matrix(0,nhstepm,1,nlstate);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  
     puts(line);      for(theta=1; theta <=npar; theta++){
     fputs(line,ficparo);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   ungetc(c,ficpar);        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   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);        if (popbased==1) {
 while((c=getc(ficpar))=='#' && c!= EOF){          if(mobilav ==0){
     ungetc(c,ficpar);            for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);              prlim[i][i]=probs[(int)age][i][ij];
     puts(line);          }else{ /* mobilav */ 
     fputs(line,ficparo);            for(i=1; i<=nlstate;i++)
   }              prlim[i][i]=mobaverage[(int)age][i][ij];
   ungetc(c,ficpar);          }
          }
        
   covar=matrix(0,NCOVMAX,1,n);        for(j=1; j<= nlstate; j++){
   cptcovn=0;          for(h=0; h<=nhstepm; h++){
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   ncovmodel=2+cptcovn;          }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        }
          /* This for computing probability of death (h=1 means
   /* Read guess parameters */           computed over hstepm matrices product = hstepm*stepm months) 
   /* Reads comments: lines beginning with '#' */           as a weighted average of prlim.
   while((c=getc(ficpar))=='#' && c!= EOF){        */
     ungetc(c,ficpar);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     fgets(line, MAXLINE, ficpar);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     puts(line);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     fputs(line,ficparo);        }    
   }        /* end probability of death */
   ungetc(c,ficpar);  
          for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     for(i=1; i <=nlstate; i++)        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     for(j=1; j <=nlstate+ndeath-1; j++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       fscanf(ficpar,"%1d%1d",&i1,&j1);   
       fprintf(ficparo,"%1d%1d",i1,j1);        if (popbased==1) {
       printf("%1d%1d",i,j);          if(mobilav ==0){
       for(k=1; k<=ncovmodel;k++){            for(i=1; i<=nlstate;i++)
         fscanf(ficpar," %lf",&param[i][j][k]);              prlim[i][i]=probs[(int)age][i][ij];
         printf(" %lf",param[i][j][k]);          }else{ /* mobilav */ 
         fprintf(ficparo," %lf",param[i][j][k]);            for(i=1; i<=nlstate;i++)
       }              prlim[i][i]=mobaverage[(int)age][i][ij];
       fscanf(ficpar,"\n");          }
       printf("\n");        }
       fprintf(ficparo,"\n");  
     }        for(j=1; j<= nlstate; j++){
            for(h=0; h<=nhstepm; h++){
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   p=param[1][1];          }
          }
   /* Reads comments: lines beginning with '#' */        /* This for computing probability of death (h=1 means
   while((c=getc(ficpar))=='#' && c!= EOF){           computed over hstepm matrices product = hstepm*stepm months) 
     ungetc(c,ficpar);           as a weighted average of prlim.
     fgets(line, MAXLINE, ficpar);        */
     puts(line);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     fputs(line,ficparo);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   ungetc(c,ficpar);        }    
         /* end probability of death */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        for(j=1; j<= nlstate; j++) /* vareij */
   for(i=1; i <=nlstate; i++){          for(h=0; h<=nhstepm; h++){
     for(j=1; j <=nlstate+ndeath-1; j++){            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       fscanf(ficpar,"%1d%1d",&i1,&j1);          }
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       for(k=1; k<=ncovmodel;k++){          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         fscanf(ficpar,"%le",&delti3[i][j][k]);        }
         printf(" %le",delti3[i][j][k]);  
         fprintf(ficparo," %le",delti3[i][j][k]);      } /* End theta */
       }  
       fscanf(ficpar,"\n");      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       printf("\n");  
       fprintf(ficparo,"\n");      for(h=0; h<=nhstepm; h++) /* veij */
     }        for(j=1; j<=nlstate;j++)
   }          for(theta=1; theta <=npar; theta++)
   delti=delti3[1][1];            trgradg[h][j][theta]=gradg[h][theta][j];
    
   /* Reads comments: lines beginning with '#' */      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   while((c=getc(ficpar))=='#' && c!= EOF){        for(theta=1; theta <=npar; theta++)
     ungetc(c,ficpar);          trgradgp[j][theta]=gradgp[theta][j];
     fgets(line, MAXLINE, ficpar);    
     puts(line);  
     fputs(line,ficparo);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   }      for(i=1;i<=nlstate;i++)
   ungetc(c,ficpar);        for(j=1;j<=nlstate;j++)
            vareij[i][j][(int)age] =0.;
   matcov=matrix(1,npar,1,npar);  
   for(i=1; i <=npar; i++){      for(h=0;h<=nhstepm;h++){
     fscanf(ficpar,"%s",&str);        for(k=0;k<=nhstepm;k++){
     printf("%s",str);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     fprintf(ficparo,"%s",str);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
     for(j=1; j <=i; j++){          for(i=1;i<=nlstate;i++)
       fscanf(ficpar," %le",&matcov[i][j]);            for(j=1;j<=nlstate;j++)
       printf(" %.5le",matcov[i][j]);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       fprintf(ficparo," %.5le",matcov[i][j]);        }
     }      }
     fscanf(ficpar,"\n");    
     printf("\n");      /* pptj */
     fprintf(ficparo,"\n");      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   }      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   for(i=1; i <=npar; i++)      for(j=nlstate+1;j<=nlstate+ndeath;j++)
     for(j=i+1;j<=npar;j++)        for(i=nlstate+1;i<=nlstate+ndeath;i++)
       matcov[i][j]=matcov[j][i];          varppt[j][i]=doldmp[j][i];
          /* end ppptj */
   printf("\n");      /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     /*-------- Rewriting paramater file ----------*/   
      strcpy(rfileres,"r");    /* "Rparameterfile */      if (popbased==1) {
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        if(mobilav ==0){
      strcat(rfileres,".");    /* */          for(i=1; i<=nlstate;i++)
      strcat(rfileres,optionfilext);    /* Other files have txt extension */            prlim[i][i]=probs[(int)age][i][ij];
     if((ficres =fopen(rfileres,"w"))==NULL) {        }else{ /* mobilav */ 
       printf("Problem writing new parameter file: %s\n", fileres);goto end;          for(i=1; i<=nlstate;i++)
     }            prlim[i][i]=mobaverage[(int)age][i][ij];
     fprintf(ficres,"#%s\n",version);        }
          }
     /*-------- data file ----------*/               
     if((fic=fopen(datafile,"r"))==NULL)    {      /* This for computing probability of death (h=1 means
       printf("Problem with datafile: %s\n", datafile);goto end;         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     }         as a weighted average of prlim.
       */
     n= lastobs;      for(j=nlstate+1;j<=nlstate+ndeath;j++){
     severity = vector(1,maxwav);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     outcome=imatrix(1,maxwav+1,1,n);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     num=ivector(1,n);      }    
     moisnais=vector(1,n);      /* end probability of death */
     annais=vector(1,n);  
     moisdc=vector(1,n);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     andc=vector(1,n);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     agedc=vector(1,n);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     cod=ivector(1,n);        for(i=1; i<=nlstate;i++){
     weight=vector(1,n);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     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);      fprintf(ficresprobmorprev,"\n");
     s=imatrix(1,maxwav+1,1,n);  
     adl=imatrix(1,maxwav+1,1,n);          fprintf(ficresvij,"%.0f ",age );
     tab=ivector(1,NCOVMAX);      for(i=1; i<=nlstate;i++)
     ncodemax=ivector(1,8);        for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     i=1;        }
     while (fgets(line, MAXLINE, fic) != NULL)    {      fprintf(ficresvij,"\n");
       if ((i >= firstobs) && (i <=lastobs)) {      free_matrix(gp,0,nhstepm,1,nlstate);
              free_matrix(gm,0,nhstepm,1,nlstate);
         for (j=maxwav;j>=1;j--){      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
           strcpy(line,stra);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    } /* End age */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    free_vector(gpp,nlstate+1,nlstate+ndeath);
         }    free_vector(gmp,nlstate+1,nlstate+ndeath);
            free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    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 */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
         for (j=ncovcol;j>=1;j--){    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
         }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
         num[i]=atol(stra);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
            fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    /*  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);
           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;}*/  */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
         i=i+1;    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
       }  
     }    free_vector(xp,1,npar);
     /* printf("ii=%d", ij);    free_matrix(doldm,1,nlstate,1,nlstate);
        scanf("%d",i);*/    free_matrix(dnewm,1,nlstate,1,npar);
   imx=i-1; /* Number of individuals */    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   /* for (i=1; i<=imx; i++){    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    fclose(ficresprobmorprev);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    fflush(ficgp);
     }*/    fflush(fichtm); 
    }  /* end varevsij */
   /* for (i=1; i<=imx; i++){  
      if (s[4][i]==9)  s[4][i]=-1;  /************ Variance of prevlim ******************/
      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]));}  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
   */  {
      /* Variance of prevalence limit */
   /* Calculation of the number of parameter from char model*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   Tvar=ivector(1,15);    double **newm;
   Tprod=ivector(1,15);    double **dnewm,**doldm;
   Tvaraff=ivector(1,15);    int i, j, nhstepm, hstepm;
   Tvard=imatrix(1,15,1,2);    int k, cptcode;
   Tage=ivector(1,15);          double *xp;
        double *gp, *gm;
   if (strlen(model) >1){    double **gradg, **trgradg;
     j=0, j1=0, k1=1, k2=1;    double age,agelim;
     j=nbocc(model,'+');    int theta;
     j1=nbocc(model,'*');     
     cptcovn=j+1;    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     cptcovprod=j1;    fprintf(ficresvpl,"# Age");
        for(i=1; i<=nlstate;i++)
     strcpy(modelsav,model);        fprintf(ficresvpl," %1d-%1d",i,i);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    fprintf(ficresvpl,"\n");
       printf("Error. Non available option model=%s ",model);  
       goto end;    xp=vector(1,npar);
     }    dnewm=matrix(1,nlstate,1,npar);
        doldm=matrix(1,nlstate,1,nlstate);
     for(i=(j+1); i>=1;i--){    
       cutv(stra,strb,modelsav,'+');    hstepm=1*YEARM; /* Every year of age */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    agelim = AGESUP;
       /*scanf("%d",i);*/    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       if (strchr(strb,'*')) {      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         cutv(strd,strc,strb,'*');      if (stepm >= YEARM) hstepm=1;
         if (strcmp(strc,"age")==0) {      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           cptcovprod--;      gradg=matrix(1,npar,1,nlstate);
           cutv(strb,stre,strd,'V');      gp=vector(1,nlstate);
           Tvar[i]=atoi(stre);      gm=vector(1,nlstate);
           cptcovage++;  
             Tage[cptcovage]=i;      for(theta=1; theta <=npar; theta++){
             /*printf("stre=%s ", stre);*/        for(i=1; i<=npar; i++){ /* Computes gradient */
         }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         else if (strcmp(strd,"age")==0) {        }
           cptcovprod--;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           cutv(strb,stre,strc,'V');        for(i=1;i<=nlstate;i++)
           Tvar[i]=atoi(stre);          gp[i] = prlim[i][i];
           cptcovage++;      
           Tage[cptcovage]=i;        for(i=1; i<=npar; i++) /* Computes gradient */
         }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         else {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           cutv(strb,stre,strc,'V');        for(i=1;i<=nlstate;i++)
           Tvar[i]=ncovcol+k1;          gm[i] = prlim[i][i];
           cutv(strb,strc,strd,'V');  
           Tprod[k1]=i;        for(i=1;i<=nlstate;i++)
           Tvard[k1][1]=atoi(strc);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
           Tvard[k1][2]=atoi(stre);      } /* End theta */
           Tvar[cptcovn+k2]=Tvard[k1][1];  
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      trgradg =matrix(1,nlstate,1,npar);
           for (k=1; k<=lastobs;k++)  
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      for(j=1; j<=nlstate;j++)
           k1++;        for(theta=1; theta <=npar; theta++)
           k2=k2+2;          trgradg[j][theta]=gradg[theta][j];
         }  
       }      for(i=1;i<=nlstate;i++)
       else {        varpl[i][(int)age] =0.;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
        /*  scanf("%d",i);*/      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       cutv(strd,strc,strb,'V');      for(i=1;i<=nlstate;i++)
       Tvar[i]=atoi(strc);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
       }  
       strcpy(modelsav,stra);        fprintf(ficresvpl,"%.0f ",age );
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      for(i=1; i<=nlstate;i++)
         scanf("%d",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);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      free_matrix(gradg,1,npar,1,nlstate);
   printf("cptcovprod=%d ", cptcovprod);      free_matrix(trgradg,1,nlstate,1,npar);
   scanf("%d ",i);*/    } /* End age */
     fclose(fic);  
     free_vector(xp,1,npar);
     /*  if(mle==1){*/    free_matrix(doldm,1,nlstate,1,npar);
     if (weightopt != 1) { /* Maximisation without weights*/    free_matrix(dnewm,1,nlstate,1,nlstate);
       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);  /************ 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)
     for (i=1; i<=imx; i++) {  {
       for(m=2; (m<= maxwav); m++) {    int i, j=0,  i1, k1, l1, t, tj;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    int k2, l2, j1,  z1;
          anint[m][i]=9999;    int k=0,l, cptcode;
          s[m][i]=-1;    int first=1, first1;
        }    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    double **dnewm,**doldm;
       }    double *xp;
     }    double *gp, *gm;
     double **gradg, **trgradg;
     for (i=1; i<=imx; i++)  {    double **mu;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    double age,agelim, cov[NCOVMAX];
       for(m=1; (m<= maxwav); m++){    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
         if(s[m][i] >0){    int theta;
           if (s[m][i] >= nlstate+1) {    char fileresprob[FILENAMELENGTH];
             if(agedc[i]>0)    char fileresprobcov[FILENAMELENGTH];
               if(moisdc[i]!=99 && andc[i]!=9999)    char fileresprobcor[FILENAMELENGTH];
                 agev[m][i]=agedc[i];  
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    double ***varpij;
            else {  
               if (andc[i]!=9999){    strcpy(fileresprob,"prob"); 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    strcat(fileresprob,fileres);
               agev[m][i]=-1;    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
               }      printf("Problem with resultfile: %s\n", fileresprob);
             }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
           }    }
           else if(s[m][i] !=9){ /* Should no more exist */    strcpy(fileresprobcov,"probcov"); 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    strcat(fileresprobcov,fileres);
             if(mint[m][i]==99 || anint[m][i]==9999)    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
               agev[m][i]=1;      printf("Problem with resultfile: %s\n", fileresprobcov);
             else if(agev[m][i] <agemin){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
               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);*/    strcpy(fileresprobcor,"probcor"); 
             }    strcat(fileresprobcor,fileres);
             else if(agev[m][i] >agemax){    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
               agemax=agev[m][i];      printf("Problem with resultfile: %s\n", fileresprobcor);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
             }    }
             /*agev[m][i]=anint[m][i]-annais[i];*/    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
             /*   agev[m][i] = age[i]+2*m;*/    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           }    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           else { /* =9 */    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
             agev[m][i]=1;    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
             s[m][i]=-1;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           }    
         }    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
         else /*= 0 Unknown */    fprintf(ficresprob,"# Age");
           agev[m][i]=1;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
       }    fprintf(ficresprobcov,"# Age");
        fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     }    fprintf(ficresprobcov,"# Age");
     for (i=1; i<=imx; i++)  {  
       for(m=1; (m<= maxwav); m++){  
         if (s[m][i] > (nlstate+ndeath)) {    for(i=1; i<=nlstate;i++)
           printf("Error: Wrong value in nlstate or ndeath\n");        for(j=1; j<=(nlstate+ndeath);j++){
           goto end;        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");
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
     free_vector(severity,1,maxwav);   */
     free_imatrix(outcome,1,maxwav+1,1,n);   xp=vector(1,npar);
     free_vector(moisnais,1,n);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(annais,1,n);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     /* free_matrix(mint,1,maxwav,1,n);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
        free_matrix(anint,1,maxwav,1,n);*/    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     free_vector(moisdc,1,n);    first=1;
     free_vector(andc,1,n);    fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
        fprintf(fichtm,"\n");
     wav=ivector(1,imx);  
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
        file %s<br>\n",optionfilehtmcov);
     /* Concatenates waves */    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  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");
     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. \
       Tcode=ivector(1,100);  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
       ncodemax[1]=1;  standard deviations wide on each axis. <br>\
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);   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>\
    codtab=imatrix(1,100,1,10);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
    h=0;  
    m=pow(2,cptcoveff);    cov[1]=1;
      tj=cptcoveff;
    for(k=1;k<=cptcoveff; k++){    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
      for(i=1; i <=(m/pow(2,k));i++){    j1=0;
        for(j=1; j <= ncodemax[k]; j++){    for(t=1; t<=tj;t++){
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      for(i1=1; i1<=ncodemax[t];i1++){ 
            h++;        j1++;
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;        if  (cptcovn>0) {
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/          fprintf(ficresprob, "\n#********** Variable "); 
          }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
        }          fprintf(ficresprob, "**********\n#\n");
      }          fprintf(ficresprobcov, "\n#********** Variable "); 
    }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);          fprintf(ficresprobcov, "**********\n#\n");
       codtab[1][2]=1;codtab[2][2]=2; */          
    /* for(i=1; i <=m ;i++){          fprintf(ficgp, "\n#********** Variable "); 
       for(k=1; k <=cptcovn; k++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);          fprintf(ficgp, "**********\n#\n");
       }          
       printf("\n");          
       }          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       scanf("%d",i);*/          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\">");
    /* Calculates basic frequencies. Computes observed prevalence at single age          
        and prints on file fileres'p'. */          fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
              fprintf(ficresprobcor, "**********\n#");    
            }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for (age=bage; age<=fage; age ++){ 
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          cov[2]=age;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for (k=1; k<=cptcovn;k++) {
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
                }
     /* For Powell, parameters are in a vector p[] starting at p[1]          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          for (k=1; k<=cptcovprod;k++)
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
     if(mle==1){          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     }          gp=vector(1,(nlstate)*(nlstate+ndeath));
              gm=vector(1,(nlstate)*(nlstate+ndeath));
     /*--------- 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);          for(theta=1; theta <=npar; theta++){
              for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
    jk=1;            
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            
    for(i=1,jk=1; i <=nlstate; i++){            k=0;
      for(k=1; k <=(nlstate+ndeath); k++){            for(i=1; i<= (nlstate); i++){
        if (k != i)              for(j=1; j<=(nlstate+ndeath);j++){
          {                k=k+1;
            printf("%d%d ",i,k);                gp[k]=pmmij[i][j];
            fprintf(ficres,"%1d%1d ",i,k);              }
            for(j=1; j <=ncovmodel; j++){            }
              printf("%f ",p[jk]);            
              fprintf(ficres,"%f ",p[jk]);            for(i=1; i<=npar; i++)
              jk++;              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
            }      
            printf("\n");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
            fprintf(ficres,"\n");            k=0;
          }            for(i=1; i<=(nlstate); i++){
      }              for(j=1; j<=(nlstate+ndeath);j++){
    }                k=k+1;
  if(mle==1){                gm[k]=pmmij[i][j];
     /* Computing hessian and covariance matrix */              }
     ftolhess=ftol; /* Usually correct */            }
     hesscov(matcov, p, npar, delti, ftolhess, func);       
  }            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     printf("# Scales (for hessian or gradient estimation)\n");          }
      for(i=1,jk=1; i <=nlstate; i++){  
       for(j=1; j <=nlstate+ndeath; j++){          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
         if (j!=i) {            for(theta=1; theta <=npar; theta++)
           fprintf(ficres,"%1d%1d",i,j);              trgradg[j][theta]=gradg[theta][j];
           printf("%1d%1d",i,j);          
           for(k=1; k<=ncovmodel;k++){          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
             printf(" %.5e",delti[jk]);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
             fprintf(ficres," %.5e",delti[jk]);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
             jk++;          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           }          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           printf("\n");          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           fprintf(ficres,"\n");  
         }          pmij(pmmij,cov,ncovmodel,x,nlstate);
       }          
      }          k=0;
              for(i=1; i<=(nlstate); i++){
     k=1;            for(j=1; j<=(nlstate+ndeath);j++){
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");              k=k+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");              mu[k][(int) age]=pmmij[i][j];
     for(i=1;i<=npar;i++){            }
       /*  if (k>nlstate) k=1;          }
       i1=(i-1)/(ncovmodel*nlstate)+1;          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
       printf("%s%d%d",alph[k],i1,tab[i]);*/              varpij[i][j][(int)age] = doldm[i][j];
       fprintf(ficres,"%3d",i);  
       printf("%3d",i);          /*printf("\n%d ",(int)age);
       for(j=1; j<=i;j++){            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         fprintf(ficres," %.5e",matcov[i][j]);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         printf(" %.5e",matcov[i][j]);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       }            }*/
       fprintf(ficres,"\n");  
       printf("\n");          fprintf(ficresprob,"\n%d ",(int)age);
       k++;          fprintf(ficresprobcov,"\n%d ",(int)age);
     }          fprintf(ficresprobcor,"\n%d ",(int)age);
      
     while((c=getc(ficpar))=='#' && c!= EOF){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
       ungetc(c,ficpar);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       fgets(line, MAXLINE, ficpar);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       puts(line);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
       fputs(line,ficparo);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     }          }
     ungetc(c,ficpar);          i=0;
     estepm=0;          for (k=1; k<=(nlstate);k++){
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);            for (l=1; l<=(nlstate+ndeath);l++){ 
     if (estepm==0 || estepm < stepm) estepm=stepm;              i=i++;
     if (fage <= 2) {              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
       bage = ageminpar;              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
       fage = agemaxpar;              for (j=1; j<=i;j++){
     }                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                    fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     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);          }/* end of loop for state */
          } /* end of loop for age */
     while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);        /* Confidence intervalle of pij  */
     fgets(line, MAXLINE, ficpar);        /*
     puts(line);          fprintf(ficgp,"\nset noparametric;unset label");
     fputs(line,ficparo);          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");
   ungetc(c,ficpar);          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);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        */
        
   while((c=getc(ficpar))=='#' && c!= EOF){        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     ungetc(c,ficpar);        first1=1;
     fgets(line, MAXLINE, ficpar);        for (k2=1; k2<=(nlstate);k2++){
     puts(line);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     fputs(line,ficparo);            if(l2==k2) continue;
   }            j=(k2-1)*(nlstate+ndeath)+l2;
   ungetc(c,ficpar);            for (k1=1; k1<=(nlstate);k1++){
                for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                i=(k1-1)*(nlstate+ndeath)+l1;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;                if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
   fscanf(ficpar,"pop_based=%d\n",&popbased);                  if ((int)age %5==0){
   fprintf(ficparo,"pop_based=%d\n",popbased);                      v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   fprintf(ficres,"pop_based=%d\n",popbased);                      v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                      cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   while((c=getc(ficpar))=='#' && c!= EOF){                    mu1=mu[i][(int) age]/stepm*YEARM ;
     ungetc(c,ficpar);                    mu2=mu[j][(int) age]/stepm*YEARM;
     fgets(line, MAXLINE, ficpar);                    c12=cv12/sqrt(v1*v2);
     puts(line);                    /* Computing eigen value of matrix of covariance */
     fputs(line,ficparo);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   }                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   ungetc(c,ficpar);                    /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   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);                    /*v21=sqrt(1.-v11*v11); *//* error */
 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);                    v21=(lc1-v1)/cv12*v11;
 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);                    v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
 while((c=getc(ficpar))=='#' && c!= EOF){                    if(first1==1){
     ungetc(c,ficpar);                      first1=0;
     fgets(line, MAXLINE, ficpar);                      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);
     puts(line);                    }
     fputs(line,ficparo);                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
   }                    /*printf(fignu*/
   ungetc(c,ficpar);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);                    if(first==1){
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                      first=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);                      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);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
 /*------------ gnuplot -------------*/   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                                subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
 /*------------ free_vector  -------------*/                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
  chdir(path);                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                        fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
  free_ivector(wav,1,imx);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                        fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
  free_ivector(num,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(agedc,1,n);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
  /*free_matrix(covar,1,NCOVMAX,1,n);*/                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
  fclose(ficparo);                    }else{
  fclose(ficres);                      first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
 /*--------- index.htm --------*/                      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);
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                                mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   /*--------------- Prevalence limit --------------*/                    }/* if first */
                    } /* age mod 5 */
   strcpy(filerespl,"pl");                } /* end loop age */
   strcat(filerespl,fileres);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {                first=1;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;              } /*l12 */
   }            } /* k12 */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          } /*l1 */
   fprintf(ficrespl,"#Prevalence limit\n");        }/* k1 */
   fprintf(ficrespl,"#Age ");      } /* loop covariates */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    }
   fprintf(ficrespl,"\n");    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
      free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   prlim=matrix(1,nlstate,1,nlstate);    free_vector(xp,1,npar);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fclose(ficresprob);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fclose(ficresprobcov);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fclose(ficresprobcor);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fflush(ficgp);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fflush(fichtmcov);
   k=0;  }
   agebase=ageminpar;  
   agelim=agemaxpar;  
   ftolpl=1.e-10;  /******************* Printing html file ***********/
   i1=cptcoveff;  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   if (cptcovn < 1){i1=1;}                    int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   for(cptcov=1;cptcov<=i1;cptcov++){                    int popforecast, int estepm ,\
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    double jprev1, double mprev1,double anprev1, \
         k=k+1;                    double jprev2, double mprev2,double anprev2){
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    int jj1, k1, i1, cpt;
         fprintf(ficrespl,"\n#******");  
         for(j=1;j<=cptcoveff;j++)     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
         fprintf(ficrespl,"******\n");             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
             fprintf(fichtm,"\
         for (age=agebase; age<=agelim; age++){   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
           fprintf(ficrespl,"%.0f",age );     fprintf(fichtm,"\
           for(i=1; i<=nlstate;i++)   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
           fprintf(ficrespl," %.5f", prlim[i][i]);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
           fprintf(ficrespl,"\n");     fprintf(fichtm,"\
         }   - Life expectancies by age and initial health status (estepm=%2d months): \
       }     <a href=\"%s\">%s</a> <br>\n</li>",
     }             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   fclose(ficrespl);  
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   /*------------- h Pij x at various ages ------------*/  
     m=cptcoveff;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;   jj1=0;
   }   for(k1=1; k1<=m;k1++){
   printf("Computing pij: result on file '%s' \n", filerespij);     for(i1=1; i1<=ncodemax[k1];i1++){
         jj1++;
   stepsize=(int) (stepm+YEARM-1)/YEARM;       if (cptcovn > 0) {
   /*if (stepm<=24) stepsize=2;*/         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
   agelim=AGESUP;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   hstepm=stepsize*YEARM; /* Every year of age */         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */       }
         /* Pij */
   k=0;       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(cptcov=1;cptcov<=i1;cptcov++){  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       /* Quasi-incidences */
       k=k+1;       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
         fprintf(ficrespij,"\n#****** ");   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
         for(j=1;j<=cptcoveff;j++)  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         /* Stable prevalence in each health state */
         fprintf(ficrespij,"******\n");         for(cpt=1; cpt<nlstate;cpt++){
                   fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */         }
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */       for(cpt=1; cpt<=nlstate;cpt++) {
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
           oldm=oldms;savm=savms;  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         }
           fprintf(ficrespij,"# Age");     } /* end i1 */
           for(i=1; i<=nlstate;i++)   }/* End k1 */
             for(j=1; j<=nlstate+ndeath;j++)   fprintf(fichtm,"</ul>");
               fprintf(ficrespij," %1d-%1d",i,j);  
           fprintf(ficrespij,"\n");  
           for (h=0; h<=nhstepm; h++){   fprintf(fichtm,"\
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  \n<br><li><h4> Result files (second order: variances)</h4>\n\
             for(i=1; i<=nlstate;i++)   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
               for(j=1; j<=nlstate+ndeath;j++)  
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
             fprintf(ficrespij,"\n");           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
           }   fprintf(fichtm,"\
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
           fprintf(ficrespij,"\n");           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
         }  
     }   fprintf(fichtm,"\
   }   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/   fprintf(fichtm,"\
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
   fclose(ficrespij);           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
   /*---------- Forecasting ------------------*/           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
   if((stepm == 1) && (strcmp(model,".")==0)){   fprintf(fichtm,"\
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
     free_matrix(mint,1,maxwav,1,n);  
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  /*  if(popforecast==1) fprintf(fichtm,"\n */
     free_vector(weight,1,n);}  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   else{  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
     erreur=108;  /*      <br>",fileres,fileres,fileres,fileres); */
     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);  /*  else  */
   }  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
     fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   /*---------- Health expectancies and variances ------------*/  
    m=cptcoveff;
   strcpy(filerest,"t");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   strcat(filerest,fileres);  
   if((ficrest=fopen(filerest,"w"))==NULL) {   jj1=0;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;   for(k1=1; k1<=m;k1++){
   }     for(i1=1; i1<=ncodemax[k1];i1++){
   printf("Computing Total LEs with variances: file '%s' \n", filerest);       jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   strcpy(filerese,"e");         for (cpt=1; cpt<=cptcoveff;cpt++) 
   strcat(filerese,fileres);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   if((ficreseij=fopen(filerese,"w"))==NULL) {         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);       }
   }       for(cpt=1; cpt<=nlstate;cpt++) {
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
  strcpy(fileresv,"v");  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
   strcat(fileresv,fileres);       }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  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("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);     } /* end i1 */
    }/* End k1 */
   k=0;   fprintf(fichtm,"</ul>");
   for(cptcov=1;cptcov<=i1;cptcov++){   fflush(fichtm);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  }
       k=k+1;  
       fprintf(ficrest,"\n#****** ");  /******************* Gnuplot file **************/
       for(j=1;j<=cptcoveff;j++)  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficrest,"******\n");    char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
       fprintf(ficreseij,"\n#****** ");    int ng;
       for(j=1;j<=cptcoveff;j++)  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*     printf("Problem with file %s",optionfilegnuplot); */
       fprintf(ficreseij,"******\n");  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
       fprintf(ficresvij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)    /*#ifdef windows */
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficgp,"cd \"%s\" \n",pathc);
       fprintf(ficresvij,"******\n");      /*#endif */
     m=pow(2,cptcoveff);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;    strcpy(dirfileres,optionfilefiname);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);      strcpy(optfileres,"vpl");
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);   /* 1eme*/
       oldm=oldms;savm=savms;    for (cpt=1; cpt<= nlstate ; cpt ++) {
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);     for (k1=1; k1<= m ; k1 ++) {
           fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \n\
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  set ylabel \"Probability\" \n\
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  set ter png small\n\
       fprintf(ficrest,"\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);
       epj=vector(1,nlstate+1);  
       for(age=bage; age <=fage ;age++){       for (i=1; i<= nlstate ; i ++) {
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         if (popbased==1) {         else fprintf(ficgp," \%%*lf (\%%*lf)");
           for(i=1; i<=nlstate;i++)       }
             prlim[i][i]=probs[(int)age][i][k];       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)");
         fprintf(ficrest," %4.0f",age);         else fprintf(ficgp," \%%*lf (\%%*lf)");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){       } 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
             epj[j] += prlim[i][i]*eij[i][j][(int)age];       for (i=1; i<= nlstate ; i ++) {
           }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           epj[nlstate+1] +=epj[j];         else fprintf(ficgp," \%%*lf (\%%*lf)");
         }       }  
         for(i=1, vepp=0.;i <=nlstate;i++)       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
           for(j=1;j <=nlstate;j++)     }
             vepp += vareij[i][j][(int)age];    }
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    /*2 eme*/
         for(j=1;j <=nlstate;j++){    
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    for (k1=1; k1<= m ; k1 ++) { 
         }      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
         fprintf(ficrest,"\n");      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);
   fclose(ficreseij);        for (j=1; j<= nlstate+1 ; j ++) {
   fclose(ficresvij);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   fclose(ficrest);          else fprintf(ficgp," \%%*lf (\%%*lf)");
   fclose(ficpar);        }   
   free_vector(epj,1,nlstate+1);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
          else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   /*------- Variance limit prevalence------*/          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
   strcpy(fileresvpl,"vpl");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   strcat(fileresvpl,fileres);          else fprintf(ficgp," \%%*lf (\%%*lf)");
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        }   
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        fprintf(ficgp,"\" t\"\" w l 0,");
     exit(0);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   }        for (j=1; j<= nlstate+1 ; j ++) {
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
   k=0;        }   
   for(cptcov=1;cptcov<=i1;cptcov++){        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        else fprintf(ficgp,"\" t\"\" w l 0,");
       k=k+1;      }
       fprintf(ficresvpl,"\n#****** ");    }
       for(j=1;j<=cptcoveff;j++)    
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /*3eme*/
       fprintf(ficresvpl,"******\n");    
          for (k1=1; k1<= m ; k1 ++) { 
       varpl=matrix(1,nlstate,(int) bage, (int) fage);      for (cpt=1; cpt<= nlstate ; cpt ++) {
       oldm=oldms;savm=savms;        k=2+nlstate*(2*cpt-2);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
     }        fprintf(ficgp,"set ter png small\n\
  }  set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
   fclose(ficresvpl);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   /*---------- End : free ----------------*/          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
            for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);          
          */
          for (i=1; i< nlstate ; i ++) {
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
   free_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(matcov,1,npar,1,npar);    
   free_vector(delti,1,npar);    /* CV preval stable (period) */
   free_matrix(agev,1,maxwav,1,imx);    for (k1=1; k1<= m ; k1 ++) { 
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
   if(erreur >0)        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
     printf("End of Imach with error or warning %d\n",erreur);        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   else   printf("End of Imach\n");  set ter png small\nset size 0.65,0.65\n\
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  unset log y\n\
    plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/        
   /*printf("Total time was %d uSec.\n", total_usecs);*/        for (i=1; i< nlstate ; i ++)
   /*------ End -----------*/          fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
  end:        l=3+(nlstate+ndeath)*cpt;
 #ifdef windows        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
   /* chdir(pathcd);*/        for (i=1; i< nlstate ; i ++) {
 #endif          l=3+(nlstate+ndeath)*cpt;
  /*system("wgnuplot graph.plt");*/          fprintf(ficgp,"+$%d",l+i+1);
  /*system("../gp37mgw/wgnuplot graph.plt");*/        }
  /*system("cd ../gp37mgw");*/        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      } 
  strcpy(plotcmd,GNUPLOTPROGRAM);    }  
  strcat(plotcmd," ");    
  strcat(plotcmd,optionfilegnuplot);    /* proba elementaires */
  system(plotcmd);    for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
 #ifdef windows        if (k != i) {
   while (z[0] != 'q') {          for(j=1; j <=ncovmodel; j++){
     /* chdir(path); */            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");            jk++; 
     scanf("%s",z);            fprintf(ficgp,"\n");
     if (z[0] == 'c') system("./imach");          }
     else if (z[0] == 'e') system(optionfilehtm);        }
     else if (z[0] == 'g') system(plotcmd);      }
     else if (z[0] == 'q') exit(0);     }
   }  
 #endif     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){
     int i;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
         for(j=0; line[j] != '\n';j++){  /* Untabifies line */
           if(line[j] == '\t')
             line[j] = ' ';
         }
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (j=1; j<=lastpass; j++)
           if (s[j][i]>nlstate) {
             dcwave[i]=j;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];agecens[i]=1.; 
           if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
           cens[i]=1;
           
           if (ageexmed[i]<1) cens[i]=-1;
           if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
   
       p[1]=0.1; p[2]=0.1;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow-mort"); 
     strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
     /*  for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     */
     fprintf(ficrespow,"\n");
   
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM,delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov);
     } /* Endof if mle==-3 */
   
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficrespl,"#Stable prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
   
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /*---------- Health expectancies and variances ------------*/
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total LEs with variances: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficreseij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
           }
   
    
           fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficreseij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of stable prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocaltime at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
     strcpy(plotcmd,"\"");
     strcat(plotcmd,pathimach);
     strcat(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd,"\"");
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     if((outcmd=system(plotcmd)) != 0){
       printf(" Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.38  
changed lines
  Added in v.1.103


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