Diff for /imach/src/imach.c between versions 1.30 and 1.101

version 1.30, 2002/03/08 16:17:18 version 1.101, 2004/09/15 10:38:38
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.101  2004/09/15 10:38:38  brouard
      Fix on curr_time
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.100  2004/07/12 18:29:06  brouard
   first survey ("cross") where individuals from different ages are    Add version for Mac OS X. Just define UNIX in Makefile
   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 1.99  2004/06/05 08:57:40  brouard
   second wave of interviews ("longitudinal") which measure each change    *** empty log message ***
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.98  2004/05/16 15:05:56  brouard
   model. More health states you consider, more time is necessary to reach the    New version 0.97 . First attempt to estimate force of mortality
   Maximum Likelihood of the parameters involved in the model.  The    directly from the data i.e. without the need of knowing the health
   simplest model is the multinomial logistic model where pij is the    state at each age, but using a Gompertz model: log u =a + b*age .
   probabibility to be observed in state j at the second wave    This is the basic analysis of mortality and should be done before any
   conditional to be observed in state i at the first wave. Therefore    other analysis, in order to test if the mortality estimated from the
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    cross-longitudinal survey is different from the mortality estimated
   'age' is age and 'sex' is a covariate. If you want to have a more    from other sources like vital statistic data.
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    The same imach parameter file can be used but the option for mle should be -3.
   you to do it.  More covariates you add, slower the  
   convergence.    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.
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    The output is very simple: only an estimate of the intercept and of
   identical for each individual. Also, if a individual missed an    the slope with 95% confident intervals.
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Current limitations:
     A) Even if you enter covariates, i.e. with the
   hPijx is the probability to be observed in state i at age x+h    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   conditional to the observed state i at age x. The delay 'h' can be    B) There is no computation of Life Expectancy nor Life Table.
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    Revision 1.97  2004/02/20 13:25:42  lievre
   semester or year) is model as a multinomial logistic.  The hPx    Version 0.96d. Population forecasting command line is (temporarily)
   matrix is simply the matrix product of nh*stepm elementary matrices    suppressed.
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Revision 1.96  2003/07/15 15:38:55  brouard
     * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   Also this programme outputs the covariance matrix of the parameters but also    rewritten within the same printf. Workaround: many printfs.
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.95  2003/07/08 07:54:34  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    * imach.c (Repository):
            Institut national d'études démographiques, Paris.    (Repository): Using imachwizard code to output a more meaningful covariance
   This software have been partly granted by Euro-REVES, a concerted action    matrix (cov(a12,c31) instead of numbers.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.94  2003/06/27 13:00:02  brouard
   software can be distributed freely for non commercial use. Latest version    Just cleaning
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.93  2003/06/25 16:33:55  brouard
      (Module): On windows (cygwin) function asctime_r doesn't
 #include <math.h>    exist so I changed back to asctime which exists.
 #include <stdio.h>    (Module): Version 0.96b
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 #define MAXLINE 256    exist so I changed back to asctime which exists.
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"  
 #define FILENAMELENGTH 80    Revision 1.91  2003/06/25 15:30:29  brouard
 /*#define DEBUG*/    * imach.c (Repository): Duplicated warning errors corrected.
 #define windows    (Repository): Elapsed time after each iteration is now output. It
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    helps to forecast when convergence will be reached. Elapsed time
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    is stamped in powell.  We created a new html file for the graphs
     concerning matrix of covariance. It has extension -cov.htm.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
 #define NINTERVMAX 8    mle=-1 a template is output in file "or"mypar.txt with the design
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    of the covariance matrix to be input.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.89  2003/06/24 12:30:52  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 1.88  2003/06/23 17:54:56  brouard
     * 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 erreur; /* Error number */  
 int nvar;    Revision 1.87  2003/06/18 12:26:01  brouard
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Version 0.96
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Revision 1.86  2003/06/17 20:04:08  brouard
 int ndeath=1; /* Number of dead states */    (Module): Change position of html and gnuplot routines and added
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    routine fileappend.
 int popbased=0;  
     Revision 1.85  2003/06/17 13:12:43  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    * imach.c (Repository): Check when date of death was earlier that
 int maxwav; /* Maxim number of waves */    current date of interview. It may happen when the death was just
 int jmin, jmax; /* min, max spacing between 2 waves */    prior to the death. In this case, dh was negative and likelihood
 int mle, weightopt;    was wrong (infinity). We still send an "Error" but patch by
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    assuming that the date of death was just one stepm after the
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    interview.
 double jmean; /* Mean space between 2 waves */    (Repository): Because some people have very long ID (first column)
 double **oldm, **newm, **savm; /* Working pointers to matrices */    we changed int to long in num[] and we added a new lvector for
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    memory allocation. But we also truncated to 8 characters (left
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    truncation)
 FILE *ficgp,*ficresprob,*ficpop;    (Repository): No more line truncation errors.
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.84  2003/06/13 21:44:43  brouard
  FILE  *ficresvij;    * imach.c (Repository): Replace "freqsummary" at a correct
   char fileresv[FILENAMELENGTH];    place. It differs from routine "prevalence" which may be called
  FILE  *ficresvpl;    many times. Probs is memory consuming and must be used with
   char fileresvpl[FILENAMELENGTH];    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.83  2003/06/10 13:39:11  lievre
 #define FTOL 1.0e-10    *** empty log message ***
   
 #define NRANSI    Revision 1.82  2003/06/05 15:57:20  brouard
 #define ITMAX 200    Add log in  imach.c and  fullversion number is now printed.
   
 #define TOL 2.0e-4  */
   /*
 #define CGOLD 0.3819660     Interpolated Markov Chain
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Short summary of the programme:
     
 #define GOLD 1.618034    This program computes Healthy Life Expectancies from
 #define GLIMIT 100.0    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #define TINY 1.0e-20    first survey ("cross") where individuals from different ages are
     interviewed on their health status or degree of disability (in the
 static double maxarg1,maxarg2;    case of a health survey which is our main interest) -2- at least a
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    second wave of interviews ("longitudinal") which measure each change
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    (if any) in individual health status.  Health expectancies are
      computed from the time spent in each health state according to a
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    model. More health states you consider, more time is necessary to reach the
 #define rint(a) floor(a+0.5)    Maximum Likelihood of the parameters involved in the model.  The
     simplest model is the multinomial logistic model where pij is the
 static double sqrarg;    probability to be observed in state j at the second wave
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    conditional to be observed in state i at the first wave. Therefore
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     'age' is age and 'sex' is a covariate. If you want to have a more
 int imx;    complex model than "constant and age", you should modify the program
 int stepm;    where the markup *Covariates have to be included here again* invites
 /* Stepm, step in month: minimum step interpolation*/    you to do it.  More covariates you add, slower the
     convergence.
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    The advantage of this computer programme, compared to a simple
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    multinomial logistic model, is clear when the delay between waves is not
 double **pmmij, ***probs, ***mobaverage;    identical for each individual. Also, if a individual missed an
 double dateintmean=0;    intermediate interview, the information is lost, but taken into
     account using an interpolation or extrapolation.  
 double *weight;  
 int **s; /* Status */    hPijx is the probability to be observed in state i at age x+h
 double *agedc, **covar, idx;    conditional to the observed state i at age x. The delay 'h' can be
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    semester or year) is modelled as a multinomial logistic.  The hPx
 double ftolhess; /* Tolerance for computing hessian */    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
 /**************** split *************************/    hPijx.
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    Also this programme outputs the covariance matrix of the parameters but also
    char *s;                             /* pointer */    of the life expectancies. It also computes the stable prevalence. 
    int  l1, l2;                         /* length counters */    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
    l1 = strlen( path );                 /* length of path */             Institut national d'études démographiques, Paris.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    This software have been partly granted by Euro-REVES, a concerted action
 #ifdef windows    from the European Union.
    s = strrchr( path, '\\' );           /* find last / */    It is copyrighted identically to a GNU software product, ie programme and
 #else    software can be distributed freely for non commercial use. Latest version
    s = strrchr( path, '/' );            /* find last / */    can be accessed at http://euroreves.ined.fr/imach .
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #if     defined(__bsd__)                /* get current working directory */    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
       extern char       *getwd( );    
     **********************************************************************/
       if ( getwd( dirc ) == NULL ) {  /*
 #else    main
       extern char       *getcwd( );    read parameterfile
     read datafile
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    concatwav
 #endif    freqsummary
          return( GLOCK_ERROR_GETCWD );    if (mle >= 1)
       }      mlikeli
       strcpy( name, path );             /* we've got it */    print results files
    } else {                             /* strip direcotry from path */    if mle==1 
       s++;                              /* after this, the filename */       computes hessian
       l2 = strlen( s );                 /* length of filename */    read end of parameter file: agemin, agemax, bage, fage, estepm
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );        begin-prev-date,...
       strcpy( name, s );                /* save file name */    open gnuplot file
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    open html file
       dirc[l1-l2] = 0;                  /* add zero */    stable prevalence
    }     for age prevalim()
    l1 = strlen( dirc );                 /* length of directory */    h Pij x
 #ifdef windows    variance of p varprob
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    forecasting if prevfcast==1 prevforecast call prevalence()
 #else    health expectancies
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    Variance-covariance of DFLE
 #endif    prevalence()
    s = strrchr( name, '.' );            /* find last / */     movingaverage()
    s++;    varevsij() 
    strcpy(ext,s);                       /* save extension */    if popbased==1 varevsij(,popbased)
    l1= strlen( name);    total life expectancies
    l2= strlen( s)+1;    Variance of stable prevalence
    strncpy( finame, name, l1-l2);   end
    finame[l1-l2]= 0;  */
    return( 0 );                         /* we're done */  
 }  
   
    
 /******************************************/  #include <math.h>
   #include <stdio.h>
 void replace(char *s, char*t)  #include <stdlib.h>
 {  #include <unistd.h>
   int i;  
   int lg=20;  /* #include <sys/time.h> */
   i=0;  #include <time.h>
   lg=strlen(t);  #include "timeval.h"
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);  /* #include <libintl.h> */
     if (t[i]== '\\') s[i]='/';  /* #define _(String) gettext (String) */
   }  
 }  #define MAXLINE 256
   #define GNUPLOTPROGRAM "gnuplot"
 int nbocc(char *s, char occ)  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 {  #define FILENAMELENGTH 132
   int i,j=0;  /*#define DEBUG*/
   int lg=20;  /*#define windows*/
   i=0;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   lg=strlen(s);  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   }  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   return j;  
 }  #define NINTERVMAX 8
   #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 void cutv(char *u,char *v, char*t, char occ)  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 {  #define NCOVMAX 8 /* Maximum number of covariates */
   int i,lg,j,p=0;  #define MAXN 20000
   i=0;  #define YEARM 12. /* Number of months per year */
   for(j=0; j<=strlen(t)-1; j++) {  #define AGESUP 130
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  #define AGEBASE 40
   }  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   #ifdef UNIX
   lg=strlen(t);  #define DIRSEPARATOR '/'
   for(j=0; j<p; j++) {  #define ODIRSEPARATOR '\\'
     (u[j] = t[j]);  #else
   }  #define DIRSEPARATOR '\\'
      u[p]='\0';  #define ODIRSEPARATOR '/'
   #endif
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);  /* $Id$ */
   }  /* $State$ */
 }  
   char version[]="Imach version 0.97b, May 2004, INED-EUROREVES ";
 /********************** nrerror ********************/  char fullversion[]="$Revision$ $Date$"; 
   int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 void nrerror(char error_text[])  int nvar;
 {  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   fprintf(stderr,"ERREUR ...\n");  int npar=NPARMAX;
   fprintf(stderr,"%s\n",error_text);  int nlstate=2; /* Number of live states */
   exit(1);  int ndeath=1; /* Number of dead states */
 }  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 /*********************** vector *******************/  int popbased=0;
 double *vector(int nl, int nh)  
 {  int *wav; /* Number of waves for this individuual 0 is possible */
   double *v;  int maxwav; /* Maxim number of waves */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  int jmin, jmax; /* min, max spacing between 2 waves */
   if (!v) nrerror("allocation failure in vector");  int gipmx, gsw; /* Global variables on the number of contributions 
   return v-nl+NR_END;                     to the likelihood and the sum of weights (done by funcone)*/
 }  int mle, weightopt;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 /************************ free vector ******************/  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 void free_vector(double*v, int nl, int nh)  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. */
   free((FREE_ARG)(v+nl-NR_END));  double jmean; /* Mean space between 2 waves */
 }  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 /************************ivector *******************************/  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 int *ivector(long nl,long nh)  FILE *ficlog, *ficrespow;
 {  int globpr; /* Global variable for printing or not */
   int *v;  double fretone; /* Only one call to likelihood */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  long ipmx; /* Number of contributions */
   if (!v) nrerror("allocation failure in ivector");  double sw; /* Sum of weights */
   return v-nl+NR_END;  char filerespow[FILENAMELENGTH];
 }  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   FILE *ficresilk;
 /******************free ivector **************************/  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 void free_ivector(int *v, long nl, long nh)  FILE *ficresprobmorprev;
 {  FILE *fichtm, *fichtmcov; /* Html File */
   free((FREE_ARG)(v+nl-NR_END));  FILE *ficreseij;
 }  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
 /******************* imatrix *******************************/  char fileresv[FILENAMELENGTH];
 int **imatrix(long nrl, long nrh, long ncl, long nch)  FILE  *ficresvpl;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  char fileresvpl[FILENAMELENGTH];
 {  char title[MAXLINE];
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   int **m;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
    char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   /* allocate pointers to rows */  char command[FILENAMELENGTH];
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  int  outcmd=0;
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   m -= nrl;  
    char filelog[FILENAMELENGTH]; /* Log file */
    char filerest[FILENAMELENGTH];
   /* allocate rows and set pointers to them */  char fileregp[FILENAMELENGTH];
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  char popfile[FILENAMELENGTH];
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   m[nrl] -= ncl;  
    struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  struct timezone tzp;
    extern int gettimeofday();
   /* return pointer to array of pointers to rows */  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   return m;  long time_value;
 }  extern long time();
   char strcurr[80], strfor[80];
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)  #define NR_END 1
       int **m;  #define FREE_ARG char*
       long nch,ncl,nrh,nrl;  #define FTOL 1.0e-10
      /* free an int matrix allocated by imatrix() */  
 {  #define NRANSI 
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #define ITMAX 200 
   free((FREE_ARG) (m+nrl-NR_END));  
 }  #define TOL 2.0e-4 
   
 /******************* matrix *******************************/  #define CGOLD 0.3819660 
 double **matrix(long nrl, long nrh, long ncl, long nch)  #define ZEPS 1.0e-10 
 {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;  #define GOLD 1.618034 
   #define GLIMIT 100.0 
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define TINY 1.0e-20 
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  static double maxarg1,maxarg2;
   m -= nrl;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   m[nrl] += NR_END;  #define rint(a) floor(a+0.5)
   m[nrl] -= ncl;  
   static double sqrarg;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   return m;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 }  int agegomp= AGEGOMP;
   
 /*************************free matrix ************************/  int imx; 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  int stepm=1;
 {  /* Stepm, step in month: minimum step interpolation*/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  int estepm;
 }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
 /******************* ma3x *******************************/  int m,nb;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  long *num;
 {  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double ***m;  double **pmmij, ***probs;
   double *ageexmed,*agecens;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  double dateintmean=0;
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  double *weight;
   m -= nrl;  int **s; /* Status */
   double *agedc, **covar, idx;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   m[nrl] -= ncl;  double ftolhess; /* Tolerance for computing hessian */
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  {
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
   m[nrl][ncl] += NR_END;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   m[nrl][ncl] -= nll;    */ 
   for (j=ncl+1; j<=nch; j++)    char  *ss;                            /* pointer */
     m[nrl][j]=m[nrl][j-1]+nlay;    int   l1, l2;                         /* length counters */
    
   for (i=nrl+1; i<=nrh; i++) {    l1 = strlen(path );                   /* length of path */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     for (j=ncl+1; j<=nch; j++)    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       m[i][j]=m[i][j-1]+nlay;    if ( ss == NULL ) {                   /* no directory, so use current */
   }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   return m;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 }      /* get current working directory */
       /*    extern  char* getcwd ( char *buf , int len);*/
 /*************************free ma3x ************************/      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)        return( GLOCK_ERROR_GETCWD );
 {      }
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));      strcpy( name, path );               /* we've got it */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    } else {                              /* strip direcotry from path */
   free((FREE_ARG)(m+nrl-NR_END));      ss++;                               /* after this, the filename */
 }      l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 /***************** f1dim *************************/      strcpy( name, ss );         /* save file name */
 extern int ncom;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 extern double *pcom,*xicom;      dirc[l1-l2] = 0;                    /* add zero */
 extern double (*nrfunc)(double []);    }
      l1 = strlen( dirc );                  /* length of directory */
 double f1dim(double x)    /*#ifdef windows
 {    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   int j;  #else
   double f;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   double *xt;  #endif
      */
   xt=vector(1,ncom);    ss = strrchr( name, '.' );            /* find last / */
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    if (ss >0){
   f=(*nrfunc)(xt);      ss++;
   free_vector(xt,1,ncom);      strcpy(ext,ss);                     /* save extension */
   return f;      l1= strlen( name);
 }      l2= strlen(ss)+1;
       strncpy( finame, name, l1-l2);
 /*****************brent *************************/      finame[l1-l2]= 0;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    }
 {    return( 0 );                          /* we're done */
   int iter;  }
   double a,b,d,etemp;  
   double fu,fv,fw,fx;  
   double ftemp;  /******************************************/
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  void replace_back_to_slash(char *s, char*t)
    {
   a=(ax < cx ? ax : cx);    int i;
   b=(ax > cx ? ax : cx);    int lg=0;
   x=w=v=bx;    i=0;
   fw=fv=fx=(*f)(x);    lg=strlen(t);
   for (iter=1;iter<=ITMAX;iter++) {    for(i=0; i<= lg; i++) {
     xm=0.5*(a+b);      (s[i] = t[i]);
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);      if (t[i]== '\\') s[i]='/';
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    }
     printf(".");fflush(stdout);  }
 #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);  int nbocc(char *s, char occ)
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  {
 #endif    int i,j=0;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    int lg=20;
       *xmin=x;    i=0;
       return fx;    lg=strlen(s);
     }    for(i=0; i<= lg; i++) {
     ftemp=fu;    if  (s[i] == occ ) j++;
     if (fabs(e) > tol1) {    }
       r=(x-w)*(fx-fv);    return j;
       q=(x-v)*(fx-fw);  }
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);  void cutv(char *u,char *v, char*t, char occ)
       if (q > 0.0) p = -p;  {
       q=fabs(q);    /* cuts string t into u and v where u is ended by char occ excluding it
       etemp=e;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
       e=d;       gives u="abcedf" and v="ghi2j" */
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    int i,lg,j,p=0;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    i=0;
       else {    for(j=0; j<=strlen(t)-1; j++) {
         d=p/q;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
         u=x+d;    }
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);    lg=strlen(t);
       }    for(j=0; j<p; j++) {
     } else {      (u[j] = t[j]);
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    }
     }       u[p]='\0';
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);     for(j=0; j<= lg; j++) {
     if (fu <= fx) {      if (j>=(p+1))(v[j-p-1] = t[j]);
       if (u >= x) a=x; else b=x;    }
       SHFT(v,w,x,u)  }
         SHFT(fv,fw,fx,fu)  
         } else {  /********************** nrerror ********************/
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  void nrerror(char error_text[])
             v=w;  {
             w=u;    fprintf(stderr,"ERREUR ...\n");
             fv=fw;    fprintf(stderr,"%s\n",error_text);
             fw=fu;    exit(EXIT_FAILURE);
           } else if (fu <= fv || v == x || v == w) {  }
             v=u;  /*********************** vector *******************/
             fv=fu;  double *vector(int nl, int nh)
           }  {
         }    double *v;
   }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   nrerror("Too many iterations in brent");    if (!v) nrerror("allocation failure in vector");
   *xmin=x;    return v-nl+NR_END;
   return fx;  }
 }  
   /************************ free vector ******************/
 /****************** mnbrak ***********************/  void free_vector(double*v, int nl, int nh)
   {
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    free((FREE_ARG)(v+nl-NR_END));
             double (*func)(double))  }
 {  
   double ulim,u,r,q, dum;  /************************ivector *******************************/
   double fu;  int *ivector(long nl,long nh)
    {
   *fa=(*func)(*ax);    int *v;
   *fb=(*func)(*bx);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   if (*fb > *fa) {    if (!v) nrerror("allocation failure in ivector");
     SHFT(dum,*ax,*bx,dum)    return v-nl+NR_END;
       SHFT(dum,*fb,*fa,dum)  }
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);  /******************free ivector **************************/
   *fc=(*func)(*cx);  void free_ivector(int *v, long nl, long nh)
   while (*fb > *fc) {  {
     r=(*bx-*ax)*(*fb-*fc);    free((FREE_ARG)(v+nl-NR_END));
     q=(*bx-*cx)*(*fb-*fa);  }
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  /************************lvector *******************************/
     ulim=(*bx)+GLIMIT*(*cx-*bx);  long *lvector(long nl,long nh)
     if ((*bx-u)*(u-*cx) > 0.0) {  {
       fu=(*func)(u);    long *v;
     } else if ((*cx-u)*(u-ulim) > 0.0) {    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       fu=(*func)(u);    if (!v) nrerror("allocation failure in ivector");
       if (fu < *fc) {    return v-nl+NR_END;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  }
           SHFT(*fb,*fc,fu,(*func)(u))  
           }  /******************free lvector **************************/
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  void free_lvector(long *v, long nl, long nh)
       u=ulim;  {
       fu=(*func)(u);    free((FREE_ARG)(v+nl-NR_END));
     } else {  }
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);  /******************* imatrix *******************************/
     }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     SHFT(*ax,*bx,*cx,u)       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       SHFT(*fa,*fb,*fc,fu)  { 
       }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 }    int **m; 
     
 /*************** linmin ************************/    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 int ncom;    if (!m) nrerror("allocation failure 1 in matrix()"); 
 double *pcom,*xicom;    m += NR_END; 
 double (*nrfunc)(double []);    m -= nrl; 
      
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    
 {    /* allocate rows and set pointers to them */ 
   double brent(double ax, double bx, double cx,    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
                double (*f)(double), double tol, double *xmin);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   double f1dim(double x);    m[nrl] += NR_END; 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    m[nrl] -= ncl; 
               double *fc, double (*func)(double));    
   int j;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   double xx,xmin,bx,ax;    
   double fx,fb,fa;    /* return pointer to array of pointers to rows */ 
      return m; 
   ncom=n;  } 
   pcom=vector(1,n);  
   xicom=vector(1,n);  /****************** free_imatrix *************************/
   nrfunc=func;  void free_imatrix(m,nrl,nrh,ncl,nch)
   for (j=1;j<=n;j++) {        int **m;
     pcom[j]=p[j];        long nch,ncl,nrh,nrl; 
     xicom[j]=xi[j];       /* free an int matrix allocated by imatrix() */ 
   }  { 
   ax=0.0;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   xx=1.0;    free((FREE_ARG) (m+nrl-NR_END)); 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  } 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  /******************* matrix *******************************/
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  double **matrix(long nrl, long nrh, long ncl, long nch)
 #endif  {
   for (j=1;j<=n;j++) {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     xi[j] *= xmin;    double **m;
     p[j] += xi[j];  
   }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   free_vector(xicom,1,n);    if (!m) nrerror("allocation failure 1 in matrix()");
   free_vector(pcom,1,n);    m += NR_END;
 }    m -= nrl;
   
 /*************** powell ************************/    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
             double (*func)(double []))    m[nrl] += NR_END;
 {    m[nrl] -= ncl;
   void linmin(double p[], double xi[], int n, double *fret,  
               double (*func)(double []));    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   int i,ibig,j;    return m;
   double del,t,*pt,*ptt,*xit;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   double fp,fptt;     */
   double *xits;  }
   pt=vector(1,n);  
   ptt=vector(1,n);  /*************************free matrix ************************/
   xit=vector(1,n);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   xits=vector(1,n);  {
   *fret=(*func)(p);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   for (j=1;j<=n;j++) pt[j]=p[j];    free((FREE_ARG)(m+nrl-NR_END));
   for (*iter=1;;++(*iter)) {  }
     fp=(*fret);  
     ibig=0;  /******************* ma3x *******************************/
     del=0.0;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  {
     for (i=1;i<=n;i++)    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       printf(" %d %.12f",i, p[i]);    double ***m;
     printf("\n");  
     for (i=1;i<=n;i++) {    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    if (!m) nrerror("allocation failure 1 in matrix()");
       fptt=(*fret);    m += NR_END;
 #ifdef DEBUG    m -= nrl;
       printf("fret=%lf \n",*fret);  
 #endif    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       printf("%d",i);fflush(stdout);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       linmin(p,xit,n,fret,func);    m[nrl] += NR_END;
       if (fabs(fptt-(*fret)) > del) {    m[nrl] -= ncl;
         del=fabs(fptt-(*fret));  
         ibig=i;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       }  
 #ifdef DEBUG    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       printf("%d %.12e",i,(*fret));    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       for (j=1;j<=n;j++) {    m[nrl][ncl] += NR_END;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    m[nrl][ncl] -= nll;
         printf(" x(%d)=%.12e",j,xit[j]);    for (j=ncl+1; j<=nch; j++) 
       }      m[nrl][j]=m[nrl][j-1]+nlay;
       for(j=1;j<=n;j++)    
         printf(" p=%.12e",p[j]);    for (i=nrl+1; i<=nrh; i++) {
       printf("\n");      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 #endif      for (j=ncl+1; j<=nch; j++) 
     }        m[i][j]=m[i][j-1]+nlay;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    }
 #ifdef DEBUG    return m; 
       int k[2],l;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       k[0]=1;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       k[1]=-1;    */
       printf("Max: %.12e",(*func)(p));  }
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  /*************************free ma3x ************************/
       printf("\n");  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       for(l=0;l<=1;l++) {  {
         for (j=1;j<=n;j++) {    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    free((FREE_ARG)(m+nrl-NR_END));
         }  }
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  /*************** function subdirf ***********/
 #endif  char *subdirf(char fileres[])
   {
     /* Caution optionfilefiname is hidden */
       free_vector(xit,1,n);    strcpy(tmpout,optionfilefiname);
       free_vector(xits,1,n);    strcat(tmpout,"/"); /* Add to the right */
       free_vector(ptt,1,n);    strcat(tmpout,fileres);
       free_vector(pt,1,n);    return tmpout;
       return;  }
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  /*************** function subdirf2 ***********/
     for (j=1;j<=n;j++) {  char *subdirf2(char fileres[], char *preop)
       ptt[j]=2.0*p[j]-pt[j];  {
       xit[j]=p[j]-pt[j];    
       pt[j]=p[j];    /* Caution optionfilefiname is hidden */
     }    strcpy(tmpout,optionfilefiname);
     fptt=(*func)(ptt);    strcat(tmpout,"/");
     if (fptt < fp) {    strcat(tmpout,preop);
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    strcat(tmpout,fileres);
       if (t < 0.0) {    return tmpout;
         linmin(p,xit,n,fret,func);  }
         for (j=1;j<=n;j++) {  
           xi[j][ibig]=xi[j][n];  /*************** function subdirf3 ***********/
           xi[j][n]=xit[j];  char *subdirf3(char fileres[], char *preop, char *preop2)
         }  {
 #ifdef DEBUG    
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    /* Caution optionfilefiname is hidden */
         for(j=1;j<=n;j++)    strcpy(tmpout,optionfilefiname);
           printf(" %.12e",xit[j]);    strcat(tmpout,"/");
         printf("\n");    strcat(tmpout,preop);
 #endif    strcat(tmpout,preop2);
       }    strcat(tmpout,fileres);
     }    return tmpout;
   }  }
 }  
   /***************** f1dim *************************/
 /**** Prevalence limit ****************/  extern int ncom; 
   extern double *pcom,*xicom;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  extern double (*nrfunc)(double []); 
 {   
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  double f1dim(double x) 
      matrix by transitions matrix until convergence is reached */  { 
     int j; 
   int i, ii,j,k;    double f;
   double min, max, maxmin, maxmax,sumnew=0.;    double *xt; 
   double **matprod2();   
   double **out, cov[NCOVMAX], **pmij();    xt=vector(1,ncom); 
   double **newm;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   double agefin, delaymax=50 ; /* Max number of years to converge */    f=(*nrfunc)(xt); 
     free_vector(xt,1,ncom); 
   for (ii=1;ii<=nlstate+ndeath;ii++)    return f; 
     for (j=1;j<=nlstate+ndeath;j++){  } 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
     }  /*****************brent *************************/
   double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
    cov[1]=1.;  { 
      int iter; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    double a,b,d,etemp;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    double fu,fv,fw,fx;
     newm=savm;    double ftemp;
     /* Covariates have to be included here again */    double p,q,r,tol1,tol2,u,v,w,x,xm; 
      cov[2]=agefin;    double e=0.0; 
     
       for (k=1; k<=cptcovn;k++) {    a=(ax < cx ? ax : cx); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    b=(ax > cx ? ax : cx); 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    x=w=v=bx; 
       }    fw=fv=fx=(*f)(x); 
       for (k=1; k<=cptcovage;k++)    for (iter=1;iter<=ITMAX;iter++) { 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      xm=0.5*(a+b); 
       for (k=1; k<=cptcovprod;k++)      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       printf(".");fflush(stdout);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      fprintf(ficlog,".");fflush(ficlog);
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  #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);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     savm=oldm;  #endif
     oldm=newm;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     maxmax=0.;        *xmin=x; 
     for(j=1;j<=nlstate;j++){        return fx; 
       min=1.;      } 
       max=0.;      ftemp=fu;
       for(i=1; i<=nlstate; i++) {      if (fabs(e) > tol1) { 
         sumnew=0;        r=(x-w)*(fx-fv); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        q=(x-v)*(fx-fw); 
         prlim[i][j]= newm[i][j]/(1-sumnew);        p=(x-v)*q-(x-w)*r; 
         max=FMAX(max,prlim[i][j]);        q=2.0*(q-r); 
         min=FMIN(min,prlim[i][j]);        if (q > 0.0) p = -p; 
       }        q=fabs(q); 
       maxmin=max-min;        etemp=e; 
       maxmax=FMAX(maxmax,maxmin);        e=d; 
     }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     if(maxmax < ftolpl){          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       return prlim;        else { 
     }          d=p/q; 
   }          u=x+d; 
 }          if (u-a < tol2 || b-u < tol2) 
             d=SIGN(tol1,xm-x); 
 /*************** transition probabilities ***************/        } 
       } else { 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 {      } 
   double s1, s2;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   /*double t34;*/      fu=(*f)(u); 
   int i,j,j1, nc, ii, jj;      if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
     for(i=1; i<= nlstate; i++){        SHFT(v,w,x,u) 
     for(j=1; j<i;j++){          SHFT(fv,fw,fx,fu) 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          } else { 
         /*s2 += param[i][j][nc]*cov[nc];*/            if (u < x) a=u; else b=u; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];            if (fu <= fw || w == x) { 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/              v=w; 
       }              w=u; 
       ps[i][j]=s2;              fv=fw; 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/              fw=fu; 
     }            } else if (fu <= fv || v == x || v == w) { 
     for(j=i+1; j<=nlstate+ndeath;j++){              v=u; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){              fv=fu; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];            } 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/          } 
       }    } 
       ps[i][j]=s2;    nrerror("Too many iterations in brent"); 
     }    *xmin=x; 
   }    return fx; 
     /*ps[3][2]=1;*/  } 
   
   for(i=1; i<= nlstate; i++){  /****************** mnbrak ***********************/
      s1=0;  
     for(j=1; j<i; j++)  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       s1+=exp(ps[i][j]);              double (*func)(double)) 
     for(j=i+1; j<=nlstate+ndeath; j++)  { 
       s1+=exp(ps[i][j]);    double ulim,u,r,q, dum;
     ps[i][i]=1./(s1+1.);    double fu; 
     for(j=1; j<i; j++)   
       ps[i][j]= exp(ps[i][j])*ps[i][i];    *fa=(*func)(*ax); 
     for(j=i+1; j<=nlstate+ndeath; j++)    *fb=(*func)(*bx); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    if (*fb > *fa) { 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      SHFT(dum,*ax,*bx,dum) 
   } /* end i */        SHFT(dum,*fb,*fa,dum) 
         } 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    *cx=(*bx)+GOLD*(*bx-*ax); 
     for(jj=1; jj<= nlstate+ndeath; jj++){    *fc=(*func)(*cx); 
       ps[ii][jj]=0;    while (*fb > *fc) { 
       ps[ii][ii]=1;      r=(*bx-*ax)*(*fb-*fc); 
     }      q=(*bx-*cx)*(*fb-*fa); 
   }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      if ((*bx-u)*(u-*cx) > 0.0) { 
     for(jj=1; jj<= nlstate+ndeath; jj++){        fu=(*func)(u); 
      printf("%lf ",ps[ii][jj]);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
    }        fu=(*func)(u); 
     printf("\n ");        if (fu < *fc) { 
     }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     printf("\n ");printf("%lf ",cov[2]);*/            SHFT(*fb,*fc,fu,(*func)(u)) 
 /*            } 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   goto end;*/        u=ulim; 
     return ps;        fu=(*func)(u); 
 }      } else { 
         u=(*cx)+GOLD*(*cx-*bx); 
 /**************** Product of 2 matrices ******************/        fu=(*func)(u); 
       } 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      SHFT(*ax,*bx,*cx,u) 
 {        SHFT(*fa,*fb,*fc,fu) 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        } 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  } 
   /* in, b, out are matrice of pointers which should have been initialized  
      before: only the contents of out is modified. The function returns  /*************** linmin ************************/
      a pointer to pointers identical to out */  
   long i, j, k;  int ncom; 
   for(i=nrl; i<= nrh; i++)  double *pcom,*xicom;
     for(k=ncolol; k<=ncoloh; k++)  double (*nrfunc)(double []); 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)   
         out[i][k] +=in[i][j]*b[j][k];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   { 
   return out;    double brent(double ax, double bx, double cx, 
 }                 double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 /************* Higher Matrix Product ***************/                double *fc, double (*func)(double)); 
     int j; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    double xx,xmin,bx,ax; 
 {    double fx,fb,fa;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month   
      duration (i.e. until    ncom=n; 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    pcom=vector(1,n); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    xicom=vector(1,n); 
      (typically every 2 years instead of every month which is too big).    nrfunc=func; 
      Model is determined by parameters x and covariates have to be    for (j=1;j<=n;j++) { 
      included manually here.      pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
      */    } 
     ax=0.0; 
   int i, j, d, h, k;    xx=1.0; 
   double **out, cov[NCOVMAX];    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   double **newm;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   #ifdef DEBUG
   /* Hstepm could be zero and should return the unit matrix */    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   for (i=1;i<=nlstate+ndeath;i++)    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     for (j=1;j<=nlstate+ndeath;j++){  #endif
       oldm[i][j]=(i==j ? 1.0 : 0.0);    for (j=1;j<=n;j++) { 
       po[i][j][0]=(i==j ? 1.0 : 0.0);      xi[j] *= xmin; 
     }      p[j] += xi[j]; 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    } 
   for(h=1; h <=nhstepm; h++){    free_vector(xicom,1,n); 
     for(d=1; d <=hstepm; d++){    free_vector(pcom,1,n); 
       newm=savm;  } 
       /* Covariates have to be included here again */  
       cov[1]=1.;  char *asc_diff_time(long time_sec, char ascdiff[])
       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]]];    long sec_left, days, hours, minutes;
       for (k=1; k<=cptcovage;k++)    days = (time_sec) / (60*60*24);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    sec_left = (time_sec) % (60*60*24);
       for (k=1; k<=cptcovprod;k++)    hours = (sec_left) / (60*60) ;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    sec_left = (sec_left) %(60*60);
     minutes = (sec_left) /60;
     sec_left = (sec_left) % (60);
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    return ascdiff;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  }
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;  /*************** powell ************************/
       oldm=newm;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     }              double (*func)(double [])) 
     for(i=1; i<=nlstate+ndeath; i++)  { 
       for(j=1;j<=nlstate+ndeath;j++) {    void linmin(double p[], double xi[], int n, 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]);    int i,ibig,j; 
          */    double del,t,*pt,*ptt,*xit;
       }    double fp,fptt;
   } /* end h */    double *xits;
   return po;    int niterf, itmp;
 }  
     pt=vector(1,n); 
     ptt=vector(1,n); 
 /*************** log-likelihood *************/    xit=vector(1,n); 
 double func( double *x)    xits=vector(1,n); 
 {    *fret=(*func)(p); 
   int i, ii, j, k, mi, d, kk;    for (j=1;j<=n;j++) pt[j]=p[j]; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    for (*iter=1;;++(*iter)) { 
   double **out;      fp=(*fret); 
   double sw; /* Sum of weights */      ibig=0; 
   double lli; /* Individual log likelihood */      del=0.0; 
   long ipmx;      last_time=curr_time;
   /*extern weight */      (void) gettimeofday(&curr_time,&tzp);
   /* We are differentiating ll according to initial status */      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      /*    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);
   /*for(i=1;i<imx;i++)      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
     printf(" %d\n",s[4][i]);      */
   */     for (i=1;i<=n;i++) {
   cov[1]=1.;        printf(" %d %.12f",i, p[i]);
         fprintf(ficlog," %d %.12lf",i, p[i]);
   for(k=1; k<=nlstate; k++) ll[k]=0.;        fprintf(ficrespow," %.12lf", p[i]);
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      }
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      printf("\n");
     for(mi=1; mi<= wav[i]-1; mi++){      fprintf(ficlog,"\n");
       for (ii=1;ii<=nlstate+ndeath;ii++)      fprintf(ficrespow,"\n");fflush(ficrespow);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      if(*iter <=3){
       for(d=0; d<dh[mi][i]; d++){        tm = *localtime(&curr_time.tv_sec);
         newm=savm;        strcpy(strcurr,asctime(&tm));
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  /*       asctime_r(&tm,strcurr); */
         for (kk=1; kk<=cptcovage;kk++) {        forecast_time=curr_time; 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        itmp = strlen(strcurr);
         }        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
                  strcurr[itmp-1]='\0';
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         savm=oldm;        for(niterf=10;niterf<=30;niterf+=10){
         oldm=newm;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
                  tmf = *localtime(&forecast_time.tv_sec);
          /*      asctime_r(&tmf,strfor); */
       } /* end mult */          strcpy(strfor,asctime(&tmf));
                itmp = strlen(strfor);
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);          if(strfor[itmp-1]=='\n')
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/          strfor[itmp-1]='\0';
       ipmx +=1;          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);
       sw += weight[i];          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        }
     } /* end of wave */      }
   } /* end of individual */      for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        fptt=(*fret); 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  #ifdef DEBUG
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        printf("fret=%lf \n",*fret);
   return -l;        fprintf(ficlog,"fret=%lf \n",*fret);
 }  #endif
         printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
 /*********** Maximum Likelihood Estimation ***************/        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))          del=fabs(fptt-(*fret)); 
 {          ibig=i; 
   int i,j, iter;        } 
   double **xi,*delti;  #ifdef DEBUG
   double fret;        printf("%d %.12e",i,(*fret));
   xi=matrix(1,npar,1,npar);        fprintf(ficlog,"%d %.12e",i,(*fret));
   for (i=1;i<=npar;i++)        for (j=1;j<=n;j++) {
     for (j=1;j<=npar;j++)          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       xi[i][j]=(i==j ? 1.0 : 0.0);          printf(" x(%d)=%.12e",j,xit[j]);
   printf("Powell\n");          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   powell(p,xi,npar,ftol,&iter,&fret,func);        }
         for(j=1;j<=n;j++) {
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          printf(" p=%.12e",p[j]);
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));          fprintf(ficlog," p=%.12e",p[j]);
         }
 }        printf("\n");
         fprintf(ficlog,"\n");
 /**** Computes Hessian and covariance matrix ***/  #endif
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      } 
 {      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   double  **a,**y,*x,pd;  #ifdef DEBUG
   double **hess;        int k[2],l;
   int i, j,jk;        k[0]=1;
   int *indx;        k[1]=-1;
         printf("Max: %.12e",(*func)(p));
   double hessii(double p[], double delta, int theta, double delti[]);        fprintf(ficlog,"Max: %.12e",(*func)(p));
   double hessij(double p[], double delti[], int i, int j);        for (j=1;j<=n;j++) {
   void lubksb(double **a, int npar, int *indx, double b[]) ;          printf(" %.12e",p[j]);
   void ludcmp(double **a, int npar, int *indx, double *d) ;          fprintf(ficlog," %.12e",p[j]);
         }
   hess=matrix(1,npar,1,npar);        printf("\n");
         fprintf(ficlog,"\n");
   printf("\nCalculation of the hessian matrix. Wait...\n");        for(l=0;l<=1;l++) {
   for (i=1;i<=npar;i++){          for (j=1;j<=n;j++) {
     printf("%d",i);fflush(stdout);            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     hess[i][i]=hessii(p,ftolhess,i,delti);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     /*printf(" %f ",p[i]);*/            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     /*printf(" %lf ",hess[i][i]);*/          }
   }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
            fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   for (i=1;i<=npar;i++) {        }
     for (j=1;j<=npar;j++)  {  #endif
       if (j>i) {  
         printf(".%d%d",i,j);fflush(stdout);  
         hess[i][j]=hessij(p,delti,i,j);        free_vector(xit,1,n); 
         hess[j][i]=hess[i][j];            free_vector(xits,1,n); 
         /*printf(" %lf ",hess[i][j]);*/        free_vector(ptt,1,n); 
       }        free_vector(pt,1,n); 
     }        return; 
   }      } 
   printf("\n");      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        ptt[j]=2.0*p[j]-pt[j]; 
          xit[j]=p[j]-pt[j]; 
   a=matrix(1,npar,1,npar);        pt[j]=p[j]; 
   y=matrix(1,npar,1,npar);      } 
   x=vector(1,npar);      fptt=(*func)(ptt); 
   indx=ivector(1,npar);      if (fptt < fp) { 
   for (i=1;i<=npar;i++)        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        if (t < 0.0) { 
   ludcmp(a,npar,indx,&pd);          linmin(p,xit,n,fret,func); 
           for (j=1;j<=n;j++) { 
   for (j=1;j<=npar;j++) {            xi[j][ibig]=xi[j][n]; 
     for (i=1;i<=npar;i++) x[i]=0;            xi[j][n]=xit[j]; 
     x[j]=1;          }
     lubksb(a,npar,indx,x);  #ifdef DEBUG
     for (i=1;i<=npar;i++){          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       matcov[i][j]=x[i];          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     }          for(j=1;j<=n;j++){
   }            printf(" %.12e",xit[j]);
             fprintf(ficlog," %.12e",xit[j]);
   printf("\n#Hessian matrix#\n");          }
   for (i=1;i<=npar;i++) {          printf("\n");
     for (j=1;j<=npar;j++) {          fprintf(ficlog,"\n");
       printf("%.3e ",hess[i][j]);  #endif
     }        }
     printf("\n");      } 
   }    } 
   } 
   /* Recompute Inverse */  
   for (i=1;i<=npar;i++)  /**** Prevalence limit (stable prevalence)  ****************/
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  
   ludcmp(a,npar,indx,&pd);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   {
   /*  printf("\n#Hessian matrix recomputed#\n");    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
        matrix by transitions matrix until convergence is reached */
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;    int i, ii,j,k;
     x[j]=1;    double min, max, maxmin, maxmax,sumnew=0.;
     lubksb(a,npar,indx,x);    double **matprod2();
     for (i=1;i<=npar;i++){    double **out, cov[NCOVMAX], **pmij();
       y[i][j]=x[i];    double **newm;
       printf("%.3e ",y[i][j]);    double agefin, delaymax=50 ; /* Max number of years to converge */
     }  
     printf("\n");    for (ii=1;ii<=nlstate+ndeath;ii++)
   }      for (j=1;j<=nlstate+ndeath;j++){
   */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
   free_matrix(a,1,npar,1,npar);  
   free_matrix(y,1,npar,1,npar);     cov[1]=1.;
   free_vector(x,1,npar);   
   free_ivector(indx,1,npar);   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   free_matrix(hess,1,npar,1,npar);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       newm=savm;
       /* Covariates have to be included here again */
 }       cov[2]=agefin;
     
 /*************** hessian matrix ****************/        for (k=1; k<=cptcovn;k++) {
 double hessii( double x[], double delta, int theta, double delti[])          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]]);*/
   int i;        }
   int l=1, lmax=20;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double k1,k2;        for (k=1; k<=cptcovprod;k++)
   double p2[NPARMAX+1];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   double res;  
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   double fx;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   int k=0,kmax=10;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   double l1;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
   fx=func(x);      savm=oldm;
   for (i=1;i<=npar;i++) p2[i]=x[i];      oldm=newm;
   for(l=0 ; l <=lmax; l++){      maxmax=0.;
     l1=pow(10,l);      for(j=1;j<=nlstate;j++){
     delts=delt;        min=1.;
     for(k=1 ; k <kmax; k=k+1){        max=0.;
       delt = delta*(l1*k);        for(i=1; i<=nlstate; i++) {
       p2[theta]=x[theta] +delt;          sumnew=0;
       k1=func(p2)-fx;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       p2[theta]=x[theta]-delt;          prlim[i][j]= newm[i][j]/(1-sumnew);
       k2=func(p2)-fx;          max=FMAX(max,prlim[i][j]);
       /*res= (k1-2.0*fx+k2)/delt/delt; */          min=FMIN(min,prlim[i][j]);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        }
              maxmin=max-min;
 #ifdef DEBUG        maxmax=FMAX(maxmax,maxmin);
       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      if(maxmax < ftolpl){
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        return prlim;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      }
         k=kmax;    }
       }  }
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  
         k=kmax; l=lmax*10.;  /*************** transition probabilities ***************/ 
       }  
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         delts=delt;  {
       }    double s1, s2;
     }    /*double t34;*/
   }    int i,j,j1, nc, ii, jj;
   delti[theta]=delts;  
   return res;      for(i=1; i<= nlstate; i++){
          for(j=1; j<i;j++){
 }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
             /*s2 += param[i][j][nc]*cov[nc];*/
 double hessij( double x[], double delti[], int thetai,int thetaj)            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 {  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
   int i;          }
   int l=1, l1, lmax=20;          ps[i][j]=s2;
   double k1,k2,k3,k4,res,fx;  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
   double p2[NPARMAX+1];        }
   int k;        for(j=i+1; j<=nlstate+ndeath;j++){
           for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   fx=func(x);            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   for (k=1; k<=2; k++) {  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     for (i=1;i<=npar;i++) p2[i]=x[i];          }
     p2[thetai]=x[thetai]+delti[thetai]/k;          ps[i][j]=s2;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        }
     k1=func(p2)-fx;      }
        /*ps[3][2]=1;*/
     p2[thetai]=x[thetai]+delti[thetai]/k;      
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      for(i=1; i<= nlstate; i++){
     k2=func(p2)-fx;        s1=0;
          for(j=1; j<i; j++)
     p2[thetai]=x[thetai]-delti[thetai]/k;          s1+=exp(ps[i][j]);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        for(j=i+1; j<=nlstate+ndeath; j++)
     k3=func(p2)-fx;          s1+=exp(ps[i][j]);
          ps[i][i]=1./(s1+1.);
     p2[thetai]=x[thetai]-delti[thetai]/k;        for(j=1; j<i; j++)
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          ps[i][j]= exp(ps[i][j])*ps[i][i];
     k4=func(p2)-fx;        for(j=i+1; j<=nlstate+ndeath; j++)
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          ps[i][j]= exp(ps[i][j])*ps[i][i];
 #ifdef DEBUG        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     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);      } /* end i */
 #endif      
   }      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   return res;        for(jj=1; jj<= nlstate+ndeath; jj++){
 }          ps[ii][jj]=0;
           ps[ii][ii]=1;
 /************** Inverse of matrix **************/        }
 void ludcmp(double **a, int n, int *indx, double *d)      }
 {      
   int i,imax,j,k;  
   double big,dum,sum,temp;  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   double *vv;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
    /*         printf("ddd %lf ",ps[ii][jj]); */
   vv=vector(1,n);  /*       } */
   *d=1.0;  /*       printf("\n "); */
   for (i=1;i<=n;i++) {  /*        } */
     big=0.0;  /*        printf("\n ");printf("%lf ",cov[2]); */
     for (j=1;j<=n;j++)         /*
       if ((temp=fabs(a[i][j])) > big) big=temp;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        goto end;*/
     vv[i]=1.0/big;      return ps;
   }  }
   for (j=1;j<=n;j++) {  
     for (i=1;i<j;i++) {  /**************** Product of 2 matrices ******************/
       sum=a[i][j];  
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       a[i][j]=sum;  {
     }    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     big=0.0;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     for (i=j;i<=n;i++) {    /* in, b, out are matrice of pointers which should have been initialized 
       sum=a[i][j];       before: only the contents of out is modified. The function returns
       for (k=1;k<j;k++)       a pointer to pointers identical to out */
         sum -= a[i][k]*a[k][j];    long i, j, k;
       a[i][j]=sum;    for(i=nrl; i<= nrh; i++)
       if ( (dum=vv[i]*fabs(sum)) >= big) {      for(k=ncolol; k<=ncoloh; k++)
         big=dum;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
         imax=i;          out[i][k] +=in[i][j]*b[j][k];
       }  
     }    return out;
     if (j != imax) {  }
       for (k=1;k<=n;k++) {  
         dum=a[imax][k];  
         a[imax][k]=a[j][k];  /************* Higher Matrix Product ***************/
         a[j][k]=dum;  
       }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       *d = -(*d);  {
       vv[imax]=vv[j];    /* Computes the transition matrix starting at age 'age' over 
     }       'nhstepm*hstepm*stepm' months (i.e. until
     indx[j]=imax;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     if (a[j][j] == 0.0) a[j][j]=TINY;       nhstepm*hstepm matrices. 
     if (j != n) {       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       dum=1.0/(a[j][j]);       (typically every 2 years instead of every month which is too big 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;       for the memory).
     }       Model is determined by parameters x and covariates have to be 
   }       included manually here. 
   free_vector(vv,1,n);  /* Doesn't work */  
 ;       */
 }  
     int i, j, d, h, k;
 void lubksb(double **a, int n, int *indx, double b[])    double **out, cov[NCOVMAX];
 {    double **newm;
   int i,ii=0,ip,j;  
   double sum;    /* Hstepm could be zero and should return the unit matrix */
      for (i=1;i<=nlstate+ndeath;i++)
   for (i=1;i<=n;i++) {      for (j=1;j<=nlstate+ndeath;j++){
     ip=indx[i];        oldm[i][j]=(i==j ? 1.0 : 0.0);
     sum=b[ip];        po[i][j][0]=(i==j ? 1.0 : 0.0);
     b[ip]=b[i];      }
     if (ii)    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    for(h=1; h <=nhstepm; h++){
     else if (sum) ii=i;      for(d=1; d <=hstepm; d++){
     b[i]=sum;        newm=savm;
   }        /* Covariates have to be included here again */
   for (i=n;i>=1;i--) {        cov[1]=1.;
     sum=b[i];        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     b[i]=sum/a[i][i];        for (k=1; k<=cptcovage;k++)
   }          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 }        for (k=1; k<=cptcovprod;k++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 /************ Frequencies ********************/  
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)  
 {  /* Some frequencies */        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
          /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   double ***freq; /* Frequencies */                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   double *pp;        savm=oldm;
   double pos, k2, dateintsum=0,k2cpt=0;        oldm=newm;
   FILE *ficresp;      }
   char fileresp[FILENAMELENGTH];      for(i=1; i<=nlstate+ndeath; i++)
          for(j=1;j<=nlstate+ndeath;j++) {
   pp=vector(1,nlstate);          po[i][j][h]=newm[i][j];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   strcpy(fileresp,"p");           */
   strcat(fileresp,fileres);        }
   if((ficresp=fopen(fileresp,"w"))==NULL) {    } /* end h */
     printf("Problem with prevalence resultfile: %s\n", fileresp);    return po;
     exit(0);  }
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;  /*************** log-likelihood *************/
   double func( double *x)
   j=cptcoveff;  {
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
   for(k1=1; k1<=j;k1++){    double **out;
    for(i1=1; i1<=ncodemax[k1];i1++){    double sw; /* Sum of weights */
        j1++;    double lli; /* Individual log likelihood */
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    int s1, s2;
          scanf("%d", i);*/    double bbh, survp;
         for (i=-1; i<=nlstate+ndeath; i++)      long ipmx;
          for (jk=-1; jk<=nlstate+ndeath; jk++)      /*extern weight */
            for(m=agemin; m <= agemax+3; m++)    /* We are differentiating ll according to initial status */
              freq[i][jk][m]=0;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
         dateintsum=0;      printf(" %d\n",s[4][i]);
         k2cpt=0;    */
        for (i=1; i<=imx; i++) {    cov[1]=1.;
          bool=1;  
          if  (cptcovn>0) {    for(k=1; k<=nlstate; k++) ll[k]=0.;
            for (z1=1; z1<=cptcoveff; z1++)  
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    if(mle==1){
                bool=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          if (bool==1) {        for(mi=1; mi<= wav[i]-1; mi++){
            for(m=firstpass; m<=lastpass; m++){          for (ii=1;ii<=nlstate+ndeath;ii++)
              k2=anint[m][i]+(mint[m][i]/12.);            for (j=1;j<=nlstate+ndeath;j++){
              if ((k2>=dateprev1) && (k2<=dateprev2)) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                if(agev[m][i]==0) agev[m][i]=agemax+1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                if(agev[m][i]==1) agev[m][i]=agemax+2;            }
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          for(d=0; d<dh[mi][i]; d++){
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];            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 */
           /* But now since version 0.9 we anticipate for bias at large stepm.
         if  (cptcovn>0) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
          fprintf(ficresp, "\n#********** Variable ");           * (in months) between two waves is not a multiple of stepm, we rounded to 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);           * the nearest (and in case of equal distance, to the lowest) interval but now
        fprintf(ficresp, "**********\n#");           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         }           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
        for(i=1; i<=nlstate;i++)           * probability in order to take into account the bias as a fraction of the way
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
        fprintf(ficresp, "\n");           * -stepm/2 to stepm/2 .
                   * For stepm=1 the results are the same as for previous versions of Imach.
   for(i=(int)agemin; i <= (int)agemax+3; i++){           * For stepm > 1 the results are less biased than in previous versions. 
     if(i==(int)agemax+3)           */
       printf("Total");          s1=s[mw[mi][i]][i];
     else          s2=s[mw[mi+1][i]][i];
       printf("Age %d", i);          bbh=(double)bh[mi][i]/(double)stepm; 
     for(jk=1; jk <=nlstate ; jk++){          /* bias bh is positive if real duration
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)           * is higher than the multiple of stepm and negative otherwise.
         pp[jk] += freq[jk][m][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]));*/
     for(jk=1; jk <=nlstate ; jk++){          if( s2 > nlstate){ 
       for(m=-1, pos=0; m <=0 ; m++)            /* i.e. if s2 is a death state and if the date of death is known then the contribution
         pos += freq[jk][m][i];               to the likelihood is the probability to die between last step unit time and current 
       if(pp[jk]>=1.e-10)               step unit time, which is also equal to probability to die before dh 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);               minus probability to die before dh-stepm . 
       else               In version up to 0.92 likelihood was computed
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          as if date of death was unknown. Death was treated as any other
     }          health state: the date of the interview describes the actual state
           and not the date of a change in health state. The former idea was
      for(jk=1; jk <=nlstate ; jk++){          to consider that at each interview the state was recorded
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          (healthy, disable or death) and IMaCh was corrected; but when we
         pp[jk] += freq[jk][m][i];          introduced the exact date of death then we should have modified
      }          the contribution of an exact death to the likelihood. This new
           contribution is smaller and very dependent of the step unit
     for(jk=1,pos=0; jk <=nlstate ; jk++)          stepm. It is no more the probability to die between last interview
       pos += pp[jk];          and month of death but the probability to survive from last
     for(jk=1; jk <=nlstate ; jk++){          interview up to one month before death multiplied by the
       if(pos>=1.e-5)          probability to die within a month. Thanks to Chris
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          Jackson for correcting this bug.  Former versions increased
       else          mortality artificially. The bad side is that we add another loop
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          which slows down the processing. The difference can be up to 10%
       if( i <= (int) agemax){          lower mortality.
         if(pos>=1.e-5){            */
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            lli=log(out[s1][s2] - savm[s1][s2]);
           probs[i][jk][j1]= pp[jk]/pos;          }else{
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
       else          } 
           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];
               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;
           ij++;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
         }          }
         if (ij > ncodemax[j]) break;          fprintf(ficresilk," %10.6f\n", -llt);
       }          }
     }      } /* end of wave */
   }      } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
  for (k=0; k<19; k++) Ndum[k]=0;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
  for (i=1; i<=ncovmodel-2; i++) {    if(globpr==0){ /* First time we count the contributions and weights */
       ij=Tvar[i];      gipmx=ipmx;
       Ndum[ij]++;      gsw=sw;
     }    }
     return -l;
  ij=1;  }
  for (i=1; i<=10; i++) {  
    if((Ndum[i]!=0) && (i<=ncov)){  
      Tvaraff[ij]=i;  /*************** function likelione ***********/
      ij++;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
    }  {
  }    /* This routine should help understanding what is done with 
         the selection of individuals/waves and
     cptcoveff=ij-1;       to check the exact contribution to the likelihood.
 }       Plotting could be done.
      */
 /*********** Health Expectancies ****************/    int k;
   
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    if(*globpri !=0){ /* Just counts and sums, no printings */
 {      strcpy(fileresilk,"ilk"); 
   /* Health expectancies */      strcat(fileresilk,fileres);
   int i, j, nhstepm, hstepm, h;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   double age, agelim,hf;        printf("Problem with resultfile: %s\n", fileresilk);
   double ***p3mat;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
        }
   fprintf(ficreseij,"# Health expectancies\n");      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,"# Age");      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   for(i=1; i<=nlstate;i++)      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     for(j=1; j<=nlstate;j++)      for(k=1; k<=nlstate; k++) 
       fprintf(ficreseij," %1d-%1d",i,j);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   fprintf(ficreseij,"\n");      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
   hstepm=1*YEARM; /*  Every j years of age (in month) */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    *fretone=(*funcone)(p);
     if(*globpri !=0){
   agelim=AGESUP;      fclose(ficresilk);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     /* nhstepm age range expressed in number of stepm */      fflush(fichtm); 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);    } 
     /* Typically if 20 years = 20*12/6=40 stepm */    return;
     /*if (stepm >= YEARM) hstepm=1;*/  }
 hstepm=1;  
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*********** Maximum Likelihood Estimation ***************/
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    {
 hf=stepm/YEARM;    int i,j, iter;
 /*printf("stepm=%d nhstepm=%d hstepm=%d age=%lf ",stepm, nhstepm, hstepm, age);*/    double **xi;
     for(i=1; i<=nlstate;i++)    double fret;
       for(j=1; j<=nlstate;j++)    double fretone; /* Only one call to likelihood */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    /*  char filerespow[FILENAMELENGTH];*/
           eij[i][j][(int)age] +=hf*(p3mat[i][j][h]+p3mat[i][j][h+1])/2.0;    xi=matrix(1,npar,1,npar);
         }    for (i=1;i<=npar;i++)
          for (j=1;j<=npar;j++)
     /* hf=1;        xi[i][j]=(i==j ? 1.0 : 0.0);
        if (stepm >= YEARM) hf=stepm/YEARM;*/    printf("Powell\n");  fprintf(ficlog,"Powell\n");
 hf=stepm/YEARM;    strcpy(filerespow,"pow"); 
      strcat(filerespow,fileres);
     fprintf(ficreseij,"%3.0f",age );    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     for(i=1; i<=nlstate;i++)      printf("Problem with resultfile: %s\n", filerespow);
       for(j=1; j<=nlstate;j++){      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);    }
       }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     fprintf(ficreseij,"\n");    for (i=1;i<=nlstate;i++)
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(j=1;j<=nlstate+ndeath;j++)
   }        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
 }    fprintf(ficrespow,"\n");
   
 /************ Variance ******************/    powell(p,xi,npar,ftol,&iter,&fret,func);
 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)  
 {    fclose(ficrespow);
   /* Variance of health expectancies */    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double **newm;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm, h;  }
   int k, cptcode;  
   double *xp;  /**** Computes Hessian and covariance matrix ***/
   double **gp, **gm;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   double ***gradg, ***trgradg;  {
   double ***p3mat;    double  **a,**y,*x,pd;
   double age,agelim;    double **hess;
   int theta;    int i, j,jk;
     int *indx;
    fprintf(ficresvij,"# Covariances of life expectancies\n");  
   fprintf(ficresvij,"# Age");    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   for(i=1; i<=nlstate;i++)    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     for(j=1; j<=nlstate;j++)    void lubksb(double **a, int npar, int *indx, double b[]) ;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    void ludcmp(double **a, int npar, int *indx, double *d) ;
   fprintf(ficresvij,"\n");    double gompertz(double p[]);
     hess=matrix(1,npar,1,npar);
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);    printf("\nCalculation of the hessian matrix. Wait...\n");
   doldm=matrix(1,nlstate,1,nlstate);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
      for (i=1;i<=npar;i++){
   hstepm=1*YEARM; /* Every year of age */      printf("%d",i);fflush(stdout);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      fprintf(ficlog,"%d",i);fflush(ficlog);
   agelim = AGESUP;     
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      
     if (stepm >= YEARM) hstepm=1;      /*  printf(" %f ",p[i]);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    
     gp=matrix(0,nhstepm,1,nlstate);    for (i=1;i<=npar;i++) {
     gm=matrix(0,nhstepm,1,nlstate);      for (j=1;j<=npar;j++)  {
         if (j>i) { 
     for(theta=1; theta <=npar; theta++){          printf(".%d%d",i,j);fflush(stdout);
       for(i=1; i<=npar; i++){ /* Computes gradient */          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          hess[i][j]=hessij(p,delti,i,j,func,npar);
       }          
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            hess[j][i]=hess[i][j];    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          /*printf(" %lf ",hess[i][j]);*/
         }
       if (popbased==1) {      }
         for(i=1; i<=nlstate;i++)    }
           prlim[i][i]=probs[(int)age][i][ij];    printf("\n");
       }    fprintf(ficlog,"\n");
    
       for(j=1; j<= nlstate; j++){    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
         for(h=0; h<=nhstepm; h++){    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    a=matrix(1,npar,1,npar);
         }    y=matrix(1,npar,1,npar);
       }    x=vector(1,npar);
        indx=ivector(1,npar);
       for(i=1; i<=npar; i++) /* Computes gradient */    for (i=1;i<=npar;i++)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      ludcmp(a,npar,indx,&pd);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
      for (j=1;j<=npar;j++) {
       if (popbased==1) {      for (i=1;i<=npar;i++) x[i]=0;
         for(i=1; i<=nlstate;i++)      x[j]=1;
           prlim[i][i]=probs[(int)age][i][ij];      lubksb(a,npar,indx,x);
       }      for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
       for(j=1; j<= nlstate; j++){      }
         for(h=0; h<=nhstepm; h++){    }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    printf("\n#Hessian matrix#\n");
         }    fprintf(ficlog,"\n#Hessian matrix#\n");
       }    for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
       for(j=1; j<= nlstate; j++)        printf("%.3e ",hess[i][j]);
         for(h=0; h<=nhstepm; h++){        fprintf(ficlog,"%.3e ",hess[i][j]);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      }
         }      printf("\n");
     } /* End theta */      fprintf(ficlog,"\n");
     }
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  
     /* Recompute Inverse */
     for(h=0; h<=nhstepm; h++)    for (i=1;i<=npar;i++)
       for(j=1; j<=nlstate;j++)      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         for(theta=1; theta <=npar; theta++)    ludcmp(a,npar,indx,&pd);
           trgradg[h][j][theta]=gradg[h][theta][j];  
     /*  printf("\n#Hessian matrix recomputed#\n");
     for(i=1;i<=nlstate;i++)  
       for(j=1;j<=nlstate;j++)    for (j=1;j<=npar;j++) {
         vareij[i][j][(int)age] =0.;      for (i=1;i<=npar;i++) x[i]=0;
     for(h=0;h<=nhstepm;h++){      x[j]=1;
       for(k=0;k<=nhstepm;k++){      lubksb(a,npar,indx,x);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      for (i=1;i<=npar;i++){ 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        y[i][j]=x[i];
         for(i=1;i<=nlstate;i++)        printf("%.3e ",y[i][j]);
           for(j=1;j<=nlstate;j++)        fprintf(ficlog,"%.3e ",y[i][j]);
             vareij[i][j][(int)age] += doldm[i][j];      }
       }      printf("\n");
     }      fprintf(ficlog,"\n");
     h=1;    }
     if (stepm >= YEARM) h=stepm/YEARM;    */
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)    free_matrix(a,1,npar,1,npar);
       for(j=1; j<=nlstate;j++){    free_matrix(y,1,npar,1,npar);
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    free_vector(x,1,npar);
       }    free_ivector(indx,1,npar);
     fprintf(ficresvij,"\n");    free_matrix(hess,1,npar,1,npar);
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);  
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  }
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*************** hessian matrix ****************/
   } /* End age */  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
    {
   free_vector(xp,1,npar);    int i;
   free_matrix(doldm,1,nlstate,1,npar);    int l=1, lmax=20;
   free_matrix(dnewm,1,nlstate,1,nlstate);    double k1,k2;
     double p2[NPARMAX+1];
 }    double res;
     double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
 /************ Variance of prevlim ******************/    double fx;
 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)    int k=0,kmax=10;
 {    double l1;
   /* Variance of prevalence limit */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    fx=func(x);
   double **newm;    for (i=1;i<=npar;i++) p2[i]=x[i];
   double **dnewm,**doldm;    for(l=0 ; l <=lmax; l++){
   int i, j, nhstepm, hstepm;      l1=pow(10,l);
   int k, cptcode;      delts=delt;
   double *xp;      for(k=1 ; k <kmax; k=k+1){
   double *gp, *gm;        delt = delta*(l1*k);
   double **gradg, **trgradg;        p2[theta]=x[theta] +delt;
   double age,agelim;        k1=func(p2)-fx;
   int theta;        p2[theta]=x[theta]-delt;
            k2=func(p2)-fx;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");        /*res= (k1-2.0*fx+k2)/delt/delt; */
   fprintf(ficresvpl,"# Age");        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   for(i=1; i<=nlstate;i++)        
       fprintf(ficresvpl," %1d-%1d",i,i);  #ifdef DEBUG
   fprintf(ficresvpl,"\n");        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         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);
   xp=vector(1,npar);  #endif
   dnewm=matrix(1,nlstate,1,npar);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   doldm=matrix(1,nlstate,1,nlstate);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
            k=kmax;
   hstepm=1*YEARM; /* Every year of age */        }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   agelim = AGESUP;          k=kmax; l=lmax*10.;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     if (stepm >= YEARM) hstepm=1;          delts=delt;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        }
     gradg=matrix(1,npar,1,nlstate);      }
     gp=vector(1,nlstate);    }
     gm=vector(1,nlstate);    delti[theta]=delts;
     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);  
       }  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  {
       for(i=1;i<=nlstate;i++)    int i;
         gp[i] = prlim[i][i];    int l=1, l1, lmax=20;
        double k1,k2,k3,k4,res,fx;
       for(i=1; i<=npar; i++) /* Computes gradient */    double p2[NPARMAX+1];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    int k;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    fx=func(x);
         gm[i] = prlim[i][i];    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
       for(i=1;i<=nlstate;i++)      p2[thetai]=x[thetai]+delti[thetai]/k;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     } /* End theta */      k1=func(p2)-fx;
     
     trgradg =matrix(1,nlstate,1,npar);      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     for(j=1; j<=nlstate;j++)      k2=func(p2)-fx;
       for(theta=1; theta <=npar; theta++)    
         trgradg[j][theta]=gradg[theta][j];      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     for(i=1;i<=nlstate;i++)      k3=func(p2)-fx;
       varpl[i][(int)age] =0.;    
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      p2[thetai]=x[thetai]-delti[thetai]/k;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     for(i=1;i<=nlstate;i++)      k4=func(p2)-fx;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   #ifdef DEBUG
     fprintf(ficresvpl,"%.0f ",age );      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     for(i=1; i<=nlstate;i++)      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);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  #endif
     fprintf(ficresvpl,"\n");    }
     free_vector(gp,1,nlstate);    return res;
     free_vector(gm,1,nlstate);  }
     free_matrix(gradg,1,npar,1,nlstate);  
     free_matrix(trgradg,1,nlstate,1,npar);  /************** Inverse of matrix **************/
   } /* End age */  void ludcmp(double **a, int n, int *indx, double *d) 
   { 
   free_vector(xp,1,npar);    int i,imax,j,k; 
   free_matrix(doldm,1,nlstate,1,npar);    double big,dum,sum,temp; 
   free_matrix(dnewm,1,nlstate,1,nlstate);    double *vv; 
    
 }    vv=vector(1,n); 
     *d=1.0; 
 /************ Variance of one-step probabilities  ******************/    for (i=1;i<=n;i++) { 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)      big=0.0; 
 {      for (j=1;j<=n;j++) 
   int i, j;        if ((temp=fabs(a[i][j])) > big) big=temp; 
   int k=0, cptcode;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   double **dnewm,**doldm;      vv[i]=1.0/big; 
   double *xp;    } 
   double *gp, *gm;    for (j=1;j<=n;j++) { 
   double **gradg, **trgradg;      for (i=1;i<j;i++) { 
   double age,agelim, cov[NCOVMAX];        sum=a[i][j]; 
   int theta;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   char fileresprob[FILENAMELENGTH];        a[i][j]=sum; 
       } 
   strcpy(fileresprob,"prob");      big=0.0; 
   strcat(fileresprob,fileres);      for (i=j;i<=n;i++) { 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        sum=a[i][j]; 
     printf("Problem with resultfile: %s\n", fileresprob);        for (k=1;k<j;k++) 
   }          sum -= a[i][k]*a[k][j]; 
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        a[i][j]=sum; 
          if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
   xp=vector(1,npar);          imax=i; 
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        } 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      } 
        if (j != imax) { 
   cov[1]=1;        for (k=1;k<=n;k++) { 
   for (age=bage; age<=fage; age ++){          dum=a[imax][k]; 
     cov[2]=age;          a[imax][k]=a[j][k]; 
     gradg=matrix(1,npar,1,9);          a[j][k]=dum; 
     trgradg=matrix(1,9,1,npar);        } 
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        *d = -(*d); 
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        vv[imax]=vv[j]; 
          } 
     for(theta=1; theta <=npar; theta++){      indx[j]=imax; 
       for(i=1; i<=npar; i++)      if (a[j][j] == 0.0) a[j][j]=TINY; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      if (j != n) { 
              dum=1.0/(a[j][j]); 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
          } 
       k=0;    } 
       for(i=1; i<= (nlstate+ndeath); i++){    free_vector(vv,1,n);  /* Doesn't work */
         for(j=1; j<=(nlstate+ndeath);j++){  ;
            k=k+1;  } 
           gp[k]=pmmij[i][j];  
         }  void lubksb(double **a, int n, int *indx, double b[]) 
       }  { 
     int i,ii=0,ip,j; 
       for(i=1; i<=npar; i++)    double sum; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);   
        for (i=1;i<=n;i++) { 
       ip=indx[i]; 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      sum=b[ip]; 
       k=0;      b[ip]=b[i]; 
       for(i=1; i<=(nlstate+ndeath); i++){      if (ii) 
         for(j=1; j<=(nlstate+ndeath);j++){        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           k=k+1;      else if (sum) ii=i; 
           gm[k]=pmmij[i][j];      b[i]=sum; 
         }    } 
       }    for (i=n;i>=1;i--) { 
            sum=b[i]; 
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        b[i]=sum/a[i][i]; 
     }    } 
   } 
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  
       for(theta=1; theta <=npar; theta++)  /************ Frequencies ********************/
       trgradg[j][theta]=gradg[theta][j];  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)
    {  /* Some frequencies */
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     int first;
      pmij(pmmij,cov,ncovmodel,x,nlstate);    double ***freq; /* Frequencies */
     double *pp, **prop;
      k=0;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
      for(i=1; i<=(nlstate+ndeath); i++){    FILE *ficresp;
        for(j=1; j<=(nlstate+ndeath);j++){    char fileresp[FILENAMELENGTH];
          k=k+1;    
          gm[k]=pmmij[i][j];    pp=vector(1,nlstate);
         }    prop=matrix(1,nlstate,iagemin,iagemax+3);
      }    strcpy(fileresp,"p");
          strcat(fileresp,fileres);
      /*printf("\n%d ",(int)age);    if((ficresp=fopen(fileresp,"w"))==NULL) {
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      printf("Problem with prevalence resultfile: %s\n", fileresp);
              fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       exit(0);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    }
      }*/    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
   fprintf(ficresprob,"\n%d ",(int)age);    
     j=cptcoveff;
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    first=1;
   }  
     for(k1=1; k1<=j;k1++){
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      for(i1=1; i1<=ncodemax[k1];i1++){
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        j1++;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          scanf("%d", i);*/
 }        for (i=-1; i<=nlstate+ndeath; i++)  
  free_vector(xp,1,npar);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
 fclose(ficresprob);            for(m=iagemin; m <= iagemax+3; m++)
               freq[i][jk][m]=0;
 }  
       for (i=1; i<=nlstate; i++)  
 /******************* Printing html file ***********/        for(m=iagemin; m <= iagemax+3; m++)
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){          prop[i][m]=0;
   int jj1, k1, i1, cpt;        
   FILE *fichtm;        dateintsum=0;
   /*char optionfilehtm[FILENAMELENGTH];*/        k2cpt=0;
         for (i=1; i<=imx; i++) {
   strcpy(optionfilehtm,optionfile);          bool=1;
   strcat(optionfilehtm,".htm");          if  (cptcovn>0) {
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {            for (z1=1; z1<=cptcoveff; z1++) 
     printf("Problem with %s \n",optionfilehtm), exit(0);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   }                bool=0;
           }
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71 </font> <hr size=\"2\" color=\"#EC5E5E\">          if (bool==1){
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
 Total number of observations=%d <br>              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 <hr  size=\"2\" color=\"#EC5E5E\">                if(agev[m][i]==1) agev[m][i]=iagemax+2;
 <li>Outputs files<br><br>\n                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n                if (m<lastpass) {
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>                }
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>                
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>                  dateintsum=dateintsum+k2;
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>                  k2cpt++;
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>                }
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>                /*}*/
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>            }
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);          }
          }
 fprintf(fichtm," <li>Graphs</li><p>");         
         /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
  m=cptcoveff;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
  jj1=0;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  for(k1=1; k1<=m;k1++){          fprintf(ficresp, "**********\n#");
    for(i1=1; i1<=ncodemax[k1];i1++){        }
        jj1++;        for(i=1; i<=nlstate;i++) 
        if (cptcovn > 0) {          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        fprintf(ficresp, "\n");
          for (cpt=1; cpt<=cptcoveff;cpt++)        
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);        for(i=iagemin; i <= iagemax+3; i++){
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          if(i==iagemax+3){
        }            fprintf(ficlog,"Total");
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          }else{
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                if(first==1){
        for(cpt=1; cpt<nlstate;cpt++){              first=0;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>              printf("See log file for details...\n");
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            }
        }            fprintf(ficlog,"Age %d", i);
     for(cpt=1; cpt<=nlstate;cpt++) {          }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          for(jk=1; jk <=nlstate ; jk++){
 interval) in state (%d): v%s%d%d.gif <br>            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                pp[jk] += freq[jk][m][i]; 
      }          }
      for(cpt=1; cpt<=nlstate;cpt++) {          for(jk=1; jk <=nlstate ; jk++){
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>            for(m=-1, pos=0; m <=0 ; m++)
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              pos += freq[jk][m][i];
      }            if(pp[jk]>=1.e-10){
      fprintf(fichtm,"\n<br>- Total life expectancy by age and              if(first==1){
 health expectancies in states (1) and (2): e%s%d.gif<br>              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              }
 fprintf(fichtm,"\n</body>");              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
    }            }else{
    }              if(first==1)
 fclose(fichtm);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
 /******************* Gnuplot file **************/          }
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){  
           for(jk=1; jk <=nlstate ; jk++){
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
   strcpy(optionfilegnuplot,optionfilefiname);          }       
   strcat(optionfilegnuplot,".plt");          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {            pos += pp[jk];
     printf("Problem with file %s",optionfilegnuplot);            posprop += prop[jk][i];
   }          }
           for(jk=1; jk <=nlstate ; jk++){
 #ifdef windows            if(pos>=1.e-5){
     fprintf(ficgp,"cd \"%s\" \n",pathc);              if(first==1)
 #endif                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 m=pow(2,cptcoveff);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
              }else{
  /* 1eme*/              if(first==1)
   for (cpt=1; cpt<= nlstate ; cpt ++) {                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
    for (k1=1; k1<= m ; k1 ++) {              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
 #ifdef windows            if( i <= iagemax){
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);              if(pos>=1.e-5){
 #endif                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
 #ifdef unix                /*probs[i][jk][j1]= pp[jk]/pos;*/
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
 #endif              }
               else
 for (i=1; i<= nlstate ; i ++) {                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            }
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }          
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          for(jk=-1; jk <=nlstate+ndeath; jk++)
     for (i=1; i<= nlstate ; i ++) {            for(m=-1; m <=nlstate+ndeath; m++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              if(freq[jk][m][i] !=0 ) {
   else fprintf(ficgp," \%%*lf (\%%*lf)");              if(first==1)
 }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
      for (i=1; i<= nlstate ; i ++) {              }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          if(i <= iagemax)
   else fprintf(ficgp," \%%*lf (\%%*lf)");            fprintf(ficresp,"\n");
 }            if(first==1)
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));            printf("Others in log...\n");
 #ifdef unix          fprintf(ficlog,"\n");
 fprintf(ficgp,"\nset ter gif small size 400,300");        }
 #endif      }
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    }
    }    dateintmean=dateintsum/k2cpt; 
   }   
   /*2 eme*/    fclose(ficresp);
     free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
   for (k1=1; k1<= m ; k1 ++) {    free_vector(pp,1,nlstate);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
        /* End of Freq */
     for (i=1; i<= nlstate+1 ; i ++) {  }
       k=2*i;  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  /************ Prevalence ********************/
       for (j=1; j<= nlstate+1 ; j ++) {  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)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  {  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
 }         in each health status at the date of interview (if between dateprev1 and dateprev2).
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");       We still use firstpass and lastpass as another selection.
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);   
       for (j=1; j<= nlstate+1 ; j ++) {    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double ***freq; /* Frequencies */
         else fprintf(ficgp," \%%*lf (\%%*lf)");    double *pp, **prop;
 }      double pos,posprop; 
       fprintf(ficgp,"\" t\"\" w l 0,");    double  y2; /* in fractional years */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    int iagemin, iagemax;
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    iagemin= (int) agemin;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    iagemax= (int) agemax;
 }      /*pp=vector(1,nlstate);*/
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       else fprintf(ficgp,"\" t\"\" w l 0,");    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     }    j1=0;
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    
   }    j=cptcoveff;
      if (cptcovn<1) {j=1;ncodemax[1]=1;}
   /*3eme*/    
     for(k1=1; k1<=j;k1++){
   for (k1=1; k1<= m ; k1 ++) {      for(i1=1; i1<=ncodemax[k1];i1++){
     for (cpt=1; cpt<= nlstate ; cpt ++) {        j1++;
       k=2+nlstate*(cpt-1);        
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);        for (i=1; i<=nlstate; i++)  
       for (i=1; i< nlstate ; i ++) {          for(m=iagemin; m <= iagemax+3; m++)
         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);            prop[i][m]=0.0;
       }       
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        for (i=1; i<=imx; i++) { /* Each individual */
     }          bool=1;
     }          if  (cptcovn>0) {
              for (z1=1; z1<=cptcoveff; z1++) 
   /* CV preval stat */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     for (k1=1; k1<= m ; k1 ++) {                bool=0;
     for (cpt=1; cpt<nlstate ; cpt ++) {          } 
       k=3;          if (bool==1) { 
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       for (i=1; i< nlstate ; i ++)              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         fprintf(ficgp,"+$%d",k+i+1);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                      if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
       l=3+(nlstate+ndeath)*cpt;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
       for (i=1; i< nlstate ; i ++) {                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
         l=3+(nlstate+ndeath)*cpt;                  prop[s[m][i]][iagemax+3] += weight[i]; 
         fprintf(ficgp,"+$%d",l+i+1);                } 
       }              }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);              } /* end selection of waves */
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          }
     }        }
   }          for(i=iagemin; i <= iagemax+3; i++){  
            
   /* proba elementaires */          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
    for(i=1,jk=1; i <=nlstate; i++){            posprop += prop[jk][i]; 
     for(k=1; k <=(nlstate+ndeath); k++){          } 
       if (k != i) {  
         for(j=1; j <=ncovmodel; j++){          for(jk=1; jk <=nlstate ; jk++){     
                    if( i <=  iagemax){ 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);              if(posprop>=1.e-5){ 
           jk++;                probs[i][jk][j1]= prop[jk][i]/posprop;
           fprintf(ficgp,"\n");              } 
         }            } 
       }          }/* end jk */ 
     }        }/* end i */ 
     }      } /* end i1 */
     } /* end k1 */
     for(jk=1; jk <=m; jk++) {    
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
    i=1;    /*free_vector(pp,1,nlstate);*/
    for(k2=1; k2<=nlstate; k2++) {    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
      k3=i;  }  /* End of prevalence */
      for(k=1; k<=(nlstate+ndeath); k++) {  
        if (k != k2){  /************* Waves Concatenation ***************/
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  
 ij=1;  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
         for(j=3; j <=ncovmodel; j++) {  {
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);       Death is a valid wave (if date is known).
             ij++;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
           }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
           else       and mw[mi+1][i]. dh depends on stepm.
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);       */
         }  
           fprintf(ficgp,")/(1");    int i, mi, m;
            /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         for(k1=1; k1 <=nlstate; k1++){         double sum=0., jmean=0.;*/
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    int first;
 ij=1;    int j, k=0,jk, ju, jl;
           for(j=3; j <=ncovmodel; j++){    double sum=0.;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    first=0;
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    jmin=1e+5;
             ij++;    jmax=-1;
           }    jmean=0.;
           else    for(i=1; i<=imx; i++){
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      mi=0;
           }      m=firstpass;
           fprintf(ficgp,")");      while(s[m][i] <= nlstate){
         }        if(s[m][i]>=1)
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);          mw[++mi][i]=m;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        if(m >=lastpass)
         i=i+ncovmodel;          break;
        }        else
      }          m++;
    }      }/* end while */
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      if (s[m][i] > nlstate){
    }        mi++;     /* Death is another wave */
            /* if(mi==0)  never been interviewed correctly before death */
   fclose(ficgp);           /* Only death is a correct wave */
 }  /* end gnuplot */        mw[mi][i]=m;
       }
   
 /*************** Moving average **************/      wav[i]=mi;
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){      if(mi==0){
         nbwarn++;
   int i, cpt, cptcod;        if(first==0){
     for (agedeb=agemin; agedeb<=fage; agedeb++)          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       for (i=1; i<=nlstate;i++)          first=1;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        }
           mobaverage[(int)agedeb][i][cptcod]=0.;        if(first==1){
              fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){        }
       for (i=1; i<=nlstate;i++){      } /* end mi==0 */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    } /* End individuals */
           for (cpt=0;cpt<=4;cpt++){  
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    for(i=1; i<=imx; i++){
           }      for(mi=1; mi<wav[i];mi++){
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        if (stepm <=0)
         }          dh[mi][i]=1;
       }        else{
     }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                if (agedc[i] < 2*AGESUP) {
 }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
 /************** Forecasting ******************/                nberr++;
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                  j=1; /* Temporary Dangerous patch */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                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);
   int *popage;                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]);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;                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);
   double *popeffectif,*popcount;              }
   double ***p3mat;              k=k+1;
   char fileresf[FILENAMELENGTH];              if (j >= jmax) jmax=j;
               if (j <= jmin) jmin=j;
  agelim=AGESUP;              sum=sum+j;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            }
            }
            else{
   strcpy(fileresf,"f");            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   strcat(fileresf,fileres);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   if((ficresf=fopen(fileresf,"w"))==NULL) {            k=k+1;
     printf("Problem with forecast resultfile: %s\n", fileresf);            if (j >= jmax) jmax=j;
   }            else if (j <= jmin)jmin=j;
   printf("Computing forecasting: result on file '%s' \n", fileresf);            /*        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]);*/
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            if(j<0){
               nberr++;
   if (mobilav==1) {              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]);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              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]);
     movingaverage(agedeb, fage, agemin, mobaverage);            }
   }            sum=sum+j;
           }
   stepsize=(int) (stepm+YEARM-1)/YEARM;          jk= j/stepm;
   if (stepm<=12) stepsize=1;          jl= j -jk*stepm;
            ju= j -(jk+1)*stepm;
   agelim=AGESUP;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
              if(jl==0){
   hstepm=1;              dh[mi][i]=jk;
   hstepm=hstepm/stepm;              bh[mi][i]=0;
   yp1=modf(dateintmean,&yp);            }else{ /* We want a negative bias in order to only have interpolation ie
   anprojmean=yp;                    * at the price of an extra matrix product in likelihood */
   yp2=modf((yp1*12),&yp);              dh[mi][i]=jk+1;
   mprojmean=yp;              bh[mi][i]=ju;
   yp1=modf((yp2*30.5),&yp);            }
   jprojmean=yp;          }else{
   if(jprojmean==0) jprojmean=1;            if(jl <= -ju){
   if(mprojmean==0) jprojmean=1;              dh[mi][i]=jk;
                bh[mi][i]=jl;       /* bias is positive if real duration
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);                                   * is higher than the multiple of stepm and negative otherwise.
                                     */
   for(cptcov=1;cptcov<=i2;cptcov++){            }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            else{
       k=k+1;              dh[mi][i]=jk+1;
       fprintf(ficresf,"\n#******");              bh[mi][i]=ju;
       for(j=1;j<=cptcoveff;j++) {            }
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            if(dh[mi][i]==0){
       }              dh[mi][i]=1; /* At least one step */
       fprintf(ficresf,"******\n");              bh[mi][i]=ju; /* At least one step */
       fprintf(ficresf,"# StartingAge FinalAge");              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);            }
                } /* end if mle */
              }
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      } /* end wave */
         fprintf(ficresf,"\n");    }
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      jmean=sum/k;
     printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);   }
           nhstepm = nhstepm/hstepm;  
            /*********** Tricode ****************************/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  void tricode(int *Tvar, int **nbcode, int imx)
           oldm=oldms;savm=savms;  {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      
            int Ndum[20],ij=1, k, j, i, maxncov=19;
           for (h=0; h<=nhstepm; h++){    int cptcode=0;
             if (h==(int) (calagedate+YEARM*cpt)) {    cptcoveff=0; 
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);   
             }    for (k=0; k<maxncov; k++) Ndum[k]=0;
             for(j=1; j<=nlstate+ndeath;j++) {    for (k=1; k<=7; k++) ncodemax[k]=0;
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                  for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
                 if (mobilav==1)      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                                 modality*/ 
                 else {        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        Ndum[ij]++; /*store the modality */
                 }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
                        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
               }                                         Tvar[j]. If V=sex and male is 0 and 
               if (h==(int)(calagedate+12*cpt)){                                         female is 1, then  cptcode=1.*/
                 fprintf(ficresf," %.3f", kk1);      }
                          
               }      for (i=0; i<=cptcode; i++) {
             }        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
           }      }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }      ij=1; 
       }      for (i=1; i<=ncodemax[j]; i++) {
     }        for (k=0; k<= maxncov; k++) {
   }          if (Ndum[k] != 0) {
                    nbcode[Tvar[j]][ij]=k; 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            /* 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; */
             
   fclose(ficresf);            ij++;
 }          }
 /************** Forecasting ******************/          if (ij > ncodemax[j]) break; 
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){        }  
        } 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    }  
   int *popage;  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;   for (k=0; k< maxncov; k++) Ndum[k]=0;
   double *popeffectif,*popcount;  
   double ***p3mat,***tabpop,***tabpopprev;   for (i=1; i<=ncovmodel-2; i++) { 
   char filerespop[FILENAMELENGTH];     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
      ij=Tvar[i];
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     Ndum[ij]++;
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   }
   agelim=AGESUP;  
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;   ij=1;
     for (i=1; i<= maxncov; i++) {
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);     if((Ndum[i]!=0) && (i<=ncovcol)){
         Tvaraff[ij]=i; /*For printing */
         ij++;
   strcpy(filerespop,"pop");     }
   strcat(filerespop,fileres);   }
   if((ficrespop=fopen(filerespop,"w"))==NULL) {   
     printf("Problem with forecast resultfile: %s\n", filerespop);   cptcoveff=ij-1; /*Number of simple covariates*/
   }  }
   printf("Computing forecasting: result on file '%s' \n", filerespop);  
   /*********** Health Expectancies ****************/
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
   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 )
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  {
     movingaverage(agedeb, fage, agemin, mobaverage);    /* Health expectancies */
   }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     double age, agelim, hf;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double ***p3mat,***varhe;
   if (stepm<=12) stepsize=1;    double **dnewm,**doldm;
      double *xp;
   agelim=AGESUP;    double **gp, **gm;
      double ***gradg, ***trgradg;
   hstepm=1;    int theta;
   hstepm=hstepm/stepm;  
      varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   if (popforecast==1) {    xp=vector(1,npar);
     if((ficpop=fopen(popfile,"r"))==NULL) {    dnewm=matrix(1,nlstate*nlstate,1,npar);
       printf("Problem with population file : %s\n",popfile);exit(0);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     }    
     popage=ivector(0,AGESUP);    fprintf(ficreseij,"# Health expectancies\n");
     popeffectif=vector(0,AGESUP);    fprintf(ficreseij,"# Age");
     popcount=vector(0,AGESUP);    for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++)
     i=1;          fprintf(ficreseij," %1d-%1d (SE)",i,j);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    fprintf(ficreseij,"\n");
      
     imx=i;    if(estepm < stepm){
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      printf ("Problem %d lower than %d\n",estepm, stepm);
   }    }
     else  hstepm=estepm;   
   for(cptcov=1;cptcov<=i2;cptcov++){    /* We compute the life expectancy from trapezoids spaced every estepm months
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){     * This is mainly to measure the difference between two models: for example
       k=k+1;     * if stepm=24 months pijx are given only every 2 years and by summing them
       fprintf(ficrespop,"\n#******");     * we are calculating an estimate of the Life Expectancy assuming a linear 
       for(j=1;j<=cptcoveff;j++) {     * progression in between and thus overestimating or underestimating according
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     * 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
       fprintf(ficrespop,"******\n");     * to compare the new estimate of Life expectancy with the same linear 
       fprintf(ficrespop,"# Age");     * hypothesis. A more precise result, taking into account a more precise
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);     * curvature will be obtained if estepm is as small as stepm. */
       if (popforecast==1)  fprintf(ficrespop," [Population]");  
          /* For example we decided to compute the life expectancy with the smallest unit */
       for (cpt=0; cpt<=0;cpt++) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);         nhstepm is the number of hstepm from age to agelim 
               nstepm is the number of stepm from age to agelin. 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){       Look at hpijx to understand the reason of that which relies in memory size
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);       and note for a fixed period like estepm months */
           nhstepm = nhstepm/hstepm;    /* 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
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       means that if the survival funtion is printed only each two years of age and if
           oldm=oldms;savm=savms;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         results. So we changed our mind and took the option of the best precision.
            */
           for (h=0; h<=nhstepm; h++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    agelim=AGESUP;
             }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
             for(j=1; j<=nlstate+ndeath;j++) {      /* nhstepm age range expressed in number of stepm */
               kk1=0.;kk2=0;      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
               for(i=1; i<=nlstate;i++) {                    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                 if (mobilav==1)      /* if (stepm >= YEARM) hstepm=1;*/
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                 else {      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
                 }      gp=matrix(0,nhstepm,1,nlstate*nlstate);
               }      gm=matrix(0,nhstepm,1,nlstate*nlstate);
               if (h==(int)(calagedate+12*cpt)){  
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
                   /*fprintf(ficrespop," %.3f", kk1);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
               }   
             }  
             for(i=1; i<=nlstate;i++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
               kk1=0.;  
                 for(j=1; j<=nlstate;j++){      /* Computing  Variances of health expectancies */
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  
                 }       for(theta=1; theta <=npar; theta++){
                   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<=npar; i++){ 
             }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    
           }        cptj=0;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(j=1; j<= nlstate; j++){
         }          for(i=1; i<=nlstate; i++){
       }            cptj=cptj+1;
              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=1; cpt<=(anpyram1-anpyram);cpt++) {          }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){       
           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 (h=0; h<=nhstepm; h++){        for(j=1; j<= nlstate; j++){
             if (h==(int) (calagedate+YEARM*cpt)) {          for(i=1;i<=nlstate;i++){
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);            cptj=cptj+1;
             }            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
               for(i=1; i<=nlstate;i++) {                          }
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              }
               }        }
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);        for(j=1; j<= nlstate*nlstate; j++)
             }          for(h=0; h<=nhstepm-1; h++){
           }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
         }       } 
       }     
    }  /* End theta */
   }  
         trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
        for(h=0; h<=nhstepm-1; h++)
   if (popforecast==1) {        for(j=1; j<=nlstate*nlstate;j++)
     free_ivector(popage,0,AGESUP);          for(theta=1; theta <=npar; theta++)
     free_vector(popeffectif,0,AGESUP);            trgradg[h][j][theta]=gradg[h][theta][j];
     free_vector(popcount,0,AGESUP);       
   }  
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       for(i=1;i<=nlstate*nlstate;i++)
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(j=1;j<=nlstate*nlstate;j++)
   fclose(ficrespop);          varhe[i][j][(int)age] =0.;
 }  
        printf("%d|",(int)age);fflush(stdout);
 /***********************************************/       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 /**************** Main Program *****************/       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);
 int main(int argc, char *argv[])          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++)
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   double agedeb, agefin,hf;        }
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      }
       /* Computing expectancies */
   double fret;      for(i=1; i<=nlstate;i++)
   double **xi,tmp,delta;        for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   double dum; /* Dummy variable */            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   double ***p3mat;            
   int *indx;  /* 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]);*/
   char line[MAXLINE], linepar[MAXLINE];  
   char title[MAXLINE];          }
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];      fprintf(ficreseij,"%3.0f",age );
        cptj=0;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
   char filerest[FILENAMELENGTH];          cptj++;
   char fileregp[FILENAMELENGTH];          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   char popfile[FILENAMELENGTH];        }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      fprintf(ficreseij,"\n");
   int firstobs=1, lastobs=10;     
   int sdeb, sfin; /* Status at beginning and end */      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   int c,  h , cpt,l;      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   int ju,jl, mi;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   int mobilav=0,popforecast=0;    }
   int hstepm, nhstepm;    printf("\n");
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    fprintf(ficlog,"\n");
   
   double bage, fage, age, agelim, agebase;    free_vector(xp,1,npar);
   double ftolpl=FTOL;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   double **prlim;    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   double *severity;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   double ***param; /* Matrix of parameters */  }
   double  *p;  
   double **matcov; /* Matrix of covariance */  /************ Variance ******************/
   double ***delti3; /* Scale */  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)
   double *delti; /* Scale */  {
   double ***eij, ***vareij;    /* Variance of health expectancies */
   double **varpl; /* Variances of prevalence limits by age */    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   double *epj, vepp;    /* double **newm;*/
   double kk1, kk2;    double **dnewm,**doldm;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    double **dnewmp,**doldmp;
      int i, j, nhstepm, hstepm, h, nstepm ;
     int k, cptcode;
   char version[80]="Imach version 0.71, February 2002, INED-EUROREVES ";    double *xp;
   char *alph[]={"a","a","b","c","d","e"}, str[4];    double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
   char z[1]="c", occ;    double *gpp, *gmp; /* for var p point j */
 #include <sys/time.h>    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
 #include <time.h>    double ***p3mat;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    double age,agelim, hf;
      double ***mobaverage;
   /* long total_usecs;    int theta;
   struct timeval start_time, end_time;    char digit[4];
      char digitp[25];
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  
     char fileresprobmorprev[FILENAMELENGTH];
   
   printf("\n%s",version);    if(popbased==1){
   if(argc <=1){      if(mobilav!=0)
     printf("\nEnter the parameter file name: ");        strcpy(digitp,"-populbased-mobilav-");
     scanf("%s",pathtot);      else strcpy(digitp,"-populbased-nomobil-");
   }    }
   else{    else 
     strcpy(pathtot,argv[1]);      strcpy(digitp,"-stablbased-");
   }  
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    if (mobilav!=0) {
   /*cygwin_split_path(pathtot,path,optionfile);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   /* cutv(path,optionfile,pathtot,'\\');*/        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);      }
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    }
   chdir(path);  
   replace(pathc,path);    strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
 /*-------- arguments in the command line --------*/    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
   strcpy(fileres,"r");    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   strcat(fileres, optionfilefiname);    strcat(fileresprobmorprev,fileres);
   strcat(fileres,".txt");    /* Other files have txt extension */    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
   /*---------arguments file --------*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     printf("Problem with optionfile %s\n",optionfile);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     goto end;    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++){
   strcpy(filereso,"o");      fprintf(ficresprobmorprev," p.%-d SE",j);
   strcat(filereso,fileres);      for(i=1; i<=nlstate;i++)
   if((ficparo=fopen(filereso,"w"))==NULL) {        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    }  
   }    fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
   /* Reads comments: lines beginning with '#' */    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");
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     ungetc(c,ficpar);  /*   } */
     fgets(line, MAXLINE, ficpar);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     puts(line);  
     fputs(line,ficparo);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
   }    fprintf(ficresvij,"# Age");
   ungetc(c,ficpar);    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    fprintf(ficresvij,"\n");
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);  
 while((c=getc(ficpar))=='#' && c!= EOF){    xp=vector(1,npar);
     ungetc(c,ficpar);    dnewm=matrix(1,nlstate,1,npar);
     fgets(line, MAXLINE, ficpar);    doldm=matrix(1,nlstate,1,nlstate);
     puts(line);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     fputs(line,ficparo);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }  
   ungetc(c,ficpar);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
      gpp=vector(nlstate+1,nlstate+ndeath);
        gmp=vector(nlstate+1,nlstate+ndeath);
   covar=matrix(0,NCOVMAX,1,n);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   cptcovn=0;    
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   ncovmodel=2+cptcovn;    }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    else  hstepm=estepm;   
      /* For example we decided to compute the life expectancy with the smallest unit */
   /* Read guess parameters */    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   /* Reads comments: lines beginning with '#' */       nhstepm is the number of hstepm from age to agelim 
   while((c=getc(ficpar))=='#' && c!= EOF){       nstepm is the number of stepm from age to agelin. 
     ungetc(c,ficpar);       Look at hpijx to understand the reason of that which relies in memory size
     fgets(line, MAXLINE, ficpar);       and note for a fixed period like k years */
     puts(line);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     fputs(line,ficparo);       survival function given by stepm (the optimization length). Unfortunately it
   }       means that if the survival funtion is printed every two years of age and if
   ungetc(c,ficpar);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         results. So we changed our mind and took the option of the best precision.
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    */
     for(i=1; i <=nlstate; i++)    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     for(j=1; j <=nlstate+ndeath-1; j++){    agelim = AGESUP;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       fprintf(ficparo,"%1d%1d",i1,j1);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       printf("%1d%1d",i,j);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       for(k=1; k<=ncovmodel;k++){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fscanf(ficpar," %lf",&param[i][j][k]);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
         printf(" %lf",param[i][j][k]);      gp=matrix(0,nhstepm,1,nlstate);
         fprintf(ficparo," %lf",param[i][j][k]);      gm=matrix(0,nhstepm,1,nlstate);
       }  
       fscanf(ficpar,"\n");  
       printf("\n");      for(theta=1; theta <=npar; theta++){
       fprintf(ficparo,"\n");        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          }
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   p=param[1][1];  
          if (popbased==1) {
   /* Reads comments: lines beginning with '#' */          if(mobilav ==0){
   while((c=getc(ficpar))=='#' && c!= EOF){            for(i=1; i<=nlstate;i++)
     ungetc(c,ficpar);              prlim[i][i]=probs[(int)age][i][ij];
     fgets(line, MAXLINE, ficpar);          }else{ /* mobilav */ 
     puts(line);            for(i=1; i<=nlstate;i++)
     fputs(line,ficparo);              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
   ungetc(c,ficpar);        }
     
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        for(j=1; j<= nlstate; j++){
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          for(h=0; h<=nhstepm; h++){
   for(i=1; i <=nlstate; i++){            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     for(j=1; j <=nlstate+ndeath-1; j++){              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
       fscanf(ficpar,"%1d%1d",&i1,&j1);          }
       printf("%1d%1d",i,j);        }
       fprintf(ficparo,"%1d%1d",i1,j1);        /* This for computing probability of death (h=1 means
       for(k=1; k<=ncovmodel;k++){           computed over hstepm matrices product = hstepm*stepm months) 
         fscanf(ficpar,"%le",&delti3[i][j][k]);           as a weighted average of prlim.
         printf(" %le",delti3[i][j][k]);        */
         fprintf(ficparo," %le",delti3[i][j][k]);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       }          for(i=1,gpp[j]=0.; i<= nlstate; i++)
       fscanf(ficpar,"\n");            gpp[j] += prlim[i][i]*p3mat[i][j][1];
       printf("\n");        }    
       fprintf(ficparo,"\n");        /* end probability of death */
     }  
   }        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   delti=delti3[1][1];          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   /* Reads comments: lines beginning with '#' */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   while((c=getc(ficpar))=='#' && c!= EOF){   
     ungetc(c,ficpar);        if (popbased==1) {
     fgets(line, MAXLINE, ficpar);          if(mobilav ==0){
     puts(line);            for(i=1; i<=nlstate;i++)
     fputs(line,ficparo);              prlim[i][i]=probs[(int)age][i][ij];
   }          }else{ /* mobilav */ 
   ungetc(c,ficpar);            for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
   matcov=matrix(1,npar,1,npar);          }
   for(i=1; i <=npar; i++){        }
     fscanf(ficpar,"%s",&str);  
     printf("%s",str);        for(j=1; j<= nlstate; j++){
     fprintf(ficparo,"%s",str);          for(h=0; h<=nhstepm; h++){
     for(j=1; j <=i; j++){            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
       fscanf(ficpar," %le",&matcov[i][j]);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
       printf(" %.5le",matcov[i][j]);          }
       fprintf(ficparo," %.5le",matcov[i][j]);        }
     }        /* This for computing probability of death (h=1 means
     fscanf(ficpar,"\n");           computed over hstepm matrices product = hstepm*stepm months) 
     printf("\n");           as a weighted average of prlim.
     fprintf(ficparo,"\n");        */
   }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   for(i=1; i <=npar; i++)          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     for(j=i+1;j<=npar;j++)           gmp[j] += prlim[i][i]*p3mat[i][j][1];
       matcov[i][j]=matcov[j][i];        }    
            /* end probability of death */
   printf("\n");  
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
     /*-------- Rewriting paramater file ----------*/            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
      strcpy(rfileres,"r");    /* "Rparameterfile */          }
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/  
      strcat(rfileres,".");    /* */        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
      strcat(rfileres,optionfilext);    /* Other files have txt extension */          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     if((ficres =fopen(rfileres,"w"))==NULL) {        }
       printf("Problem writing new parameter file: %s\n", fileres);goto end;  
     }      } /* End theta */
     fprintf(ficres,"#%s\n",version);  
          trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     /*-------- data file ----------*/  
     if((fic=fopen(datafile,"r"))==NULL)    {      for(h=0; h<=nhstepm; h++) /* veij */
       printf("Problem with datafile: %s\n", datafile);goto end;        for(j=1; j<=nlstate;j++)
     }          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
     n= lastobs;  
     severity = vector(1,maxwav);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     outcome=imatrix(1,maxwav+1,1,n);        for(theta=1; theta <=npar; theta++)
     num=ivector(1,n);          trgradgp[j][theta]=gradgp[theta][j];
     moisnais=vector(1,n);    
     annais=vector(1,n);  
     moisdc=vector(1,n);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     andc=vector(1,n);      for(i=1;i<=nlstate;i++)
     agedc=vector(1,n);        for(j=1;j<=nlstate;j++)
     cod=ivector(1,n);          vareij[i][j][(int)age] =0.;
     weight=vector(1,n);  
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      for(h=0;h<=nhstepm;h++){
     mint=matrix(1,maxwav,1,n);        for(k=0;k<=nhstepm;k++){
     anint=matrix(1,maxwav,1,n);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     s=imatrix(1,maxwav+1,1,n);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
     adl=imatrix(1,maxwav+1,1,n);              for(i=1;i<=nlstate;i++)
     tab=ivector(1,NCOVMAX);            for(j=1;j<=nlstate;j++)
     ncodemax=ivector(1,8);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
     i=1;      }
     while (fgets(line, MAXLINE, fic) != NULL)    {    
       if ((i >= firstobs) && (i <=lastobs)) {      /* pptj */
              matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
         for (j=maxwav;j>=1;j--){      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
           strcpy(line,stra);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          varppt[j][i]=doldmp[j][i];
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      /* end ppptj */
         }      /*  x centered again */
              hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);   
       if (popbased==1) {
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        if(mobilav ==0){
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        }else{ /* mobilav */ 
         for (j=ncov;j>=1;j--){          for(i=1; i<=nlstate;i++)
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);            prlim[i][i]=mobaverage[(int)age][i][ij];
         }        }
         num[i]=atol(stra);      }
                       
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){      /* This for computing probability of death (h=1 means
           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;}*/         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
         i=i+1;      */
       }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
     }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     /* printf("ii=%d", ij);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
        scanf("%d",i);*/      }    
   imx=i-1; /* Number of individuals */      /* end probability of death */
   
   /* for (i=1; i<=imx; i++){      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;        for(i=1; i<=nlstate;i++){
     }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
     for (i=1; i<=imx; i++)      } 
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/      fprintf(ficresprobmorprev,"\n");
   
   /* Calculation of the number of parameter from char model*/      fprintf(ficresvij,"%.0f ",age );
   Tvar=ivector(1,15);      for(i=1; i<=nlstate;i++)
   Tprod=ivector(1,15);        for(j=1; j<=nlstate;j++){
   Tvaraff=ivector(1,15);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   Tvard=imatrix(1,15,1,2);        }
   Tage=ivector(1,15);            fprintf(ficresvij,"\n");
          free_matrix(gp,0,nhstepm,1,nlstate);
   if (strlen(model) >1){      free_matrix(gm,0,nhstepm,1,nlstate);
     j=0, j1=0, k1=1, k2=1;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     j=nbocc(model,'+');      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     j1=nbocc(model,'*');      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     cptcovn=j+1;    } /* End age */
     cptcovprod=j1;    free_vector(gpp,nlstate+1,nlstate+ndeath);
        free_vector(gmp,nlstate+1,nlstate+ndeath);
        free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     strcpy(modelsav,model);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
       printf("Error. Non available option model=%s ",model);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       goto end;    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     }  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
      /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
     for(i=(j+1); i>=1;i--){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
       cutv(stra,strb,modelsav,'+');    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
       /*scanf("%d",i);*/    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
       if (strchr(strb,'*')) {    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);
         cutv(strd,strc,strb,'*');    /*  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);
         if (strcmp(strc,"age")==0) {  */
           cptcovprod--;  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
           cutv(strb,stre,strd,'V');    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
           Tvar[i]=atoi(stre);  
           cptcovage++;    free_vector(xp,1,npar);
             Tage[cptcovage]=i;    free_matrix(doldm,1,nlstate,1,nlstate);
             /*printf("stre=%s ", stre);*/    free_matrix(dnewm,1,nlstate,1,npar);
         }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         else if (strcmp(strd,"age")==0) {    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
           cptcovprod--;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           cutv(strb,stre,strc,'V');    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           Tvar[i]=atoi(stre);    fclose(ficresprobmorprev);
           cptcovage++;    fflush(ficgp);
           Tage[cptcovage]=i;    fflush(fichtm); 
         }  }  /* end varevsij */
         else {  
           cutv(strb,stre,strc,'V');  /************ Variance of prevlim ******************/
           Tvar[i]=ncov+k1;  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)
           cutv(strb,strc,strd,'V');  {
           Tprod[k1]=i;    /* Variance of prevalence limit */
           Tvard[k1][1]=atoi(strc);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
           Tvard[k1][2]=atoi(stre);    double **newm;
           Tvar[cptcovn+k2]=Tvard[k1][1];    double **dnewm,**doldm;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    int i, j, nhstepm, hstepm;
           for (k=1; k<=lastobs;k++)    int k, cptcode;
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    double *xp;
           k1++;    double *gp, *gm;
           k2=k2+2;    double **gradg, **trgradg;
         }    double age,agelim;
       }    int theta;
       else {     
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
        /*  scanf("%d",i);*/    fprintf(ficresvpl,"# Age");
       cutv(strd,strc,strb,'V');    for(i=1; i<=nlstate;i++)
       Tvar[i]=atoi(strc);        fprintf(ficresvpl," %1d-%1d",i,i);
       }    fprintf(ficresvpl,"\n");
       strcpy(modelsav,stra);    
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    xp=vector(1,npar);
         scanf("%d",i);*/    dnewm=matrix(1,nlstate,1,npar);
     }    doldm=matrix(1,nlstate,1,nlstate);
 }    
      hstepm=1*YEARM; /* Every year of age */
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   printf("cptcovprod=%d ", cptcovprod);    agelim = AGESUP;
   scanf("%d ",i);*/    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     fclose(fic);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
     /*  if(mle==1){*/      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     if (weightopt != 1) { /* Maximisation without weights*/      gradg=matrix(1,npar,1,nlstate);
       for(i=1;i<=n;i++) weight[i]=1.0;      gp=vector(1,nlstate);
     }      gm=vector(1,nlstate);
     /*-calculation of age at interview from date of interview and age at death -*/  
     agev=matrix(1,maxwav,1,imx);      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
    for (i=1; i<=imx; i++)          xp[i] = x[i] + (i==theta ?delti[theta]:0);
      for(m=2; (m<= maxwav); m++)        }
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
          anint[m][i]=9999;        for(i=1;i<=nlstate;i++)
          s[m][i]=-1;          gp[i] = prlim[i][i];
        }      
            for(i=1; i<=npar; i++) /* Computes gradient */
     for (i=1; i<=imx; i++)  {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       for(m=1; (m<= maxwav); m++){        for(i=1;i<=nlstate;i++)
         if(s[m][i] >0){          gm[i] = prlim[i][i];
           if (s[m][i] == nlstate+1) {  
             if(agedc[i]>0)        for(i=1;i<=nlstate;i++)
               if(moisdc[i]!=99 && andc[i]!=9999)          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
               agev[m][i]=agedc[i];      } /* End theta */
             else {  
               if (andc[i]!=9999){      trgradg =matrix(1,nlstate,1,npar);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;      for(j=1; j<=nlstate;j++)
               }        for(theta=1; theta <=npar; theta++)
             }          trgradg[j][theta]=gradg[theta][j];
           }  
           else if(s[m][i] !=9){ /* Should no more exist */      for(i=1;i<=nlstate;i++)
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        varpl[i][(int)age] =0.;
             if(mint[m][i]==99 || anint[m][i]==9999)      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
               agev[m][i]=1;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
             else if(agev[m][i] <agemin){      for(i=1;i<=nlstate;i++)
               agemin=agev[m][i];        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/  
             }      fprintf(ficresvpl,"%.0f ",age );
             else if(agev[m][i] >agemax){      for(i=1; i<=nlstate;i++)
               agemax=agev[m][i];        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      fprintf(ficresvpl,"\n");
             }      free_vector(gp,1,nlstate);
             /*agev[m][i]=anint[m][i]-annais[i];*/      free_vector(gm,1,nlstate);
             /*   agev[m][i] = age[i]+2*m;*/      free_matrix(gradg,1,npar,1,nlstate);
           }      free_matrix(trgradg,1,nlstate,1,npar);
           else { /* =9 */    } /* End age */
             agev[m][i]=1;  
             s[m][i]=-1;    free_vector(xp,1,npar);
           }    free_matrix(doldm,1,nlstate,1,npar);
         }    free_matrix(dnewm,1,nlstate,1,nlstate);
         else /*= 0 Unknown */  
           agev[m][i]=1;  }
       }  
      /************ 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=1; (m<= maxwav); m++){    int i, j=0,  i1, k1, l1, t, tj;
         if (s[m][i] > (nlstate+ndeath)) {    int k2, l2, j1,  z1;
           printf("Error: Wrong value in nlstate or ndeath\n");      int k=0,l, cptcode;
           goto end;    int first=1, first1;
         }    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
       }    double **dnewm,**doldm;
     }    double *xp;
     double *gp, *gm;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    double **gradg, **trgradg;
     double **mu;
     free_vector(severity,1,maxwav);    double age,agelim, cov[NCOVMAX];
     free_imatrix(outcome,1,maxwav+1,1,n);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     free_vector(moisnais,1,n);    int theta;
     free_vector(annais,1,n);    char fileresprob[FILENAMELENGTH];
     /* free_matrix(mint,1,maxwav,1,n);    char fileresprobcov[FILENAMELENGTH];
        free_matrix(anint,1,maxwav,1,n);*/    char fileresprobcor[FILENAMELENGTH];
     free_vector(moisdc,1,n);  
     free_vector(andc,1,n);    double ***varpij;
   
        strcpy(fileresprob,"prob"); 
     wav=ivector(1,imx);    strcat(fileresprob,fileres);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      printf("Problem with resultfile: %s\n", fileresprob);
          fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     /* Concatenates waves */    }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       Tcode=ivector(1,100);      printf("Problem with resultfile: %s\n", fileresprobcov);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
       ncodemax[1]=1;    }
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    strcpy(fileresprobcor,"probcor"); 
          strcat(fileresprobcor,fileres);
    codtab=imatrix(1,100,1,10);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
    h=0;      printf("Problem with resultfile: %s\n", fileresprobcor);
    m=pow(2,cptcoveff);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
      }
    for(k=1;k<=cptcoveff; k++){    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
      for(i=1; i <=(m/pow(2,k));i++){    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
        for(j=1; j <= ncodemax[k]; j++){    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
            h++;    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
            if (h>m) h=1;codtab[h][k]=j;    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");
      }    fprintf(ficresprob,"# Age");
    }    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
    /*for(i=1; i <=m ;i++){    fprintf(ficresprobcov,"# Age");
      for(k=1; k <=cptcovn; k++){  
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);  
      }    for(i=1; i<=nlstate;i++)
      printf("\n");      for(j=1; j<=(nlstate+ndeath);j++){
    }        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
    scanf("%d",i);*/        fprintf(ficresprobcov," p%1d-%1d ",i,j);
            fprintf(ficresprobcor," p%1d-%1d ",i,j);
    /* Calculates basic frequencies. Computes observed prevalence at single age      }  
        and prints on file fileres'p'. */   /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
        fprintf(ficresprobcor,"\n");
       */
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   xp=vector(1,npar);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
          first=1;
     /* For Powell, parameters are in a vector p[] starting at p[1]    fprintf(ficgp,"\n# Routine varprob");
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    fprintf(fichtm,"\n");
   
     if(mle==1){    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     }    file %s<br>\n",optionfilehtmcov);
        fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
     /*--------- results files --------------*/  and drawn. It helps understanding how is the covariance between two incidences.\
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
      fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
    jk=1;  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
    fprintf(ficres,"# Parameters\n");  standard deviations wide on each axis. <br>\
    printf("# Parameters\n");   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    for(i=1,jk=1; i <=nlstate; i++){   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
      for(k=1; k <=(nlstate+ndeath); k++){  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
        if (k != i)  
          {    cov[1]=1;
            printf("%d%d ",i,k);    tj=cptcoveff;
            fprintf(ficres,"%1d%1d ",i,k);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
            for(j=1; j <=ncovmodel; j++){    j1=0;
              printf("%f ",p[jk]);    for(t=1; t<=tj;t++){
              fprintf(ficres,"%f ",p[jk]);      for(i1=1; i1<=ncodemax[t];i1++){ 
              jk++;        j1++;
            }        if  (cptcovn>0) {
            printf("\n");          fprintf(ficresprob, "\n#********** Variable "); 
            fprintf(ficres,"\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
          }          fprintf(ficresprob, "**********\n#\n");
      }          fprintf(ficresprobcov, "\n#********** Variable "); 
    }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  if(mle==1){          fprintf(ficresprobcov, "**********\n#\n");
     /* Computing hessian and covariance matrix */          
     ftolhess=ftol; /* Usually correct */          fprintf(ficgp, "\n#********** Variable "); 
     hesscov(matcov, p, npar, delti, ftolhess, func);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  }          fprintf(ficgp, "**********\n#\n");
     fprintf(ficres,"# Scales\n");          
     printf("# Scales\n");          
      for(i=1,jk=1; i <=nlstate; i++){          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       for(j=1; j <=nlstate+ndeath; j++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         if (j!=i) {          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           fprintf(ficres,"%1d%1d",i,j);          
           printf("%1d%1d",i,j);          fprintf(ficresprobcor, "\n#********** Variable ");    
           for(k=1; k<=ncovmodel;k++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             printf(" %.5e",delti[jk]);          fprintf(ficresprobcor, "**********\n#");    
             fprintf(ficres," %.5e",delti[jk]);        }
             jk++;        
           }        for (age=bage; age<=fage; age ++){ 
           printf("\n");          cov[2]=age;
           fprintf(ficres,"\n");          for (k=1; k<=cptcovn;k++) {
         }            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
       }          }
      }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
              for (k=1; k<=cptcovprod;k++)
     k=1;            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     fprintf(ficres,"# Covariance\n");          
     printf("# Covariance\n");          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     for(i=1;i<=npar;i++){          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       /*  if (k>nlstate) k=1;          gp=vector(1,(nlstate)*(nlstate+ndeath));
       i1=(i-1)/(ncovmodel*nlstate)+1;          gm=vector(1,(nlstate)*(nlstate+ndeath));
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      
       printf("%s%d%d",alph[k],i1,tab[i]);*/          for(theta=1; theta <=npar; theta++){
       fprintf(ficres,"%3d",i);            for(i=1; i<=npar; i++)
       printf("%3d",i);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       for(j=1; j<=i;j++){            
         fprintf(ficres," %.5e",matcov[i][j]);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
         printf(" %.5e",matcov[i][j]);            
       }            k=0;
       fprintf(ficres,"\n");            for(i=1; i<= (nlstate); i++){
       printf("\n");              for(j=1; j<=(nlstate+ndeath);j++){
       k++;                k=k+1;
     }                gp[k]=pmmij[i][j];
                  }
     while((c=getc(ficpar))=='#' && c!= EOF){            }
       ungetc(c,ficpar);            
       fgets(line, MAXLINE, ficpar);            for(i=1; i<=npar; i++)
       puts(line);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       fputs(line,ficparo);      
     }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     ungetc(c,ficpar);            k=0;
              for(i=1; i<=(nlstate); i++){
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);              for(j=1; j<=(nlstate+ndeath);j++){
                    k=k+1;
     if (fage <= 2) {                gm[k]=pmmij[i][j];
       bage = agemin;              }
       fage = agemaxpar;            }
     }       
                for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);          }
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);  
            for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     while((c=getc(ficpar))=='#' && c!= EOF){            for(theta=1; theta <=npar; theta++)
     ungetc(c,ficpar);              trgradg[j][theta]=gradg[theta][j];
     fgets(line, MAXLINE, ficpar);          
     puts(line);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     fputs(line,ficparo);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   }          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   ungetc(c,ficpar);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
            free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          pmij(pmmij,cov,ncovmodel,x,nlstate);
                
   while((c=getc(ficpar))=='#' && c!= EOF){          k=0;
     ungetc(c,ficpar);          for(i=1; i<=(nlstate); i++){
     fgets(line, MAXLINE, ficpar);            for(j=1; j<=(nlstate+ndeath);j++){
     puts(line);              k=k+1;
     fputs(line,ficparo);              mu[k][(int) age]=pmmij[i][j];
   }            }
   ungetc(c,ficpar);          }
            for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
    dateprev1=anprev1+mprev1/12.+jprev1/365.;              varpij[i][j][(int)age] = doldm[i][j];
    dateprev2=anprev2+mprev2/12.+jprev2/365.;  
           /*printf("\n%d ",(int)age);
   fscanf(ficpar,"pop_based=%d\n",&popbased);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   fprintf(ficparo,"pop_based=%d\n",popbased);              printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   fprintf(ficres,"pop_based=%d\n",popbased);              fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
              }*/
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);          fprintf(ficresprob,"\n%d ",(int)age);
     fgets(line, MAXLINE, ficpar);          fprintf(ficresprobcov,"\n%d ",(int)age);
     puts(line);          fprintf(ficresprobcor,"\n%d ",(int)age);
     fputs(line,ficparo);  
   }          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]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
 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);          }
           i=0;
           for (k=1; k<=(nlstate);k++){
 while((c=getc(ficpar))=='#' && c!= EOF){            for (l=1; l<=(nlstate+ndeath);l++){ 
     ungetc(c,ficpar);              i=i++;
     fgets(line, MAXLINE, ficpar);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     puts(line);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     fputs(line,ficparo);              for (j=1; j<=i;j++){
   }                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   ungetc(c,ficpar);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);            }
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          }/* end of loop for state */
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        } /* end of loop for age */
   
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        /* Confidence intervalle of pij  */
         /*
 /*------------ gnuplot -------------*/          fprintf(ficgp,"\nset noparametric;unset label");
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);          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");
 /*------------ free_vector  -------------*/          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);
  chdir(path);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
            fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
  free_ivector(wav,1,imx);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        */
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    
  free_ivector(num,1,n);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
  free_vector(agedc,1,n);        first1=1;
  /*free_matrix(covar,1,NCOVMAX,1,n);*/        for (k2=1; k2<=(nlstate);k2++){
  fclose(ficparo);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
  fclose(ficres);            if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
 /*--------- index.htm --------*/            for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);                if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                  if(i<=j) continue;
   /*--------------- Prevalence limit --------------*/                for (age=bage; age<=fage; age ++){ 
                    if ((int)age %5==0){
   strcpy(filerespl,"pl");                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   strcat(filerespl,fileres);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;                    mu1=mu[i][(int) age]/stepm*YEARM ;
   }                    mu2=mu[j][(int) age]/stepm*YEARM;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);                    c12=cv12/sqrt(v1*v2);
   fprintf(ficrespl,"#Prevalence limit\n");                    /* Computing eigen value of matrix of covariance */
   fprintf(ficrespl,"#Age ");                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   fprintf(ficrespl,"\n");                    /* Eigen vectors */
                      v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   prlim=matrix(1,nlstate,1,nlstate);                    /*v21=sqrt(1.-v11*v11); *//* error */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    v21=(lc1-v1)/cv12*v11;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    v12=-v21;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    v22=v11;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    tnalp=v21/v11;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                    if(first1==1){
   k=0;                      first1=0;
   agebase=agemin;                      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);
   agelim=agemaxpar;                    }
   ftolpl=1.e-10;                    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);
   i1=cptcoveff;                    /*printf(fignu*/
   if (cptcovn < 1){i1=1;}                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   for(cptcov=1;cptcov<=i1;cptcov++){                    if(first==1){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                      first=0;
         k=k+1;                      fprintf(ficgp,"\nset parametric;unset label");
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
         fprintf(ficrespl,"\n#******");                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
         for(j=1;j<=cptcoveff;j++)                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
         fprintf(ficrespl,"******\n");  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                                      subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
         for (age=agebase; age<=agelim; age++){                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           fprintf(ficrespl,"%.0f",age );                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
           for(i=1; i<=nlstate;i++)                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           fprintf(ficrespl," %.5f", prlim[i][i]);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
           fprintf(ficrespl,"\n");                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
         }                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
       }                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   fclose(ficrespl);                    }else{
                       first=0;
   /*------------- h Pij x at various ages ------------*/                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                        fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                      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",\
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   printf("Computing pij: result on file '%s' \n", filerespij);                    }/* if first */
                    } /* age mod 5 */
   stepsize=(int) (stepm+YEARM-1)/YEARM;                } /* end loop age */
   /*if (stepm<=24) stepsize=2;*/                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
   agelim=AGESUP;              } /*l12 */
   hstepm=stepsize*YEARM; /* Every year of age */            } /* k12 */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          } /*l1 */
          }/* k1 */
   k=0;      } /* loop covariates */
   for(cptcov=1;cptcov<=i1;cptcov++){    }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
       k=k+1;    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
         fprintf(ficrespij,"\n#****** ");    free_vector(xp,1,npar);
         for(j=1;j<=cptcoveff;j++)    fclose(ficresprob);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fclose(ficresprobcov);
         fprintf(ficrespij,"******\n");    fclose(ficresprobcor);
            fflush(ficgp);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    fflush(fichtmcov);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  }
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;  /******************* Printing html file ***********/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
           fprintf(ficrespij,"# Age");                    int lastpass, int stepm, int weightopt, char model[],\
           for(i=1; i<=nlstate;i++)                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
             for(j=1; j<=nlstate+ndeath;j++)                    int popforecast, int estepm ,\
               fprintf(ficrespij," %1d-%1d",i,j);                    double jprev1, double mprev1,double anprev1, \
           fprintf(ficrespij,"\n");                    double jprev2, double mprev2,double anprev2){
           for (h=0; h<=nhstepm; h++){    int jj1, k1, i1, cpt;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
               for(j=1; j<=nlstate+ndeath;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(ficrespij," %.5f", p3mat[i][j][h]);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
             fprintf(ficrespij,"\n");     fprintf(fichtm,"\
           }   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
           fprintf(ficrespij,"\n");     fprintf(fichtm,"\
         }   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
     }             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
   }     fprintf(fichtm,"\
    - Life expectancies by age and initial health status (estepm=%2d months): \
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/     <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   fclose(ficrespij);  
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
   /*---------- Forecasting ------------------*/   m=cptcoveff;
   if((stepm == 1) && (model==".")){   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);  
 if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);   jj1=0;
     free_matrix(mint,1,maxwav,1,n);   for(k1=1; k1<=m;k1++){
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);     for(i1=1; i1<=ncodemax[k1];i1++){
     free_vector(weight,1,n);}       jj1++;
   else{       if (cptcovn > 0) {
     erreur=108;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);         for (cpt=1; cpt<=cptcoveff;cpt++) 
   }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
   /*---------- Health expectancies and variances ------------*/       /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
   strcpy(filerest,"t");  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
   strcat(filerest,fileres);       /* Quasi-incidences */
   if((ficrest=fopen(filerest,"w"))==NULL) {       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   }  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
   printf("Computing Total LEs with variances: file '%s' \n", filerest);         /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   strcpy(filerese,"e");  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
   strcat(filerese,fileres);         }
   if((ficreseij=fopen(filerese,"w"))==NULL) {       for(cpt=1; cpt<=nlstate;cpt++) {
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   }  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);       }
      } /* end i1 */
  strcpy(fileresv,"v");   }/* End k1 */
   strcat(fileresv,fileres);   fprintf(fichtm,"</ul>");
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }   fprintf(fichtm,"\
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  \n<br><li><h4> Result files (second order: variances)</h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
       k=k+1;   fprintf(fichtm,"\
       fprintf(ficrest,"\n#****** ");   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
       for(j=1;j<=cptcoveff;j++)           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficrest,"******\n");   fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
       fprintf(ficreseij,"\n#****** ");           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
       for(j=1;j<=cptcoveff;j++)   fprintf(fichtm,"\
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
       fprintf(ficreseij,"******\n");           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
       fprintf(ficresvij,"\n#****** ");   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
       for(j=1;j<=cptcoveff;j++)           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);   fprintf(fichtm,"\
       fprintf(ficresvij,"******\n");   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;  /*  if(popforecast==1) fprintf(fichtm,"\n */
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);    /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
       oldm=oldms;savm=savms;  /*      <br>",fileres,fileres,fileres,fileres); */
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  /*  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>");
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);   m=cptcoveff;
       fprintf(ficrest,"\n");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
       hf=1;   jj1=0;
       if (stepm >= YEARM) hf=stepm/YEARM;   for(k1=1; k1<=m;k1++){
       epj=vector(1,nlstate+1);     for(i1=1; i1<=ncodemax[k1];i1++){
       for(age=bage; age <=fage ;age++){       jj1++;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);       if (cptcovn > 0) {
         if (popbased==1) {         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           for(i=1; i<=nlstate;i++)         for (cpt=1; cpt<=cptcoveff;cpt++) 
             prlim[i][i]=probs[(int)age][i][k];           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
         }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
               }
         fprintf(ficrest," %.0f",age);       for(cpt=1; cpt<=nlstate;cpt++) {
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
           }       }
           epj[nlstate+1] +=epj[j];       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
         }  health expectancies in states (1) and (2): %s%d.png<br>\
         for(i=1, vepp=0.;i <=nlstate;i++)  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
           for(j=1;j <=nlstate;j++)     } /* end i1 */
             vepp += vareij[i][j][(int)age];   }/* End k1 */
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));   fprintf(fichtm,"</ul>");
         for(j=1;j <=nlstate;j++){   fflush(fichtm);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));  }
         }  
         fprintf(ficrest,"\n");  /******************* Gnuplot file **************/
       }  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
     }  
   }    char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   fclose(ficreseij);    int ng;
   fclose(ficresvij);  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   fclose(ficrest);  /*     printf("Problem with file %s",optionfilegnuplot); */
   fclose(ficpar);  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   free_vector(epj,1,nlstate+1);  /*   } */
    
   /*------- Variance limit prevalence------*/      /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
   strcpy(fileresvpl,"vpl");      /*#endif */
   strcat(fileresvpl,fileres);    m=pow(2,cptcoveff);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    strcpy(dirfileres,optionfilefiname);
     exit(0);    strcpy(optfileres,"vpl");
   }   /* 1eme*/
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
   k=0;       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
   for(cptcov=1;cptcov<=i1;cptcov++){       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       fprintf(ficgp,"set xlabel \"Age\" \n\
       k=k+1;  set ylabel \"Probability\" \n\
       fprintf(ficresvpl,"\n#****** ");  set ter png small\n\
       for(j=1;j<=cptcoveff;j++)  set size 0.65,0.65\n\
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
       fprintf(ficresvpl,"******\n");  
             for (i=1; i<= nlstate ; i ++) {
       varpl=matrix(1,nlstate,(int) bage, (int) fage);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       oldm=oldms;savm=savms;         else fprintf(ficgp," \%%*lf (\%%*lf)");
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,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)");
   fclose(ficresvpl);         else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
   /*---------- End : free ----------------*/       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);       for (i=1; i<= nlstate ; i ++) {
           if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);         else fprintf(ficgp," \%%*lf (\%%*lf)");
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);       }  
         fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
       }
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    }
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    /*2 eme*/
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    for (k1=1; k1<= m ; k1 ++) { 
        fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
   free_matrix(matcov,1,npar,1,npar);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
   free_vector(delti,1,npar);      
   free_matrix(agev,1,maxwav,1,imx);      for (i=1; i<= nlstate+1 ; i ++) {
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   if(erreur >0)        for (j=1; j<= nlstate+1 ; j ++) {
     printf("End of Imach with error %d\n",erreur);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   else   printf("End of Imach\n");          else fprintf(ficgp," \%%*lf (\%%*lf)");
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        }   
          if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   /* 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);*/        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   /*printf("Total time was %d uSec.\n", total_usecs);*/        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   /*------ End -----------*/        for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
  end:        }   
 #ifdef windows        fprintf(ficgp,"\" t\"\" w l 0,");
   /* chdir(pathcd);*/        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
 #endif        for (j=1; j<= nlstate+1 ; j ++) {
  /*system("wgnuplot graph.plt");*/          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
  /*system("../gp37mgw/wgnuplot graph.plt");*/          else fprintf(ficgp," \%%*lf (\%%*lf)");
  /*system("cd ../gp37mgw");*/        }   
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
  strcpy(plotcmd,GNUPLOTPROGRAM);        else fprintf(ficgp,"\" t\"\" w l 0,");
  strcat(plotcmd," ");      }
  strcat(plotcmd,optionfilegnuplot);    }
  system(plotcmd);    
     /*3eme*/
 #ifdef windows    
   while (z[0] != 'q') {    for (k1=1; k1<= m ; k1 ++) { 
     chdir(path);      for (cpt=1; cpt<= nlstate ; cpt ++) {
     printf("\nType e to edit output files, c to start again, and q for exiting: ");        k=2+nlstate*(2*cpt-2);
     scanf("%s",z);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
     if (z[0] == 'c') system("./imach");        fprintf(ficgp,"set ter png small\n\
     else if (z[0] == 'e') {  set size 0.65,0.65\n\
       chdir(path);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
       system(optionfilehtm);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     }          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     else if (z[0] == 'q') exit(0);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   }          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
 #endif          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
 }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       sump=sump+1;
       num=num+1;
     }
    
    
     /* for (i=1; 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=0;i<=imx-1 ; i++)
       {
         if (cens[i]==1 & wav[i]>1)
           A=-x[1]/(x[2])*
             (exp(x[2]/YEARM*(agecens[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)));
         
         if (cens[i]==0 & wav[i]>1)
           A=-x[1]/(x[2])*
                (exp(x[2]/YEARM*(agedc[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)))
             +log(x[1]/YEARM)+x[2]/YEARM*(agedc[i]*12-agegomp*12)+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=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.1.30  
changed lines
  Added in v.1.101


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