Diff for /imach/src/imach.c between versions 1.30 and 1.94

version 1.30, 2002/03/08 16:17:18 version 1.94, 2003/06/27 13:00:02
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.94  2003/06/27 13:00:02  brouard
      Just cleaning
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.93  2003/06/25 16:33:55  brouard
   first survey ("cross") where individuals from different ages are    (Module): On windows (cygwin) function asctime_r doesn't
   interviewed on their health status or degree of disability (in the    exist so I changed back to asctime which exists.
   case of a health survey which is our main interest) -2- at least a    (Module): Version 0.96b
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.92  2003/06/25 16:30:45  brouard
   computed from the time spent in each health state according to a    (Module): On windows (cygwin) function asctime_r doesn't
   model. More health states you consider, more time is necessary to reach the    exist so I changed back to asctime which exists.
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.91  2003/06/25 15:30:29  brouard
   probabibility to be observed in state j at the second wave    * imach.c (Repository): Duplicated warning errors corrected.
   conditional to be observed in state i at the first wave. Therefore    (Repository): Elapsed time after each iteration is now output. It
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    helps to forecast when convergence will be reached. Elapsed time
   'age' is age and 'sex' is a covariate. If you want to have a more    is stamped in powell.  We created a new html file for the graphs
   complex model than "constant and age", you should modify the program    concerning matrix of covariance. It has extension -cov.htm.
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Revision 1.90  2003/06/24 12:34:15  brouard
   convergence.    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
   The advantage of this computer programme, compared to a simple    of the covariance matrix to be input.
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.89  2003/06/24 12:30:52  brouard
   intermediate interview, the information is lost, but taken into    (Module): Some bugs corrected for windows. Also, when
   account using an interpolation or extrapolation.      mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    Revision 1.88  2003/06/23 17:54:56  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    * 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.
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.87  2003/06/18 12:26:01  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    Version 0.96
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
   Also this programme outputs the covariance matrix of the parameters but also    routine fileappend.
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.85  2003/06/17 13:12:43  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    * imach.c (Repository): Check when date of death was earlier that
            Institut national d'études démographiques, Paris.    current date of interview. It may happen when the death was just
   This software have been partly granted by Euro-REVES, a concerted action    prior to the death. In this case, dh was negative and likelihood
   from the European Union.    was wrong (infinity). We still send an "Error" but patch by
   It is copyrighted identically to a GNU software product, ie programme and    assuming that the date of death was just one stepm after the
   software can be distributed freely for non commercial use. Latest version    interview.
   can be accessed at http://euroreves.ined.fr/imach .    (Repository): Because some people have very long ID (first column)
   **********************************************************************/    we changed int to long in num[] and we added a new lvector for
      memory allocation. But we also truncated to 8 characters (left
 #include <math.h>    truncation)
 #include <stdio.h>    (Repository): No more line truncation errors.
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
 #define MAXLINE 256    place. It differs from routine "prevalence" which may be called
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    many times. Probs is memory consuming and must be used with
 #define FILENAMELENGTH 80    parcimony.
 /*#define DEBUG*/    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.83  2003/06/10 13:39:11  lievre
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    *** empty log message ***
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.82  2003/06/05 15:57:20  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Add log in  imach.c and  fullversion number is now printed.
   
 #define NINTERVMAX 8  */
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  /*
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */     Interpolated Markov Chain
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Short summary of the programme:
 #define YEARM 12. /* Number of months per year */    
 #define AGESUP 130    This program computes Healthy Life Expectancies from
 #define AGEBASE 40    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     first survey ("cross") where individuals from different ages are
     interviewed on their health status or degree of disability (in the
 int erreur; /* Error number */    case of a health survey which is our main interest) -2- at least a
 int nvar;    second wave of interviews ("longitudinal") which measure each change
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    (if any) in individual health status.  Health expectancies are
 int npar=NPARMAX;    computed from the time spent in each health state according to a
 int nlstate=2; /* Number of live states */    model. More health states you consider, more time is necessary to reach the
 int ndeath=1; /* Number of dead states */    Maximum Likelihood of the parameters involved in the model.  The
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    simplest model is the multinomial logistic model where pij is the
 int popbased=0;    probability to be observed in state j at the second wave
     conditional to be observed in state i at the first wave. Therefore
 int *wav; /* Number of waves for this individuual 0 is possible */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 int maxwav; /* Maxim number of waves */    'age' is age and 'sex' is a covariate. If you want to have a more
 int jmin, jmax; /* min, max spacing between 2 waves */    complex model than "constant and age", you should modify the program
 int mle, weightopt;    where the markup *Covariates have to be included here again* invites
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    you to do it.  More covariates you add, slower the
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    convergence.
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    The advantage of this computer programme, compared to a simple
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    multinomial logistic model, is clear when the delay between waves is not
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    identical for each individual. Also, if a individual missed an
 FILE *ficgp,*ficresprob,*ficpop;    intermediate interview, the information is lost, but taken into
 FILE *ficreseij;    account using an interpolation or extrapolation.  
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    hPijx is the probability to be observed in state i at age x+h
   char fileresv[FILENAMELENGTH];    conditional to the observed state i at age x. The delay 'h' can be
  FILE  *ficresvpl;    split into an exact number (nh*stepm) of unobserved intermediate
   char fileresvpl[FILENAMELENGTH];    states. This elementary transition (by month, quarter,
     semester or year) is modelled as a multinomial logistic.  The hPx
 #define NR_END 1    matrix is simply the matrix product of nh*stepm elementary matrices
 #define FREE_ARG char*    and the contribution of each individual to the likelihood is simply
 #define FTOL 1.0e-10    hPijx.
   
 #define NRANSI    Also this programme outputs the covariance matrix of the parameters but also
 #define ITMAX 200    of the life expectancies. It also computes the stable prevalence. 
     
 #define TOL 2.0e-4    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
 #define CGOLD 0.3819660    This software have been partly granted by Euro-REVES, a concerted action
 #define ZEPS 1.0e-10    from the European Union.
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 #define GOLD 1.618034    can be accessed at http://euroreves.ined.fr/imach .
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 static double maxarg1,maxarg2;    
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    **********************************************************************/
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  /*
      main
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    read parameterfile
 #define rint(a) floor(a+0.5)    read datafile
     concatwav
 static double sqrarg;    freqsummary
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    if (mle >= 1)
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}      mlikeli
     print results files
 int imx;    if mle==1 
 int stepm;       computes hessian
 /* Stepm, step in month: minimum step interpolation*/    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 int m,nb;    open gnuplot file
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    open html file
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    stable prevalence
 double **pmmij, ***probs, ***mobaverage;     for age prevalim()
 double dateintmean=0;    h Pij x
     variance of p varprob
 double *weight;    forecasting if prevfcast==1 prevforecast call prevalence()
 int **s; /* Status */    health expectancies
 double *agedc, **covar, idx;    Variance-covariance of DFLE
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    prevalence()
      movingaverage()
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    varevsij() 
 double ftolhess; /* Tolerance for computing hessian */    if popbased==1 varevsij(,popbased)
     total life expectancies
 /**************** split *************************/    Variance of stable prevalence
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )   end
 {  */
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */  
   
    l1 = strlen( path );                 /* length of path */   
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #include <math.h>
 #ifdef windows  #include <stdio.h>
    s = strrchr( path, '\\' );           /* find last / */  #include <stdlib.h>
 #else  #include <unistd.h>
    s = strrchr( path, '/' );            /* find last / */  
 #endif  #include <sys/time.h>
    if ( s == NULL ) {                   /* no directory, so use current */  #include <time.h>
 #if     defined(__bsd__)                /* get current working directory */  #include "timeval.h"
       extern char       *getwd( );  
   #define MAXLINE 256
       if ( getwd( dirc ) == NULL ) {  #define GNUPLOTPROGRAM "gnuplot"
 #else  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       extern char       *getcwd( );  #define FILENAMELENGTH 132
   /*#define DEBUG*/
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  /*#define windows*/
 #endif  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
          return( GLOCK_ERROR_GETCWD );  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       }  
       strcpy( name, path );             /* we've got it */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
    } else {                             /* strip direcotry from path */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */  #define NINTERVMAX 8
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
       strcpy( name, s );                /* save file name */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define NCOVMAX 8 /* Maximum number of covariates */
       dirc[l1-l2] = 0;                  /* add zero */  #define MAXN 20000
    }  #define YEARM 12. /* Number of months per year */
    l1 = strlen( dirc );                 /* length of directory */  #define AGESUP 130
 #ifdef windows  #define AGEBASE 40
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #ifdef unix
 #else  #define DIRSEPARATOR '/'
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  #define ODIRSEPARATOR '\\'
 #endif  #else
    s = strrchr( name, '.' );            /* find last / */  #define DIRSEPARATOR '\\'
    s++;  #define ODIRSEPARATOR '/'
    strcpy(ext,s);                       /* save extension */  #endif
    l1= strlen( name);  
    l2= strlen( s)+1;  /* $Id$ */
    strncpy( finame, name, l1-l2);  /* $State$ */
    finame[l1-l2]= 0;  
    return( 0 );                         /* we're done */  char version[]="Imach version 0.96b, June 2003, INED-EUROREVES ";
 }  char fullversion[]="$Revision$ $Date$"; 
   int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   int nvar;
 /******************************************/  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   int npar=NPARMAX;
 void replace(char *s, char*t)  int nlstate=2; /* Number of live states */
 {  int ndeath=1; /* Number of dead states */
   int i;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int lg=20;  int popbased=0;
   i=0;  
   lg=strlen(t);  int *wav; /* Number of waves for this individuual 0 is possible */
   for(i=0; i<= lg; i++) {  int maxwav; /* Maxim number of waves */
     (s[i] = t[i]);  int jmin, jmax; /* min, max spacing between 2 waves */
     if (t[i]== '\\') s[i]='/';  int gipmx, gsw; /* Global variables on the number of contributions 
   }                     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 */
 int nbocc(char *s, char occ)  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 {  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   int i,j=0;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   int lg=20;  double jmean; /* Mean space between 2 waves */
   i=0;  double **oldm, **newm, **savm; /* Working pointers to matrices */
   lg=strlen(s);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   for(i=0; i<= lg; i++) {  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   if  (s[i] == occ ) j++;  FILE *ficlog, *ficrespow;
   }  int globpr; /* Global variable for printing or not */
   return j;  double fretone; /* Only one call to likelihood */
 }  long ipmx; /* Number of contributions */
   double sw; /* Sum of weights */
 void cutv(char *u,char *v, char*t, char occ)  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 {  FILE *ficresilk;
   int i,lg,j,p=0;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   i=0;  FILE *ficresprobmorprev;
   for(j=0; j<=strlen(t)-1; j++) {  FILE *fichtm, *fichtmcov; /* Html File */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  FILE *ficreseij;
   }  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
   lg=strlen(t);  char fileresv[FILENAMELENGTH];
   for(j=0; j<p; j++) {  FILE  *ficresvpl;
     (u[j] = t[j]);  char fileresvpl[FILENAMELENGTH];
   }  char title[MAXLINE];
      u[p]='\0';  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
    for(j=0; j<= lg; j++) {  char tmpout[FILENAMELENGTH]; 
     if (j>=(p+1))(v[j-p-1] = t[j]);  char command[FILENAMELENGTH];
   }  int  outcmd=0;
 }  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 /********************** nrerror ********************/  
   char filelog[FILENAMELENGTH]; /* Log file */
 void nrerror(char error_text[])  char filerest[FILENAMELENGTH];
 {  char fileregp[FILENAMELENGTH];
   fprintf(stderr,"ERREUR ...\n");  char popfile[FILENAMELENGTH];
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 }  
 /*********************** vector *******************/  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 double *vector(int nl, int nh)  struct timezone tzp;
 {  extern int gettimeofday();
   double *v;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  long time_value;
   if (!v) nrerror("allocation failure in vector");  extern long time();
   return v-nl+NR_END;  char strcurr[80], strfor[80];
 }  
   #define NR_END 1
 /************************ free vector ******************/  #define FREE_ARG char*
 void free_vector(double*v, int nl, int nh)  #define FTOL 1.0e-10
 {  
   free((FREE_ARG)(v+nl-NR_END));  #define NRANSI 
 }  #define ITMAX 200 
   
 /************************ivector *******************************/  #define TOL 2.0e-4 
 int *ivector(long nl,long nh)  
 {  #define CGOLD 0.3819660 
   int *v;  #define ZEPS 1.0e-10 
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;  #define GOLD 1.618034 
 }  #define GLIMIT 100.0 
   #define TINY 1.0e-20 
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)  static double maxarg1,maxarg2;
 {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   free((FREE_ARG)(v+nl-NR_END));  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 }    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 /******************* imatrix *******************************/  #define rint(a) floor(a+0.5)
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  static double sqrarg;
 {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   int **m;  
    int imx; 
   /* allocate pointers to rows */  int stepm;
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  /* Stepm, step in month: minimum step interpolation*/
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  int estepm;
   m -= nrl;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
    
    int m,nb;
   /* allocate rows and set pointers to them */  long *num;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   m[nrl] += NR_END;  double **pmmij, ***probs;
   m[nrl] -= ncl;  double dateintmean=0;
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  double *weight;
    int **s; /* Status */
   /* return pointer to array of pointers to rows */  double *agedc, **covar, idx;
   return m;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 }  
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 /****************** free_imatrix *************************/  double ftolhess; /* Tolerance for computing hessian */
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  /**************** split *************************/
       long nch,ncl,nrh,nrl;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
      /* free an int matrix allocated by imatrix() */  {
 {    char  *ss;                            /* pointer */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    int   l1, l2;                         /* length counters */
   free((FREE_ARG) (m+nrl-NR_END));  
 }    l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 /******************* matrix *******************************/    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 double **matrix(long nrl, long nrh, long ncl, long nch)    if ( ss == NULL ) {                   /* no directory, so use current */
 {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   double **m;      /* get current working directory */
       /*    extern  char* getcwd ( char *buf , int len);*/
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   if (!m) nrerror("allocation failure 1 in matrix()");        return( GLOCK_ERROR_GETCWD );
   m += NR_END;      }
   m -= nrl;      strcpy( name, path );               /* we've got it */
     } else {                              /* strip direcotry from path */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));      ss++;                               /* after this, the filename */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      l2 = strlen( ss );                  /* length of filename */
   m[nrl] += NR_END;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   m[nrl] -= ncl;      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );     /* now the directory */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;      dirc[l1-l2] = 0;                    /* add zero */
   return m;    }
 }    l1 = strlen( dirc );                  /* length of directory */
     /*#ifdef windows
 /*************************free matrix ************************/    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  #else
 {    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #endif
   free((FREE_ARG)(m+nrl-NR_END));    */
 }    ss = strrchr( name, '.' );            /* find last / */
     ss++;
 /******************* ma3x *******************************/    strcpy(ext,ss);                       /* save extension */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    l1= strlen( name);
 {    l2= strlen(ss)+1;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    strncpy( finame, name, l1-l2);
   double ***m;    finame[l1-l2]= 0;
     return( 0 );                          /* we're done */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  }
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  
   m -= nrl;  /******************************************/
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  void replace_back_to_slash(char *s, char*t)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  {
   m[nrl] += NR_END;    int i;
   m[nrl] -= ncl;    int lg=0;
     i=0;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    lg=strlen(t);
     for(i=0; i<= lg; i++) {
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));      (s[i] = t[i]);
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");      if (t[i]== '\\') s[i]='/';
   m[nrl][ncl] += NR_END;    }
   m[nrl][ncl] -= nll;  }
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;  int nbocc(char *s, char occ)
    {
   for (i=nrl+1; i<=nrh; i++) {    int i,j=0;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    int lg=20;
     for (j=ncl+1; j<=nch; j++)    i=0;
       m[i][j]=m[i][j-1]+nlay;    lg=strlen(s);
   }    for(i=0; i<= lg; i++) {
   return m;    if  (s[i] == occ ) j++;
 }    }
     return j;
 /*************************free ma3x ************************/  }
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {  void cutv(char *u,char *v, char*t, char occ)
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  {
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    /* cuts string t into u and v where u is ended by char occ excluding it
   free((FREE_ARG)(m+nrl-NR_END));       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 }       gives u="abcedf" and v="ghi2j" */
     int i,lg,j,p=0;
 /***************** f1dim *************************/    i=0;
 extern int ncom;    for(j=0; j<=strlen(t)-1; j++) {
 extern double *pcom,*xicom;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 extern double (*nrfunc)(double []);    }
    
 double f1dim(double x)    lg=strlen(t);
 {    for(j=0; j<p; j++) {
   int j;      (u[j] = t[j]);
   double f;    }
   double *xt;       u[p]='\0';
    
   xt=vector(1,ncom);     for(j=0; j<= lg; j++) {
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];      if (j>=(p+1))(v[j-p-1] = t[j]);
   f=(*nrfunc)(xt);    }
   free_vector(xt,1,ncom);  }
   return f;  
 }  /********************** nrerror ********************/
   
 /*****************brent *************************/  void nrerror(char error_text[])
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  {
 {    fprintf(stderr,"ERREUR ...\n");
   int iter;    fprintf(stderr,"%s\n",error_text);
   double a,b,d,etemp;    exit(EXIT_FAILURE);
   double fu,fv,fw,fx;  }
   double ftemp;  /*********************** vector *******************/
   double p,q,r,tol1,tol2,u,v,w,x,xm;  double *vector(int nl, int nh)
   double e=0.0;  {
      double *v;
   a=(ax < cx ? ax : cx);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   b=(ax > cx ? ax : cx);    if (!v) nrerror("allocation failure in vector");
   x=w=v=bx;    return v-nl+NR_END;
   fw=fv=fx=(*f)(x);  }
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);  /************************ free vector ******************/
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  void free_vector(double*v, int nl, int nh)
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  {
     printf(".");fflush(stdout);    free((FREE_ARG)(v+nl-NR_END));
 #ifdef DEBUG  }
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  /************************ivector *******************************/
 #endif  int *ivector(long nl,long nh)
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  {
       *xmin=x;    int *v;
       return fx;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     }    if (!v) nrerror("allocation failure in ivector");
     ftemp=fu;    return v-nl+NR_END;
     if (fabs(e) > tol1) {  }
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);  /******************free ivector **************************/
       p=(x-v)*q-(x-w)*r;  void free_ivector(int *v, long nl, long nh)
       q=2.0*(q-r);  {
       if (q > 0.0) p = -p;    free((FREE_ARG)(v+nl-NR_END));
       q=fabs(q);  }
       etemp=e;  
       e=d;  /************************lvector *******************************/
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  long *lvector(long nl,long nh)
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  {
       else {    long *v;
         d=p/q;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
         u=x+d;    if (!v) nrerror("allocation failure in ivector");
         if (u-a < tol2 || b-u < tol2)    return v-nl+NR_END;
           d=SIGN(tol1,xm-x);  }
       }  
     } else {  /******************free lvector **************************/
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  void free_lvector(long *v, long nl, long nh)
     }  {
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    free((FREE_ARG)(v+nl-NR_END));
     fu=(*f)(u);  }
     if (fu <= fx) {  
       if (u >= x) a=x; else b=x;  /******************* imatrix *******************************/
       SHFT(v,w,x,u)  int **imatrix(long nrl, long nrh, long ncl, long nch) 
         SHFT(fv,fw,fx,fu)       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
         } else {  { 
           if (u < x) a=u; else b=u;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
           if (fu <= fw || w == x) {    int **m; 
             v=w;    
             w=u;    /* allocate pointers to rows */ 
             fv=fw;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
             fw=fu;    if (!m) nrerror("allocation failure 1 in matrix()"); 
           } else if (fu <= fv || v == x || v == w) {    m += NR_END; 
             v=u;    m -= nrl; 
             fv=fu;    
           }    
         }    /* allocate rows and set pointers to them */ 
   }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   nrerror("Too many iterations in brent");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   *xmin=x;    m[nrl] += NR_END; 
   return fx;    m[nrl] -= ncl; 
 }    
     for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 /****************** mnbrak ***********************/    
     /* return pointer to array of pointers to rows */ 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    return m; 
             double (*func)(double))  } 
 {  
   double ulim,u,r,q, dum;  /****************** free_imatrix *************************/
   double fu;  void free_imatrix(m,nrl,nrh,ncl,nch)
          int **m;
   *fa=(*func)(*ax);        long nch,ncl,nrh,nrl; 
   *fb=(*func)(*bx);       /* free an int matrix allocated by imatrix() */ 
   if (*fb > *fa) {  { 
     SHFT(dum,*ax,*bx,dum)    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       SHFT(dum,*fb,*fa,dum)    free((FREE_ARG) (m+nrl-NR_END)); 
       }  } 
   *cx=(*bx)+GOLD*(*bx-*ax);  
   *fc=(*func)(*cx);  /******************* matrix *******************************/
   while (*fb > *fc) {  double **matrix(long nrl, long nrh, long ncl, long nch)
     r=(*bx-*ax)*(*fb-*fc);  {
     q=(*bx-*cx)*(*fb-*fa);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    double **m;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  
     ulim=(*bx)+GLIMIT*(*cx-*bx);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if ((*bx-u)*(u-*cx) > 0.0) {    if (!m) nrerror("allocation failure 1 in matrix()");
       fu=(*func)(u);    m += NR_END;
     } else if ((*cx-u)*(u-ulim) > 0.0) {    m -= nrl;
       fu=(*func)(u);  
       if (fu < *fc) {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
           SHFT(*fb,*fc,fu,(*func)(u))    m[nrl] += NR_END;
           }    m[nrl] -= ncl;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       fu=(*func)(u);    return m;
     } else {    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       u=(*cx)+GOLD*(*cx-*bx);     */
       fu=(*func)(u);  }
     }  
     SHFT(*ax,*bx,*cx,u)  /*************************free matrix ************************/
       SHFT(*fa,*fb,*fc,fu)  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       }  {
 }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
 /*************** linmin ************************/  }
   
 int ncom;  /******************* ma3x *******************************/
 double *pcom,*xicom;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 double (*nrfunc)(double []);  {
      long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    double ***m;
 {  
   double brent(double ax, double bx, double cx,    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
                double (*f)(double), double tol, double *xmin);    if (!m) nrerror("allocation failure 1 in matrix()");
   double f1dim(double x);    m += NR_END;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    m -= nrl;
               double *fc, double (*func)(double));  
   int j;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double xx,xmin,bx,ax;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double fx,fb,fa;    m[nrl] += NR_END;
      m[nrl] -= ncl;
   ncom=n;  
   pcom=vector(1,n);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   xicom=vector(1,n);  
   nrfunc=func;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   for (j=1;j<=n;j++) {    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     pcom[j]=p[j];    m[nrl][ncl] += NR_END;
     xicom[j]=xi[j];    m[nrl][ncl] -= nll;
   }    for (j=ncl+1; j<=nch; j++) 
   ax=0.0;      m[nrl][j]=m[nrl][j-1]+nlay;
   xx=1.0;    
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    for (i=nrl+1; i<=nrh; i++) {
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 #ifdef DEBUG      for (j=ncl+1; j<=nch; j++) 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);        m[i][j]=m[i][j-1]+nlay;
 #endif    }
   for (j=1;j<=n;j++) {    return m; 
     xi[j] *= xmin;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     p[j] += xi[j];             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   }    */
   free_vector(xicom,1,n);  }
   free_vector(pcom,1,n);  
 }  /*************************free ma3x ************************/
   void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 /*************** powell ************************/  {
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
             double (*func)(double []))    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 {    free((FREE_ARG)(m+nrl-NR_END));
   void linmin(double p[], double xi[], int n, double *fret,  }
               double (*func)(double []));  
   int i,ibig,j;  /*************** function subdirf ***********/
   double del,t,*pt,*ptt,*xit;  char *subdirf(char fileres[])
   double fp,fptt;  {
   double *xits;    /* Caution optionfilefiname is hidden */
   pt=vector(1,n);    strcpy(tmpout,optionfilefiname);
   ptt=vector(1,n);    strcat(tmpout,"/"); /* Add to the right */
   xit=vector(1,n);    strcat(tmpout,fileres);
   xits=vector(1,n);    return tmpout;
   *fret=(*func)(p);  }
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  /*************** function subdirf2 ***********/
     fp=(*fret);  char *subdirf2(char fileres[], char *preop)
     ibig=0;  {
     del=0.0;    
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    /* Caution optionfilefiname is hidden */
     for (i=1;i<=n;i++)    strcpy(tmpout,optionfilefiname);
       printf(" %d %.12f",i, p[i]);    strcat(tmpout,"/");
     printf("\n");    strcat(tmpout,preop);
     for (i=1;i<=n;i++) {    strcat(tmpout,fileres);
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    return tmpout;
       fptt=(*fret);  }
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);  /*************** function subdirf3 ***********/
 #endif  char *subdirf3(char fileres[], char *preop, char *preop2)
       printf("%d",i);fflush(stdout);  {
       linmin(p,xit,n,fret,func);    
       if (fabs(fptt-(*fret)) > del) {    /* Caution optionfilefiname is hidden */
         del=fabs(fptt-(*fret));    strcpy(tmpout,optionfilefiname);
         ibig=i;    strcat(tmpout,"/");
       }    strcat(tmpout,preop);
 #ifdef DEBUG    strcat(tmpout,preop2);
       printf("%d %.12e",i,(*fret));    strcat(tmpout,fileres);
       for (j=1;j<=n;j++) {    return tmpout;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  }
         printf(" x(%d)=%.12e",j,xit[j]);  
       }  /***************** f1dim *************************/
       for(j=1;j<=n;j++)  extern int ncom; 
         printf(" p=%.12e",p[j]);  extern double *pcom,*xicom;
       printf("\n");  extern double (*nrfunc)(double []); 
 #endif   
     }  double f1dim(double x) 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  { 
 #ifdef DEBUG    int j; 
       int k[2],l;    double f;
       k[0]=1;    double *xt; 
       k[1]=-1;   
       printf("Max: %.12e",(*func)(p));    xt=vector(1,ncom); 
       for (j=1;j<=n;j++)    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
         printf(" %.12e",p[j]);    f=(*nrfunc)(xt); 
       printf("\n");    free_vector(xt,1,ncom); 
       for(l=0;l<=1;l++) {    return f; 
         for (j=1;j<=n;j++) {  } 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  /*****************brent *************************/
         }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  { 
       }    int iter; 
 #endif    double a,b,d,etemp;
     double fu,fv,fw,fx;
     double ftemp;
       free_vector(xit,1,n);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       free_vector(xits,1,n);    double e=0.0; 
       free_vector(ptt,1,n);   
       free_vector(pt,1,n);    a=(ax < cx ? ax : cx); 
       return;    b=(ax > cx ? ax : cx); 
     }    x=w=v=bx; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    fw=fv=fx=(*f)(x); 
     for (j=1;j<=n;j++) {    for (iter=1;iter<=ITMAX;iter++) { 
       ptt[j]=2.0*p[j]-pt[j];      xm=0.5*(a+b); 
       xit[j]=p[j]-pt[j];      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       pt[j]=p[j];      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     }      printf(".");fflush(stdout);
     fptt=(*func)(ptt);      fprintf(ficlog,".");fflush(ficlog);
     if (fptt < fp) {  #ifdef DEBUG
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       if (t < 0.0) {      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);
         linmin(p,xit,n,fret,func);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
         for (j=1;j<=n;j++) {  #endif
           xi[j][ibig]=xi[j][n];      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
           xi[j][n]=xit[j];        *xmin=x; 
         }        return fx; 
 #ifdef DEBUG      } 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      ftemp=fu;
         for(j=1;j<=n;j++)      if (fabs(e) > tol1) { 
           printf(" %.12e",xit[j]);        r=(x-w)*(fx-fv); 
         printf("\n");        q=(x-v)*(fx-fw); 
 #endif        p=(x-v)*q-(x-w)*r; 
       }        q=2.0*(q-r); 
     }        if (q > 0.0) p = -p; 
   }        q=fabs(q); 
 }        etemp=e; 
         e=d; 
 /**** Prevalence limit ****************/        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
           d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        else { 
 {          d=p/q; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit          u=x+d; 
      matrix by transitions matrix until convergence is reached */          if (u-a < tol2 || b-u < tol2) 
             d=SIGN(tol1,xm-x); 
   int i, ii,j,k;        } 
   double min, max, maxmin, maxmax,sumnew=0.;      } else { 
   double **matprod2();        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double **out, cov[NCOVMAX], **pmij();      } 
   double **newm;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   double agefin, delaymax=50 ; /* Max number of years to converge */      fu=(*f)(u); 
       if (fu <= fx) { 
   for (ii=1;ii<=nlstate+ndeath;ii++)        if (u >= x) a=x; else b=x; 
     for (j=1;j<=nlstate+ndeath;j++){        SHFT(v,w,x,u) 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);          SHFT(fv,fw,fx,fu) 
     }          } else { 
             if (u < x) a=u; else b=u; 
    cov[1]=1.;            if (fu <= fw || w == x) { 
                v=w; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */              w=u; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){              fv=fw; 
     newm=savm;              fw=fu; 
     /* Covariates have to be included here again */            } else if (fu <= fv || v == x || v == w) { 
      cov[2]=agefin;              v=u; 
                fv=fu; 
       for (k=1; k<=cptcovn;k++) {            } 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          } 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    } 
       }    nrerror("Too many iterations in brent"); 
       for (k=1; k<=cptcovage;k++)    *xmin=x; 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    return fx; 
       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]]];  
   /****************** mnbrak ***********************/
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               double (*func)(double)) 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  { 
     double ulim,u,r,q, dum;
     savm=oldm;    double fu; 
     oldm=newm;   
     maxmax=0.;    *fa=(*func)(*ax); 
     for(j=1;j<=nlstate;j++){    *fb=(*func)(*bx); 
       min=1.;    if (*fb > *fa) { 
       max=0.;      SHFT(dum,*ax,*bx,dum) 
       for(i=1; i<=nlstate; i++) {        SHFT(dum,*fb,*fa,dum) 
         sumnew=0;        } 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    *cx=(*bx)+GOLD*(*bx-*ax); 
         prlim[i][j]= newm[i][j]/(1-sumnew);    *fc=(*func)(*cx); 
         max=FMAX(max,prlim[i][j]);    while (*fb > *fc) { 
         min=FMIN(min,prlim[i][j]);      r=(*bx-*ax)*(*fb-*fc); 
       }      q=(*bx-*cx)*(*fb-*fa); 
       maxmin=max-min;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       maxmax=FMAX(maxmax,maxmin);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     }      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     if(maxmax < ftolpl){      if ((*bx-u)*(u-*cx) > 0.0) { 
       return prlim;        fu=(*func)(u); 
     }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   }        fu=(*func)(u); 
 }        if (fu < *fc) { 
           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
 /*************** transition probabilities ***************/            SHFT(*fb,*fc,fu,(*func)(u)) 
             } 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 {        u=ulim; 
   double s1, s2;        fu=(*func)(u); 
   /*double t34;*/      } else { 
   int i,j,j1, nc, ii, jj;        u=(*cx)+GOLD*(*cx-*bx); 
         fu=(*func)(u); 
     for(i=1; i<= nlstate; i++){      } 
     for(j=1; j<i;j++){      SHFT(*ax,*bx,*cx,u) 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        SHFT(*fa,*fb,*fc,fu) 
         /*s2 += param[i][j][nc]*cov[nc];*/        } 
         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);*/  
       }  /*************** linmin ************************/
       ps[i][j]=s2;  
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  int ncom; 
     }  double *pcom,*xicom;
     for(j=i+1; j<=nlstate+ndeath;j++){  double (*nrfunc)(double []); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){   
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  { 
       }    double brent(double ax, double bx, double cx, 
       ps[i][j]=s2;                 double (*f)(double), double tol, double *xmin); 
     }    double f1dim(double x); 
   }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     /*ps[3][2]=1;*/                double *fc, double (*func)(double)); 
     int j; 
   for(i=1; i<= nlstate; i++){    double xx,xmin,bx,ax; 
      s1=0;    double fx,fb,fa;
     for(j=1; j<i; j++)   
       s1+=exp(ps[i][j]);    ncom=n; 
     for(j=i+1; j<=nlstate+ndeath; j++)    pcom=vector(1,n); 
       s1+=exp(ps[i][j]);    xicom=vector(1,n); 
     ps[i][i]=1./(s1+1.);    nrfunc=func; 
     for(j=1; j<i; j++)    for (j=1;j<=n;j++) { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];      pcom[j]=p[j]; 
     for(j=i+1; j<=nlstate+ndeath; j++)      xicom[j]=xi[j]; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    } 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    ax=0.0; 
   } /* end i */    xx=1.0; 
     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     for(jj=1; jj<= nlstate+ndeath; jj++){  #ifdef DEBUG
       ps[ii][jj]=0;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       ps[ii][ii]=1;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     }  #endif
   }    for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
       p[j] += xi[j]; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    } 
     for(jj=1; jj<= nlstate+ndeath; jj++){    free_vector(xicom,1,n); 
      printf("%lf ",ps[ii][jj]);    free_vector(pcom,1,n); 
    }  } 
     printf("\n ");  
     }  char *asc_diff_time(long time_sec, char ascdiff[])
     printf("\n ");printf("%lf ",cov[2]);*/  {
 /*    long sec_left, days, hours, minutes;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    days = (time_sec) / (60*60*24);
   goto end;*/    sec_left = (time_sec) % (60*60*24);
     return ps;    hours = (sec_left) / (60*60) ;
 }    sec_left = (sec_left) %(60*60);
     minutes = (sec_left) /60;
 /**************** Product of 2 matrices ******************/    sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    return ascdiff;
 {  }
   /* 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(...) */  /*************** powell ************************/
   /* in, b, out are matrice of pointers which should have been initialized  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
      before: only the contents of out is modified. The function returns              double (*func)(double [])) 
      a pointer to pointers identical to out */  { 
   long i, j, k;    void linmin(double p[], double xi[], int n, double *fret, 
   for(i=nrl; i<= nrh; i++)                double (*func)(double [])); 
     for(k=ncolol; k<=ncoloh; k++)    int i,ibig,j; 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    double del,t,*pt,*ptt,*xit;
         out[i][k] +=in[i][j]*b[j][k];    double fp,fptt;
     double *xits;
   return out;    int niterf, itmp;
 }  
     pt=vector(1,n); 
     ptt=vector(1,n); 
 /************* Higher Matrix Product ***************/    xit=vector(1,n); 
     xits=vector(1,n); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    *fret=(*func)(p); 
 {    for (j=1;j<=n;j++) pt[j]=p[j]; 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    for (*iter=1;;++(*iter)) { 
      duration (i.e. until      fp=(*fret); 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      ibig=0; 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      del=0.0; 
      (typically every 2 years instead of every month which is too big).      last_time=curr_time;
      Model is determined by parameters x and covariates have to be      (void) gettimeofday(&curr_time,&tzp);
      included manually here.      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
       fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
      */      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       for (i=1;i<=n;i++) {
   int i, j, d, h, k;        printf(" %d %.12f",i, p[i]);
   double **out, cov[NCOVMAX];        fprintf(ficlog," %d %.12lf",i, p[i]);
   double **newm;        fprintf(ficrespow," %.12lf", p[i]);
       }
   /* Hstepm could be zero and should return the unit matrix */      printf("\n");
   for (i=1;i<=nlstate+ndeath;i++)      fprintf(ficlog,"\n");
     for (j=1;j<=nlstate+ndeath;j++){      fprintf(ficrespow,"\n");fflush(ficrespow);
       oldm[i][j]=(i==j ? 1.0 : 0.0);      if(*iter <=3){
       po[i][j][0]=(i==j ? 1.0 : 0.0);        tm = *localtime(&curr_time.tv_sec);
     }        strcpy(strcurr,asctime(&tmf));
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /*       asctime_r(&tm,strcurr); */
   for(h=1; h <=nhstepm; h++){        forecast_time=curr_time;
     for(d=1; d <=hstepm; d++){        itmp = strlen(strcurr);
       newm=savm;        if(strcurr[itmp-1]=='\n')
       /* Covariates have to be included here again */          strcurr[itmp-1]='\0';
       cov[1]=1.;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        for(niterf=10;niterf<=30;niterf+=10){
       for (k=1; k<=cptcovage;k++)          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          tmf = *localtime(&forecast_time.tv_sec);
       for (k=1; k<=cptcovprod;k++)  /*      asctime_r(&tmf,strfor); */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          strcpy(strfor,asctime(&tmf));
           itmp = strlen(strfor);
           if(strfor[itmp-1]=='\n')
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/          strfor[itmp-1]='\0';
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        }
       savm=oldm;      }
       oldm=newm;      for (i=1;i<=n;i++) { 
     }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     for(i=1; i<=nlstate+ndeath; i++)        fptt=(*fret); 
       for(j=1;j<=nlstate+ndeath;j++) {  #ifdef DEBUG
         po[i][j][h]=newm[i][j];        printf("fret=%lf \n",*fret);
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        fprintf(ficlog,"fret=%lf \n",*fret);
          */  #endif
       }        printf("%d",i);fflush(stdout);
   } /* end h */        fprintf(ficlog,"%d",i);fflush(ficlog);
   return po;        linmin(p,xit,n,fret,func); 
 }        if (fabs(fptt-(*fret)) > del) { 
           del=fabs(fptt-(*fret)); 
           ibig=i; 
 /*************** log-likelihood *************/        } 
 double func( double *x)  #ifdef DEBUG
 {        printf("%d %.12e",i,(*fret));
   int i, ii, j, k, mi, d, kk;        fprintf(ficlog,"%d %.12e",i,(*fret));
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        for (j=1;j<=n;j++) {
   double **out;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   double sw; /* Sum of weights */          printf(" x(%d)=%.12e",j,xit[j]);
   double lli; /* Individual log likelihood */          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   long ipmx;        }
   /*extern weight */        for(j=1;j<=n;j++) {
   /* We are differentiating ll according to initial status */          printf(" p=%.12e",p[j]);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/          fprintf(ficlog," p=%.12e",p[j]);
   /*for(i=1;i<imx;i++)        }
     printf(" %d\n",s[4][i]);        printf("\n");
   */        fprintf(ficlog,"\n");
   cov[1]=1.;  #endif
       } 
   for(k=1; k<=nlstate; k++) ll[k]=0.;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  #ifdef DEBUG
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        int k[2],l;
     for(mi=1; mi<= wav[i]-1; mi++){        k[0]=1;
       for (ii=1;ii<=nlstate+ndeath;ii++)        k[1]=-1;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        printf("Max: %.12e",(*func)(p));
       for(d=0; d<dh[mi][i]; d++){        fprintf(ficlog,"Max: %.12e",(*func)(p));
         newm=savm;        for (j=1;j<=n;j++) {
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          printf(" %.12e",p[j]);
         for (kk=1; kk<=cptcovage;kk++) {          fprintf(ficlog," %.12e",p[j]);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        }
         }        printf("\n");
                fprintf(ficlog,"\n");
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        for(l=0;l<=1;l++) {
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));          for (j=1;j<=n;j++) {
         savm=oldm;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         oldm=newm;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
                    fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
                  }
       } /* end mult */          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)));
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        }
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  #endif
       ipmx +=1;  
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        free_vector(xit,1,n); 
     } /* end of wave */        free_vector(xits,1,n); 
   } /* end of individual */        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        return; 
   /* 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 */      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   return -l;      for (j=1;j<=n;j++) { 
 }        ptt[j]=2.0*p[j]-pt[j]; 
         xit[j]=p[j]-pt[j]; 
         pt[j]=p[j]; 
 /*********** Maximum Likelihood Estimation ***************/      } 
       fptt=(*func)(ptt); 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      if (fptt < fp) { 
 {        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   int i,j, iter;        if (t < 0.0) { 
   double **xi,*delti;          linmin(p,xit,n,fret,func); 
   double fret;          for (j=1;j<=n;j++) { 
   xi=matrix(1,npar,1,npar);            xi[j][ibig]=xi[j][n]; 
   for (i=1;i<=npar;i++)            xi[j][n]=xit[j]; 
     for (j=1;j<=npar;j++)          }
       xi[i][j]=(i==j ? 1.0 : 0.0);  #ifdef DEBUG
   printf("Powell\n");          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   powell(p,xi,npar,ftol,&iter,&fret,func);          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("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));            printf(" %.12e",xit[j]);
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));            fprintf(ficlog," %.12e",xit[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 []))        }
 {      } 
   double  **a,**y,*x,pd;    } 
   double **hess;  } 
   int i, j,jk;  
   int *indx;  /**** Prevalence limit (stable prevalence)  ****************/
   
   double hessii(double p[], double delta, int theta, double delti[]);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   double hessij(double p[], double delti[], int i, int j);  {
   void lubksb(double **a, int npar, int *indx, double b[]) ;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   void ludcmp(double **a, int npar, int *indx, double *d) ;       matrix by transitions matrix until convergence is reached */
   
   hess=matrix(1,npar,1,npar);    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
   printf("\nCalculation of the hessian matrix. Wait...\n");    double **matprod2();
   for (i=1;i<=npar;i++){    double **out, cov[NCOVMAX], **pmij();
     printf("%d",i);fflush(stdout);    double **newm;
     hess[i][i]=hessii(p,ftolhess,i,delti);    double agefin, delaymax=50 ; /* Max number of years to converge */
     /*printf(" %f ",p[i]);*/  
     /*printf(" %lf ",hess[i][i]);*/    for (ii=1;ii<=nlstate+ndeath;ii++)
   }      for (j=1;j<=nlstate+ndeath;j++){
          oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (i=1;i<=npar;i++) {      }
     for (j=1;j<=npar;j++)  {  
       if (j>i) {     cov[1]=1.;
         printf(".%d%d",i,j);fflush(stdout);   
         hess[i][j]=hessij(p,delti,i,j);   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         hess[j][i]=hess[i][j];        for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
         /*printf(" %lf ",hess[i][j]);*/      newm=savm;
       }      /* Covariates have to be included here again */
     }       cov[2]=agefin;
   }    
   printf("\n");        for (k=1; k<=cptcovn;k++) {
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
          }
   a=matrix(1,npar,1,npar);        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   y=matrix(1,npar,1,npar);        for (k=1; k<=cptcovprod;k++)
   x=vector(1,npar);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   indx=ivector(1,npar);  
   for (i=1;i<=npar;i++)        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   ludcmp(a,npar,indx,&pd);        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;      savm=oldm;
     x[j]=1;      oldm=newm;
     lubksb(a,npar,indx,x);      maxmax=0.;
     for (i=1;i<=npar;i++){      for(j=1;j<=nlstate;j++){
       matcov[i][j]=x[i];        min=1.;
     }        max=0.;
   }        for(i=1; i<=nlstate; i++) {
           sumnew=0;
   printf("\n#Hessian matrix#\n");          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   for (i=1;i<=npar;i++) {          prlim[i][j]= newm[i][j]/(1-sumnew);
     for (j=1;j<=npar;j++) {          max=FMAX(max,prlim[i][j]);
       printf("%.3e ",hess[i][j]);          min=FMIN(min,prlim[i][j]);
     }        }
     printf("\n");        maxmin=max-min;
   }        maxmax=FMAX(maxmax,maxmin);
       }
   /* Recompute Inverse */      if(maxmax < ftolpl){
   for (i=1;i<=npar;i++)        return prlim;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      }
   ludcmp(a,npar,indx,&pd);    }
   }
   /*  printf("\n#Hessian matrix recomputed#\n");  
   /*************** transition probabilities ***************/ 
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     x[j]=1;  {
     lubksb(a,npar,indx,x);    double s1, s2;
     for (i=1;i<=npar;i++){    /*double t34;*/
       y[i][j]=x[i];    int i,j,j1, nc, ii, jj;
       printf("%.3e ",y[i][j]);  
     }      for(i=1; i<= nlstate; i++){
     printf("\n");      for(j=1; j<i;j++){
   }        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   */          /*s2 += param[i][j][nc]*cov[nc];*/
           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   free_matrix(a,1,npar,1,npar);          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
   free_matrix(y,1,npar,1,npar);        }
   free_vector(x,1,npar);        ps[i][j]=s2;
   free_ivector(indx,1,npar);        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   free_matrix(hess,1,npar,1,npar);      }
       for(j=i+1; j<=nlstate+ndeath;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 }          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
 /*************** hessian matrix ****************/        }
 double hessii( double x[], double delta, int theta, double delti[])        ps[i][j]=s2;
 {      }
   int i;    }
   int l=1, lmax=20;      /*ps[3][2]=1;*/
   double k1,k2;  
   double p2[NPARMAX+1];    for(i=1; i<= nlstate; i++){
   double res;       s1=0;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      for(j=1; j<i; j++)
   double fx;        s1+=exp(ps[i][j]);
   int k=0,kmax=10;      for(j=i+1; j<=nlstate+ndeath; j++)
   double l1;        s1+=exp(ps[i][j]);
       ps[i][i]=1./(s1+1.);
   fx=func(x);      for(j=1; j<i; j++)
   for (i=1;i<=npar;i++) p2[i]=x[i];        ps[i][j]= exp(ps[i][j])*ps[i][i];
   for(l=0 ; l <=lmax; l++){      for(j=i+1; j<=nlstate+ndeath; j++)
     l1=pow(10,l);        ps[i][j]= exp(ps[i][j])*ps[i][i];
     delts=delt;      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     for(k=1 ; k <kmax; k=k+1){    } /* end i */
       delt = delta*(l1*k);  
       p2[theta]=x[theta] +delt;    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       k1=func(p2)-fx;      for(jj=1; jj<= nlstate+ndeath; jj++){
       p2[theta]=x[theta]-delt;        ps[ii][jj]=0;
       k2=func(p2)-fx;        ps[ii][ii]=1;
       /*res= (k1-2.0*fx+k2)/delt/delt; */      }
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    }
        
 #ifdef DEBUG  
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
 #endif      for(jj=1; jj<= nlstate+ndeath; jj++){
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */       printf("%lf ",ps[ii][jj]);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){     }
         k=kmax;      printf("\n ");
       }      }
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      printf("\n ");printf("%lf ",cov[2]);*/
         k=kmax; l=lmax*10.;  /*
       }    for(i=1; i<= npar; i++) printf("%f ",x[i]);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    goto end;*/
         delts=delt;      return ps;
       }  }
     }  
   }  /**************** Product of 2 matrices ******************/
   delti[theta]=delts;  
   return res;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
    {
 }    /* 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(...) */
 double hessij( double x[], double delti[], int thetai,int thetaj)    /* in, b, out are matrice of pointers which should have been initialized 
 {       before: only the contents of out is modified. The function returns
   int i;       a pointer to pointers identical to out */
   int l=1, l1, lmax=20;    long i, j, k;
   double k1,k2,k3,k4,res,fx;    for(i=nrl; i<= nrh; i++)
   double p2[NPARMAX+1];      for(k=ncolol; k<=ncoloh; k++)
   int k;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
           out[i][k] +=in[i][j]*b[j][k];
   fx=func(x);  
   for (k=1; k<=2; k++) {    return out;
     for (i=1;i<=npar;i++) p2[i]=x[i];  }
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k1=func(p2)-fx;  /************* Higher Matrix Product ***************/
    
     p2[thetai]=x[thetai]+delti[thetai]/k;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  {
     k2=func(p2)-fx;    /* Computes the transition matrix starting at age 'age' over 
         'nhstepm*hstepm*stepm' months (i.e. until
     p2[thetai]=x[thetai]-delti[thetai]/k;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;       nhstepm*hstepm matrices. 
     k3=func(p2)-fx;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         (typically every 2 years instead of every month which is too big 
     p2[thetai]=x[thetai]-delti[thetai]/k;       for the memory).
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;       Model is determined by parameters x and covariates have to be 
     k4=func(p2)-fx;       included manually here. 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  
 #ifdef DEBUG       */
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  
 #endif    int i, j, d, h, k;
   }    double **out, cov[NCOVMAX];
   return res;    double **newm;
 }  
     /* Hstepm could be zero and should return the unit matrix */
 /************** Inverse of matrix **************/    for (i=1;i<=nlstate+ndeath;i++)
 void ludcmp(double **a, int n, int *indx, double *d)      for (j=1;j<=nlstate+ndeath;j++){
 {        oldm[i][j]=(i==j ? 1.0 : 0.0);
   int i,imax,j,k;        po[i][j][0]=(i==j ? 1.0 : 0.0);
   double big,dum,sum,temp;      }
   double *vv;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
      for(h=1; h <=nhstepm; h++){
   vv=vector(1,n);      for(d=1; d <=hstepm; d++){
   *d=1.0;        newm=savm;
   for (i=1;i<=n;i++) {        /* Covariates have to be included here again */
     big=0.0;        cov[1]=1.;
     for (j=1;j<=n;j++)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       if ((temp=fabs(a[i][j])) > big) big=temp;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        for (k=1; k<=cptcovage;k++)
     vv[i]=1.0/big;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   }        for (k=1; k<=cptcovprod;k++)
   for (j=1;j<=n;j++) {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     for (i=1;i<j;i++) {  
       sum=a[i][j];  
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       a[i][j]=sum;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     }        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     big=0.0;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     for (i=j;i<=n;i++) {        savm=oldm;
       sum=a[i][j];        oldm=newm;
       for (k=1;k<j;k++)      }
         sum -= a[i][k]*a[k][j];      for(i=1; i<=nlstate+ndeath; i++)
       a[i][j]=sum;        for(j=1;j<=nlstate+ndeath;j++) {
       if ( (dum=vv[i]*fabs(sum)) >= big) {          po[i][j][h]=newm[i][j];
         big=dum;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
         imax=i;           */
       }        }
     }    } /* end h */
     if (j != imax) {    return po;
       for (k=1;k<=n;k++) {  }
         dum=a[imax][k];  
         a[imax][k]=a[j][k];  
         a[j][k]=dum;  /*************** log-likelihood *************/
       }  double func( double *x)
       *d = -(*d);  {
       vv[imax]=vv[j];    int i, ii, j, k, mi, d, kk;
     }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     indx[j]=imax;    double **out;
     if (a[j][j] == 0.0) a[j][j]=TINY;    double sw; /* Sum of weights */
     if (j != n) {    double lli; /* Individual log likelihood */
       dum=1.0/(a[j][j]);    int s1, s2;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    double bbh, survp;
     }    long ipmx;
   }    /*extern weight */
   free_vector(vv,1,n);  /* Doesn't work */    /* We are differentiating ll according to initial status */
 ;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 }    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
 void lubksb(double **a, int n, int *indx, double b[])    */
 {    cov[1]=1.;
   int i,ii=0,ip,j;  
   double sum;    for(k=1; k<=nlstate; k++) ll[k]=0.;
    
   for (i=1;i<=n;i++) {    if(mle==1){
     ip=indx[i];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     sum=b[ip];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     b[ip]=b[i];        for(mi=1; mi<= wav[i]-1; mi++){
     if (ii)          for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];            for (j=1;j<=nlstate+ndeath;j++){
     else if (sum) ii=i;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     b[i]=sum;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            }
   for (i=n;i>=1;i--) {          for(d=0; d<dh[mi][i]; d++){
     sum=b[i];            newm=savm;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     b[i]=sum/a[i][i];            for (kk=1; kk<=cptcovage;kk++) {
   }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 }            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 /************ Frequencies ********************/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 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)            savm=oldm;
 {  /* Some frequencies */            oldm=newm;
            } /* end mult */
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        
   double ***freq; /* Frequencies */          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   double *pp;          /* But now since version 0.9 we anticipate for bias and large stepm.
   double pos, k2, dateintsum=0,k2cpt=0;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   FILE *ficresp;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   char fileresp[FILENAMELENGTH];           * the nearest (and in case of equal distance, to the lowest) interval but now
             * we keep into memory the bias bh[mi][i] and also the previous matrix product
   pp=vector(1,nlstate);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);           * probability in order to take into account the bias as a fraction of the way
   strcpy(fileresp,"p");           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   strcat(fileresp,fileres);           * -stepm/2 to stepm/2 .
   if((ficresp=fopen(fileresp,"w"))==NULL) {           * For stepm=1 the results are the same as for previous versions of Imach.
     printf("Problem with prevalence resultfile: %s\n", fileresp);           * For stepm > 1 the results are less biased than in previous versions. 
     exit(0);           */
   }          s1=s[mw[mi][i]][i];
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          s2=s[mw[mi+1][i]][i];
   j1=0;          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias is positive if real duration
   j=cptcoveff;           * is higher than the multiple of stepm and negative otherwise.
   if (cptcovn<1) {j=1;ncodemax[1]=1;}           */
           /* 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(k1=1; k1<=j;k1++){          if( s2 > nlstate){ 
    for(i1=1; i1<=ncodemax[k1];i1++){            /* i.e. if s2 is a death state and if the date of death is known then the contribution
        j1++;               to the likelihood is the probability to die between last step unit time and current 
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);               step unit time, which is also the differences between probability to die before dh 
          scanf("%d", i);*/               and probability to die before dh-stepm . 
         for (i=-1; i<=nlstate+ndeath; i++)                 In version up to 0.92 likelihood was computed
          for (jk=-1; jk<=nlstate+ndeath; jk++)            as if date of death was unknown. Death was treated as any other
            for(m=agemin; m <= agemax+3; m++)          health state: the date of the interview describes the actual state
              freq[i][jk][m]=0;          and not the date of a change in health state. The former idea was
           to consider that at each interview the state was recorded
         dateintsum=0;          (healthy, disable or death) and IMaCh was corrected; but when we
         k2cpt=0;          introduced the exact date of death then we should have modified
        for (i=1; i<=imx; i++) {          the contribution of an exact death to the likelihood. This new
          bool=1;          contribution is smaller and very dependent of the step unit
          if  (cptcovn>0) {          stepm. It is no more the probability to die between last interview
            for (z1=1; z1<=cptcoveff; z1++)          and month of death but the probability to survive from last
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          interview up to one month before death multiplied by the
                bool=0;          probability to die within a month. Thanks to Chris
          }          Jackson for correcting this bug.  Former versions increased
          if (bool==1) {          mortality artificially. The bad side is that we add another loop
            for(m=firstpass; m<=lastpass; m++){          which slows down the processing. The difference can be up to 10%
              k2=anint[m][i]+(mint[m][i]/12.);          lower mortality.
              if ((k2>=dateprev1) && (k2<=dateprev2)) {            */
                if(agev[m][i]==0) agev[m][i]=agemax+1;            lli=log(out[s1][s2] - savm[s1][s2]);
                if(agev[m][i]==1) agev[m][i]=agemax+2;          }else{
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          } 
                  dateintsum=dateintsum+k2;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                  k2cpt++;          /*if(lli ==000.0)*/
                }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
           ipmx +=1;
              }          sw += weight[i];
            }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          }        } /* end of wave */
        }      } /* end of individual */
            }  else if(mle==2){
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         if  (cptcovn>0) {        for(mi=1; mi<= wav[i]-1; mi++){
          fprintf(ficresp, "\n#********** Variable ");          for (ii=1;ii<=nlstate+ndeath;ii++)
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            for (j=1;j<=nlstate+ndeath;j++){
        fprintf(ficresp, "**********\n#");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
        for(i=1; i<=nlstate;i++)            }
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          for(d=0; d<=dh[mi][i]; d++){
        fprintf(ficresp, "\n");            newm=savm;
                    cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for(i=(int)agemin; i <= (int)agemax+3; i++){            for (kk=1; kk<=cptcovage;kk++) {
     if(i==(int)agemax+3)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       printf("Total");            }
     else            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       printf("Age %d", i);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(jk=1; jk <=nlstate ; jk++){            savm=oldm;
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            oldm=newm;
         pp[jk] += freq[jk][m][i];          } /* end mult */
     }        
     for(jk=1; jk <=nlstate ; jk++){          s1=s[mw[mi][i]][i];
       for(m=-1, pos=0; m <=0 ; m++)          s2=s[mw[mi+1][i]][i];
         pos += freq[jk][m][i];          bbh=(double)bh[mi][i]/(double)stepm; 
       if(pp[jk]>=1.e-10)          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 */
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          ipmx +=1;
       else          sw += weight[i];
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
       } /* end of individual */
      for(jk=1; jk <=nlstate ; jk++){    }  else if(mle==3){  /* exponential inter-extrapolation */
       for(m=0, 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 (ii=1;ii<=nlstate+ndeath;ii++)
     for(jk=1,pos=0; jk <=nlstate ; jk++)            for (j=1;j<=nlstate+ndeath;j++){
       pos += pp[jk];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(jk=1; jk <=nlstate ; jk++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       if(pos>=1.e-5)            }
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          for(d=0; d<dh[mi][i]; d++){
       else            newm=savm;
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if( i <= (int) agemax){            for (kk=1; kk<=cptcovage;kk++) {
         if(pos>=1.e-5){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            }
           probs[i][jk][j1]= pp[jk]/pos;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
       else            oldm=newm;
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          } /* end mult */
       }        
     }          s1=s[mw[mi][i]][i];
     for(jk=-1; jk <=nlstate+ndeath; jk++)          s2=s[mw[mi+1][i]][i];
       for(m=-1; m <=nlstate+ndeath; m++)          bbh=(double)bh[mi][i]/(double)stepm; 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     if(i <= (int) agemax)          ipmx +=1;
       fprintf(ficresp,"\n");          sw += weight[i];
     printf("\n");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
     }      } /* end of individual */
  }    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   dateintmean=dateintsum/k2cpt;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   fclose(ficresp);        for(mi=1; mi<= wav[i]-1; mi++){
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          for (ii=1;ii<=nlstate+ndeath;ii++)
   free_vector(pp,1,nlstate);            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* End of Freq */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 }            }
           for(d=0; d<dh[mi][i]; d++){
 /************ Prevalence ********************/            newm=savm;
 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)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 {  /* Some frequencies */            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;            }
   double ***freq; /* Frequencies */          
   double *pp;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double pos, k2;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   pp=vector(1,nlstate);            oldm=newm;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          } /* end mult */
          
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          s1=s[mw[mi][i]][i];
   j1=0;          s2=s[mw[mi+1][i]][i];
            if( s2 > nlstate){ 
   j=cptcoveff;            lli=log(out[s1][s2] - savm[s1][s2]);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          }else{
              lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
  for(k1=1; k1<=j;k1++){          }
     for(i1=1; i1<=ncodemax[k1];i1++){          ipmx +=1;
       j1++;          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for (i=-1; i<=nlstate+ndeath; i++)    /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         for (jk=-1; jk<=nlstate+ndeath; jk++)          } /* end of wave */
           for(m=agemin; m <= agemax+3; m++)      } /* end of individual */
             freq[i][jk][m]=0;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
            for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (i=1; i<=imx; i++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         bool=1;        for(mi=1; mi<= wav[i]-1; mi++){
         if  (cptcovn>0) {          for (ii=1;ii<=nlstate+ndeath;ii++)
           for (z1=1; z1<=cptcoveff; z1++)            for (j=1;j<=nlstate+ndeath;j++){
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               bool=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            }
         if (bool==1) {          for(d=0; d<dh[mi][i]; d++){
           for(m=firstpass; m<=lastpass; m++){            newm=savm;
             k2=anint[m][i]+(mint[m][i]/12.);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            for (kk=1; kk<=cptcovage;kk++) {
               if(agev[m][i]==0) agev[m][i]=agemax+1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
               if(agev[m][i]==1) agev[m][i]=agemax+2;            }
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */            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 */
         for(i=(int)agemin; i <= (int)agemax+3; i++){        
           for(jk=1; jk <=nlstate ; jk++){          s1=s[mw[mi][i]][i];
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          s2=s[mw[mi+1][i]][i];
               pp[jk] += freq[jk][m][i];          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }          ipmx +=1;
           for(jk=1; jk <=nlstate ; jk++){          sw += weight[i];
             for(m=-1, pos=0; m <=0 ; m++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             pos += freq[jk][m][i];          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         }        } /* end of wave */
              } /* end of individual */
          for(jk=1; jk <=nlstate ; jk++){    } /* End of if */
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
              pp[jk] += freq[jk][m][i];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
          }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
              return -l;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  }
   
          for(jk=1; jk <=nlstate ; jk++){            /*************** log-likelihood *************/
            if( i <= (int) agemax){  double funcone( double *x)
              if(pos>=1.e-5){  {
                probs[i][jk][j1]= pp[jk]/pos;    /* Same as likeli but slower because of a lot of printf and if */
              }    int i, ii, j, k, mi, d, kk;
            }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
          }    double **out;
              double lli; /* Individual log likelihood */
         }    double llt;
     }    int s1, s2;
   }    double bbh, survp;
      /*extern weight */
      /* We are differentiating ll according to initial status */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   free_vector(pp,1,nlstate);    /*for(i=1;i<imx;i++) 
        printf(" %d\n",s[4][i]);
 }  /* End of Freq */    */
     cov[1]=1.;
 /************* Waves Concatenation ***************/  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  
 {    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      Death is a valid wave (if date is known).      for(mi=1; mi<= wav[i]-1; mi++){
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        for (ii=1;ii<=nlstate+ndeath;ii++)
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          for (j=1;j<=nlstate+ndeath;j++){
      and mw[mi+1][i]. dh depends on stepm.            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      */            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
   int i, mi, m;        for(d=0; d<dh[mi][i]; d++){
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          newm=savm;
      double sum=0., jmean=0.;*/          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {
   int j, k=0,jk, ju, jl;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double sum=0.;          }
   jmin=1e+5;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   jmax=-1;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   jmean=0.;          savm=oldm;
   for(i=1; i<=imx; i++){          oldm=newm;
     mi=0;        } /* end mult */
     m=firstpass;        
     while(s[m][i] <= nlstate){        s1=s[mw[mi][i]][i];
       if(s[m][i]>=1)        s2=s[mw[mi+1][i]][i];
         mw[++mi][i]=m;        bbh=(double)bh[mi][i]/(double)stepm; 
       if(m >=lastpass)        /* bias is positive if real duration
         break;         * is higher than the multiple of stepm and negative otherwise.
       else         */
         m++;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     }/* end while */          lli=log(out[s1][s2] - savm[s1][s2]);
     if (s[m][i] > nlstate){        } else if (mle==1){
       mi++;     /* Death is another wave */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       /* if(mi==0)  never been interviewed correctly before death */        } else if(mle==2){
          /* Only death is a correct wave */          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 */
       mw[mi][i]=m;        } else if(mle==3){  /* exponential inter-extrapolation */
     }          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 */
         } else if (mle==4){  /* mle=4 no inter-extrapolation */
     wav[i]=mi;          lli=log(out[s1][s2]); /* Original formula */
     if(mi==0)        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          lli=log(out[s1][s2]); /* Original formula */
   }        } /* End of if */
         ipmx +=1;
   for(i=1; i<=imx; i++){        sw += weight[i];
     for(mi=1; mi<wav[i];mi++){        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       if (stepm <=0)  /*       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]); */
         dh[mi][i]=1;        if(globpr){
       else{          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
         if (s[mw[mi+1][i]][i] > nlstate) {   %10.6f %10.6f %10.6f ", \
           if (agedc[i] < 2*AGESUP) {                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           if(j==0) j=1;  /* Survives at least one month after exam */          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
           k=k+1;            llt +=ll[k]*gipmx/gsw;
           if (j >= jmax) jmax=j;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           if (j <= jmin) jmin=j;          }
           sum=sum+j;          fprintf(ficresilk," %10.6f\n", -llt);
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        }
           }      } /* end of wave */
         }    } /* end of individual */
         else{    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           k=k+1;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           if (j >= jmax) jmax=j;    if(globpr==0){ /* First time we count the contributions and weights */
           else if (j <= jmin)jmin=j;      gipmx=ipmx;
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */      gsw=sw;
           sum=sum+j;    }
         }    return -l;
         jk= j/stepm;  }
         jl= j -jk*stepm;  
         ju= j -(jk+1)*stepm;  
         if(jl <= -ju)  /*************** function likelione ***********/
           dh[mi][i]=jk;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         else  {
           dh[mi][i]=jk+1;    /* This routine should help understanding what is done with 
         if(dh[mi][i]==0)       the selection of individuals/waves and
           dh[mi][i]=1; /* At least one step */       to check the exact contribution to the likelihood.
       }       Plotting could be done.
     }     */
   }    int k;
   jmean=sum/k;  
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    if(*globpri !=0){ /* Just counts and sums, no printings */
  }      strcpy(fileresilk,"ilk"); 
 /*********** Tricode ****************************/      strcat(fileresilk,fileres);
 void tricode(int *Tvar, int **nbcode, int imx)      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
 {        printf("Problem with resultfile: %s\n", fileresilk);
   int Ndum[20],ij=1, k, j, i;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   int cptcode=0;      }
   cptcoveff=0;      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
        fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   for (k=0; k<19; k++) Ndum[k]=0;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   for (k=1; k<=7; k++) ncodemax[k]=0;      for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     for (i=1; i<=imx; i++) {    }
       ij=(int)(covar[Tvar[j]][i]);  
       Ndum[ij]++;    *fretone=(*funcone)(p);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    if(*globpri !=0){
       if (ij > cptcode) cptcode=ij;      fclose(ficresilk);
     }      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       fflush(fichtm); 
     for (i=0; i<=cptcode; i++) {    } 
       if(Ndum[i]!=0) ncodemax[j]++;    return;
     }  }
     ij=1;  
   
   /*********** Maximum Likelihood Estimation ***************/
     for (i=1; i<=ncodemax[j]; i++) {  
       for (k=0; k<=19; k++) {  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
         if (Ndum[k] != 0) {  {
           nbcode[Tvar[j]][ij]=k;    int i,j, iter;
           ij++;    double **xi;
         }    double fret;
         if (ij > ncodemax[j]) break;    double fretone; /* Only one call to likelihood */
       }      char filerespow[FILENAMELENGTH];
     }    xi=matrix(1,npar,1,npar);
   }      for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
  for (k=0; k<19; k++) Ndum[k]=0;        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
  for (i=1; i<=ncovmodel-2; i++) {    strcpy(filerespow,"pow"); 
       ij=Tvar[i];    strcat(filerespow,fileres);
       Ndum[ij]++;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     }      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
  ij=1;    }
  for (i=1; i<=10; i++) {    fprintf(ficrespow,"# Powell\n# iter -2*LL");
    if((Ndum[i]!=0) && (i<=ncov)){    for (i=1;i<=nlstate;i++)
      Tvaraff[ij]=i;      for(j=1;j<=nlstate+ndeath;j++)
      ij++;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
    }    fprintf(ficrespow,"\n");
  }  
      powell(p,xi,npar,ftol,&iter,&fret,func);
     cptcoveff=ij-1;  
 }    fclose(ficrespow);
     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
 /*********** Health Expectancies ****************/    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)  
 {  }
   /* Health expectancies */  
   int i, j, nhstepm, hstepm, h;  /**** Computes Hessian and covariance matrix ***/
   double age, agelim,hf;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   double ***p3mat;  {
      double  **a,**y,*x,pd;
   fprintf(ficreseij,"# Health expectancies\n");    double **hess;
   fprintf(ficreseij,"# Age");    int i, j,jk;
   for(i=1; i<=nlstate;i++)    int *indx;
     for(j=1; j<=nlstate;j++)  
       fprintf(ficreseij," %1d-%1d",i,j);    double hessii(double p[], double delta, int theta, double delti[]);
   fprintf(ficreseij,"\n");    double hessij(double p[], double delti[], int i, int j);
     void lubksb(double **a, int npar, int *indx, double b[]) ;
   hstepm=1*YEARM; /*  Every j years of age (in month) */    void ludcmp(double **a, int npar, int *indx, double *d) ;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
     hess=matrix(1,npar,1,npar);
   agelim=AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    printf("\nCalculation of the hessian matrix. Wait...\n");
     /* nhstepm age range expressed in number of stepm */    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);    for (i=1;i<=npar;i++){
     /* Typically if 20 years = 20*12/6=40 stepm */      printf("%d",i);fflush(stdout);
     /*if (stepm >= YEARM) hstepm=1;*/      fprintf(ficlog,"%d",i);fflush(ficlog);
 hstepm=1;      hess[i][i]=hessii(p,ftolhess,i,delti);
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */      /*printf(" %f ",p[i]);*/
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /*printf(" %lf ",hess[i][i]);*/
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      for (i=1;i<=npar;i++) {
 hf=stepm/YEARM;      for (j=1;j<=npar;j++)  {
 /*printf("stepm=%d nhstepm=%d hstepm=%d age=%lf ",stepm, nhstepm, hstepm, age);*/        if (j>i) { 
     for(i=1; i<=nlstate;i++)          printf(".%d%d",i,j);fflush(stdout);
       for(j=1; j<=nlstate;j++)          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          hess[i][j]=hessij(p,delti,i,j);
           eij[i][j][(int)age] +=hf*(p3mat[i][j][h]+p3mat[i][j][h+1])/2.0;          hess[j][i]=hess[i][j];    
         }          /*printf(" %lf ",hess[i][j]);*/
            }
     /* hf=1;      }
        if (stepm >= YEARM) hf=stepm/YEARM;*/    }
 hf=stepm/YEARM;    printf("\n");
      fprintf(ficlog,"\n");
     fprintf(ficreseij,"%3.0f",age );  
     for(i=1; i<=nlstate;i++)    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       for(j=1; j<=nlstate;j++){    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);    
       }    a=matrix(1,npar,1,npar);
     fprintf(ficreseij,"\n");    y=matrix(1,npar,1,npar);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    x=vector(1,npar);
   }    indx=ivector(1,npar);
 }    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
 /************ Variance ******************/    ludcmp(a,npar,indx,&pd);
 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)  
 {    for (j=1;j<=npar;j++) {
   /* Variance of health expectancies */      for (i=1;i<=npar;i++) x[i]=0;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      x[j]=1;
   double **newm;      lubksb(a,npar,indx,x);
   double **dnewm,**doldm;      for (i=1;i<=npar;i++){ 
   int i, j, nhstepm, hstepm, h;        matcov[i][j]=x[i];
   int k, cptcode;      }
   double *xp;    }
   double **gp, **gm;  
   double ***gradg, ***trgradg;    printf("\n#Hessian matrix#\n");
   double ***p3mat;    fprintf(ficlog,"\n#Hessian matrix#\n");
   double age,agelim;    for (i=1;i<=npar;i++) { 
   int theta;      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
    fprintf(ficresvij,"# Covariances of life expectancies\n");        fprintf(ficlog,"%.3e ",hess[i][j]);
   fprintf(ficresvij,"# Age");      }
   for(i=1; i<=nlstate;i++)      printf("\n");
     for(j=1; j<=nlstate;j++)      fprintf(ficlog,"\n");
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    }
   fprintf(ficresvij,"\n");  
     /* Recompute Inverse */
   xp=vector(1,npar);    for (i=1;i<=npar;i++)
   dnewm=matrix(1,nlstate,1,npar);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   doldm=matrix(1,nlstate,1,nlstate);    ludcmp(a,npar,indx,&pd);
    
   hstepm=1*YEARM; /* Every year of age */    /*  printf("\n#Hessian matrix recomputed#\n");
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   agelim = AGESUP;    for (j=1;j<=npar;j++) {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for (i=1;i<=npar;i++) x[i]=0;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      x[j]=1;
     if (stepm >= YEARM) hstepm=1;      lubksb(a,npar,indx,x);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      for (i=1;i<=npar;i++){ 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        y[i][j]=x[i];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        printf("%.3e ",y[i][j]);
     gp=matrix(0,nhstepm,1,nlstate);        fprintf(ficlog,"%.3e ",y[i][j]);
     gm=matrix(0,nhstepm,1,nlstate);      }
       printf("\n");
     for(theta=1; theta <=npar; theta++){      fprintf(ficlog,"\n");
       for(i=1; i<=npar; i++){ /* Computes gradient */    }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    */
       }  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      free_matrix(a,1,npar,1,npar);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
       if (popbased==1) {    free_ivector(indx,1,npar);
         for(i=1; i<=nlstate;i++)    free_matrix(hess,1,npar,1,npar);
           prlim[i][i]=probs[(int)age][i][ij];  
       }  
    }
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){  /*************** hessian matrix ****************/
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  double hessii( double x[], double delta, int theta, double delti[])
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  {
         }    int i;
       }    int l=1, lmax=20;
        double k1,k2;
       for(i=1; i<=npar; i++) /* Computes gradient */    double p2[NPARMAX+1];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double res;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double fx;
      int k=0,kmax=10;
       if (popbased==1) {    double l1;
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];    fx=func(x);
       }    for (i=1;i<=npar;i++) p2[i]=x[i];
     for(l=0 ; l <=lmax; l++){
       for(j=1; j<= nlstate; j++){      l1=pow(10,l);
         for(h=0; h<=nhstepm; h++){      delts=delt;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      for(k=1 ; k <kmax; k=k+1){
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        delt = delta*(l1*k);
         }        p2[theta]=x[theta] +delt;
       }        k1=func(p2)-fx;
         p2[theta]=x[theta]-delt;
       for(j=1; j<= nlstate; j++)        k2=func(p2)-fx;
         for(h=0; h<=nhstepm; h++){        /*res= (k1-2.0*fx+k2)/delt/delt; */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         }        
     } /* End theta */  #ifdef DEBUG
         printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   #endif
     for(h=0; h<=nhstepm; h++)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       for(j=1; j<=nlstate;j++)        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         for(theta=1; theta <=npar; theta++)          k=kmax;
           trgradg[h][j][theta]=gradg[h][theta][j];        }
         else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     for(i=1;i<=nlstate;i++)          k=kmax; l=lmax*10.;
       for(j=1;j<=nlstate;j++)        }
         vareij[i][j][(int)age] =0.;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     for(h=0;h<=nhstepm;h++){          delts=delt;
       for(k=0;k<=nhstepm;k++){        }
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      }
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    }
         for(i=1;i<=nlstate;i++)    delti[theta]=delts;
           for(j=1;j<=nlstate;j++)    return res; 
             vareij[i][j][(int)age] += doldm[i][j];    
       }  }
     }  
     h=1;  double hessij( double x[], double delti[], int thetai,int thetaj)
     if (stepm >= YEARM) h=stepm/YEARM;  {
     fprintf(ficresvij,"%.0f ",age );    int i;
     for(i=1; i<=nlstate;i++)    int l=1, l1, lmax=20;
       for(j=1; j<=nlstate;j++){    double k1,k2,k3,k4,res,fx;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    double p2[NPARMAX+1];
       }    int k;
     fprintf(ficresvij,"\n");  
     free_matrix(gp,0,nhstepm,1,nlstate);    fx=func(x);
     free_matrix(gm,0,nhstepm,1,nlstate);    for (k=1; k<=2; k++) {
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      for (i=1;i<=npar;i++) p2[i]=x[i];
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      p2[thetai]=x[thetai]+delti[thetai]/k;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   } /* End age */      k1=func(p2)-fx;
      
   free_vector(xp,1,npar);      p2[thetai]=x[thetai]+delti[thetai]/k;
   free_matrix(doldm,1,nlstate,1,npar);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   free_matrix(dnewm,1,nlstate,1,nlstate);      k2=func(p2)-fx;
     
 }      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 /************ Variance of prevlim ******************/      k3=func(p2)-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)    
 {      p2[thetai]=x[thetai]-delti[thetai]/k;
   /* Variance of prevalence limit */      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      k4=func(p2)-fx;
   double **newm;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   double **dnewm,**doldm;  #ifdef DEBUG
   int i, j, nhstepm, hstepm;      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);
   int k, cptcode;      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);
   double *xp;  #endif
   double *gp, *gm;    }
   double **gradg, **trgradg;    return res;
   double age,agelim;  }
   int theta;  
      /************** Inverse of matrix **************/
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");  void ludcmp(double **a, int n, int *indx, double *d) 
   fprintf(ficresvpl,"# Age");  { 
   for(i=1; i<=nlstate;i++)    int i,imax,j,k; 
       fprintf(ficresvpl," %1d-%1d",i,i);    double big,dum,sum,temp; 
   fprintf(ficresvpl,"\n");    double *vv; 
    
   xp=vector(1,npar);    vv=vector(1,n); 
   dnewm=matrix(1,nlstate,1,npar);    *d=1.0; 
   doldm=matrix(1,nlstate,1,nlstate);    for (i=1;i<=n;i++) { 
        big=0.0; 
   hstepm=1*YEARM; /* Every year of age */      for (j=1;j<=n;j++) 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        if ((temp=fabs(a[i][j])) > big) big=temp; 
   agelim = AGESUP;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      vv[i]=1.0/big; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    } 
     if (stepm >= YEARM) hstepm=1;    for (j=1;j<=n;j++) { 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      for (i=1;i<j;i++) { 
     gradg=matrix(1,npar,1,nlstate);        sum=a[i][j]; 
     gp=vector(1,nlstate);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     gm=vector(1,nlstate);        a[i][j]=sum; 
       } 
     for(theta=1; theta <=npar; theta++){      big=0.0; 
       for(i=1; i<=npar; i++){ /* Computes gradient */      for (i=j;i<=n;i++) { 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        sum=a[i][j]; 
       }        for (k=1;k<j;k++) 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          sum -= a[i][k]*a[k][j]; 
       for(i=1;i<=nlstate;i++)        a[i][j]=sum; 
         gp[i] = prlim[i][i];        if ( (dum=vv[i]*fabs(sum)) >= big) { 
              big=dum; 
       for(i=1; i<=npar; i++) /* Computes gradient */          imax=i; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        } 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      } 
       for(i=1;i<=nlstate;i++)      if (j != imax) { 
         gm[i] = prlim[i][i];        for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
       for(i=1;i<=nlstate;i++)          a[imax][k]=a[j][k]; 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          a[j][k]=dum; 
     } /* End theta */        } 
         *d = -(*d); 
     trgradg =matrix(1,nlstate,1,npar);        vv[imax]=vv[j]; 
       } 
     for(j=1; j<=nlstate;j++)      indx[j]=imax; 
       for(theta=1; theta <=npar; theta++)      if (a[j][j] == 0.0) a[j][j]=TINY; 
         trgradg[j][theta]=gradg[theta][j];      if (j != n) { 
         dum=1.0/(a[j][j]); 
     for(i=1;i<=nlstate;i++)        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       varpl[i][(int)age] =0.;      } 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    } 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    free_vector(vv,1,n);  /* Doesn't work */
     for(i=1;i<=nlstate;i++)  ;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  } 
   
     fprintf(ficresvpl,"%.0f ",age );  void lubksb(double **a, int n, int *indx, double b[]) 
     for(i=1; i<=nlstate;i++)  { 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    int i,ii=0,ip,j; 
     fprintf(ficresvpl,"\n");    double sum; 
     free_vector(gp,1,nlstate);   
     free_vector(gm,1,nlstate);    for (i=1;i<=n;i++) { 
     free_matrix(gradg,1,npar,1,nlstate);      ip=indx[i]; 
     free_matrix(trgradg,1,nlstate,1,npar);      sum=b[ip]; 
   } /* End age */      b[ip]=b[i]; 
       if (ii) 
   free_vector(xp,1,npar);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   free_matrix(doldm,1,nlstate,1,npar);      else if (sum) ii=i; 
   free_matrix(dnewm,1,nlstate,1,nlstate);      b[i]=sum; 
     } 
 }    for (i=n;i>=1;i--) { 
       sum=b[i]; 
 /************ Variance of one-step probabilities  ******************/      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)      b[i]=sum/a[i][i]; 
 {    } 
   int i, j;  } 
   int k=0, cptcode;  
   double **dnewm,**doldm;  /************ Frequencies ********************/
   double *xp;  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)
   double *gp, *gm;  {  /* Some frequencies */
   double **gradg, **trgradg;    
   double age,agelim, cov[NCOVMAX];    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   int theta;    int first;
   char fileresprob[FILENAMELENGTH];    double ***freq; /* Frequencies */
     double *pp, **prop;
   strcpy(fileresprob,"prob");    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   strcat(fileresprob,fileres);    FILE *ficresp;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    char fileresp[FILENAMELENGTH];
     printf("Problem with resultfile: %s\n", fileresprob);    
   }    pp=vector(1,nlstate);
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    prop=matrix(1,nlstate,iagemin,iagemax+3);
      strcpy(fileresp,"p");
     strcat(fileresp,fileres);
   xp=vector(1,npar);    if((ficresp=fopen(fileresp,"w"))==NULL) {
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      printf("Problem with prevalence resultfile: %s\n", fileresp);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
        exit(0);
   cov[1]=1;    }
   for (age=bage; age<=fage; age ++){    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     cov[2]=age;    j1=0;
     gradg=matrix(1,npar,1,9);    
     trgradg=matrix(1,9,1,npar);    j=cptcoveff;
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
        first=1;
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++)    for(k1=1; k1<=j;k1++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      for(i1=1; i1<=ncodemax[k1];i1++){
              j1++;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
              scanf("%d", i);*/
       k=0;        for (i=-1; i<=nlstate+ndeath; i++)  
       for(i=1; i<= (nlstate+ndeath); i++){          for (jk=-1; jk<=nlstate+ndeath; jk++)  
         for(j=1; j<=(nlstate+ndeath);j++){            for(m=iagemin; m <= iagemax+3; m++)
            k=k+1;              freq[i][jk][m]=0;
           gp[k]=pmmij[i][j];  
         }      for (i=1; i<=nlstate; i++)  
       }        for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
       for(i=1; i<=npar; i++)        
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        dateintsum=0;
            k2cpt=0;
         for (i=1; i<=imx; i++) {
       pmij(pmmij,cov,ncovmodel,xp,nlstate);          bool=1;
       k=0;          if  (cptcovn>0) {
       for(i=1; i<=(nlstate+ndeath); i++){            for (z1=1; z1<=cptcoveff; z1++) 
         for(j=1; j<=(nlstate+ndeath);j++){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           k=k+1;                bool=0;
           gm[k]=pmmij[i][j];          }
         }          if (bool==1){
       }            for(m=firstpass; m<=lastpass; m++){
                    k2=anint[m][i]+(mint[m][i]/12.);
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                  if(agev[m][i]==0) agev[m][i]=iagemax+1;
     }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)                if (m<lastpass) {
       for(theta=1; theta <=npar; theta++)                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       trgradg[j][theta]=gradg[theta][j];                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                  }
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);                
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
      pmij(pmmij,cov,ncovmodel,x,nlstate);                  k2cpt++;
                 }
      k=0;                /*}*/
      for(i=1; i<=(nlstate+ndeath); i++){            }
        for(j=1; j<=(nlstate+ndeath);j++){          }
          k=k+1;        }
          gm[k]=pmmij[i][j];         
         }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
      }  
              if  (cptcovn>0) {
      /*printf("\n%d ",(int)age);          fprintf(ficresp, "\n#********** Variable "); 
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                  fprintf(ficresp, "**********\n#");
         }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        for(i=1; i<=nlstate;i++) 
      }*/          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficresp, "\n");
   fprintf(ficresprob,"\n%d ",(int)age);        
         for(i=iagemin; i <= iagemax+3; i++){
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          if(i==iagemax+3){
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);            fprintf(ficlog,"Total");
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          }else{
   }            if(first==1){
               first=0;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));              printf("See log file for details...\n");
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));            }
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            fprintf(ficlog,"Age %d", i);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          }
 }          for(jk=1; jk <=nlstate ; jk++){
  free_vector(xp,1,npar);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 fclose(ficresprob);              pp[jk] += freq[jk][m][i]; 
           }
 }          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
 /******************* Printing html file ***********/              pos += freq[jk][m][i];
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){            if(pp[jk]>=1.e-10){
   int jj1, k1, i1, cpt;              if(first==1){
   FILE *fichtm;              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   /*char optionfilehtm[FILENAMELENGTH];*/              }
               fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   strcpy(optionfilehtm,optionfile);            }else{
   strcat(optionfilehtm,".htm");              if(first==1)
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     printf("Problem with %s \n",optionfilehtm), exit(0);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   }            }
           }
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71 </font> <hr size=\"2\" color=\"#EC5E5E\">  
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>          for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 Total number of observations=%d <br>              pp[jk] += freq[jk][m][i];
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>          }       
 <hr  size=\"2\" color=\"#EC5E5E\">          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
 <li>Outputs files<br><br>\n            pos += pp[jk];
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n            posprop += prop[jk][i];
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>          }
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>          for(jk=1; jk <=nlstate ; jk++){
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>            if(pos>=1.e-5){
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>              if(first==1)
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>            }else{
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>              if(first==1)
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         <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);            }
              if( i <= iagemax){
 fprintf(fichtm," <li>Graphs</li><p>");              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
  m=cptcoveff;                /*probs[i][jk][j1]= pp[jk]/pos;*/
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
               }
  jj1=0;              else
  for(k1=1; k1<=m;k1++){                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
    for(i1=1; i1<=ncodemax[k1];i1++){            }
        jj1++;          }
        if (cptcovn > 0) {          
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          for(jk=-1; jk <=nlstate+ndeath; jk++)
          for (cpt=1; cpt<=cptcoveff;cpt++)            for(m=-1; m <=nlstate+ndeath; m++)
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);              if(freq[jk][m][i] !=0 ) {
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");              if(first==1)
        }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                  }
        for(cpt=1; cpt<nlstate;cpt++){          if(i <= iagemax)
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>            fprintf(ficresp,"\n");
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          if(first==1)
        }            printf("Others in log...\n");
     for(cpt=1; cpt<=nlstate;cpt++) {          fprintf(ficlog,"\n");
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        }
 interval) in state (%d): v%s%d%d.gif <br>      }
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      }
      }    dateintmean=dateintsum/k2cpt; 
      for(cpt=1; cpt<=nlstate;cpt++) {   
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    fclose(ficresp);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
      }    free_vector(pp,1,nlstate);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
 health expectancies in states (1) and (2): e%s%d.gif<br>    /* End of Freq */
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  }
 fprintf(fichtm,"\n</body>");  
    }  /************ Prevalence ********************/
    }  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
 fclose(fichtm);  {  
 }    /* 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).
 /******************* Gnuplot file **************/       We still use firstpass and lastpass as another selection.
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){    */
    
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     double ***freq; /* Frequencies */
   strcpy(optionfilegnuplot,optionfilefiname);    double *pp, **prop;
   strcat(optionfilegnuplot,".plt");    double pos,posprop; 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    double  y2; /* in fractional years */
     printf("Problem with file %s",optionfilegnuplot);    int iagemin, iagemax;
   }  
     iagemin= (int) agemin;
 #ifdef windows    iagemax= (int) agemax;
     fprintf(ficgp,"cd \"%s\" \n",pathc);    /*pp=vector(1,nlstate);*/
 #endif    prop=matrix(1,nlstate,iagemin,iagemax+3); 
 m=pow(2,cptcoveff);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
      j1=0;
  /* 1eme*/    
   for (cpt=1; cpt<= nlstate ; cpt ++) {    j=cptcoveff;
    for (k1=1; k1<= m ; k1 ++) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
 #ifdef windows    for(k1=1; k1<=j;k1++){
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);      for(i1=1; i1<=ncodemax[k1];i1++){
 #endif        j1++;
 #ifdef unix        
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);        for (i=1; i<=nlstate; i++)  
 #endif          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0.0;
 for (i=1; i<= nlstate ; i ++) {       
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for (i=1; i<=imx; i++) { /* Each individual */
   else fprintf(ficgp," \%%*lf (\%%*lf)");          bool=1;
 }          if  (cptcovn>0) {
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);            for (z1=1; z1<=cptcoveff; z1++) 
     for (i=1; i<= nlstate ; i ++) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                bool=0;
   else fprintf(ficgp," \%%*lf (\%%*lf)");          } 
 }          if (bool==1) { 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
      for (i=1; i<= nlstate ; i ++) {              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   else fprintf(ficgp," \%%*lf (\%%*lf)");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 }                  if(agev[m][i]==1) agev[m][i]=iagemax+2;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));                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); 
 #ifdef unix                if (s[m][i]>0 && s[m][i]<=nlstate) { 
 fprintf(ficgp,"\nset ter gif small size 400,300");                  /*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]]);*/
 #endif                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);                  prop[s[m][i]][iagemax+3] += weight[i]; 
    }                } 
   }              }
   /*2 eme*/            } /* end selection of waves */
           }
   for (k1=1; k1<= m ; k1 ++) {        }
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);        for(i=iagemin; i <= iagemax+3; i++){  
              
     for (i=1; i<= nlstate+1 ; i ++) {          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       k=2*i;            posprop += prop[jk][i]; 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          } 
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          for(jk=1; jk <=nlstate ; jk++){     
   else fprintf(ficgp," \%%*lf (\%%*lf)");            if( i <=  iagemax){ 
 }                if(posprop>=1.e-5){ 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");                probs[i][jk][j1]= prop[jk][i]/posprop;
       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 ++) {          }/* end jk */ 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        }/* end i */ 
         else fprintf(ficgp," \%%*lf (\%%*lf)");      } /* end i1 */
 }      } /* end k1 */
       fprintf(ficgp,"\" t\"\" w l 0,");    
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
       for (j=1; j<= nlstate+1 ; j ++) {    /*free_vector(pp,1,nlstate);*/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   else fprintf(ficgp," \%%*lf (\%%*lf)");  }  /* End of prevalence */
 }    
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  /************* Waves Concatenation ***************/
       else fprintf(ficgp,"\" t\"\" w l 0,");  
     }  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)
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);  {
   }    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         Death is a valid wave (if date is known).
   /*3eme*/       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]
   for (k1=1; k1<= m ; k1 ++) {       and mw[mi+1][i]. dh depends on stepm.
     for (cpt=1; cpt<= nlstate ; cpt ++) {       */
       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);    int i, mi, m;
       for (i=1; i< nlstate ; i ++) {    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         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);       double sum=0., jmean=0.;*/
       }    int first;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    int j, k=0,jk, ju, jl;
     }    double sum=0.;
     }    first=0;
      jmin=1e+5;
   /* CV preval stat */    jmax=-1;
     for (k1=1; k1<= m ; k1 ++) {    jmean=0.;
     for (cpt=1; cpt<nlstate ; cpt ++) {    for(i=1; i<=imx; i++){
       k=3;      mi=0;
       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/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);      m=firstpass;
       while(s[m][i] <= nlstate){
       for (i=1; i< nlstate ; i ++)        if(s[m][i]>=1)
         fprintf(ficgp,"+$%d",k+i+1);          mw[++mi][i]=m;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        if(m >=lastpass)
                break;
       l=3+(nlstate+ndeath)*cpt;        else
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          m++;
       for (i=1; i< nlstate ; i ++) {      }/* end while */
         l=3+(nlstate+ndeath)*cpt;      if (s[m][i] > nlstate){
         fprintf(ficgp,"+$%d",l+i+1);        mi++;     /* Death is another wave */
       }        /* if(mi==0)  never been interviewed correctly before death */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);             /* Only death is a correct wave */
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        mw[mi][i]=m;
     }      }
   }    
        wav[i]=mi;
   /* proba elementaires */      if(mi==0){
    for(i=1,jk=1; i <=nlstate; i++){        nbwarn++;
     for(k=1; k <=(nlstate+ndeath); k++){        if(first==0){
       if (k != i) {          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
         for(j=1; j <=ncovmodel; j++){          first=1;
                }
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        if(first==1){
           jk++;          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
           fprintf(ficgp,"\n");        }
         }      } /* end mi==0 */
       }    } /* End individuals */
     }  
     }    for(i=1; i<=imx; i++){
       for(mi=1; mi<wav[i];mi++){
     for(jk=1; jk <=m; jk++) {        if (stepm <=0)
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);          dh[mi][i]=1;
    i=1;        else{
    for(k2=1; k2<=nlstate; k2++) {          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
      k3=i;            if (agedc[i] < 2*AGESUP) {
      for(k=1; k<=(nlstate+ndeath); k++) {              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
        if (k != k2){              if(j==0) j=1;  /* Survives at least one month after exam */
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);              else if(j<0){
 ij=1;                nberr++;
         for(j=3; j <=ncovmodel; j++) {                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                j=1; /* Temporary Dangerous patch */
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                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);
             ij++;                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           }                fprintf(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);
           else              }
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              k=k+1;
         }              if (j >= jmax) jmax=j;
           fprintf(ficgp,")/(1");              if (j <= jmin) jmin=j;
                      sum=sum+j;
         for(k1=1; k1 <=nlstate; k1++){                /*if (j<0) printf("j=%d num=%d \n",j,i);*/
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
 ij=1;            }
           for(j=3; j <=ncovmodel; j++){          }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          else{
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
             ij++;            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           }            k=k+1;
           else            if (j >= jmax) jmax=j;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            else if (j <= jmin)jmin=j;
           }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           fprintf(ficgp,")");            /*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(j<0){
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);              nberr++;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");              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]);
         i=i+ncovmodel;              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
        }            }
      }            sum=sum+j;
    }          }
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);          jk= j/stepm;
    }          jl= j -jk*stepm;
              ju= j -(jk+1)*stepm;
   fclose(ficgp);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
 }  /* end gnuplot */            if(jl==0){
               dh[mi][i]=jk;
               bh[mi][i]=0;
 /*************** Moving average **************/            }else{ /* We want a negative bias in order to only have interpolation ie
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){                    * at the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
   int i, cpt, cptcod;              bh[mi][i]=ju;
     for (agedeb=agemin; agedeb<=fage; agedeb++)            }
       for (i=1; i<=nlstate;i++)          }else{
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)            if(jl <= -ju){
           mobaverage[(int)agedeb][i][cptcod]=0.;              dh[mi][i]=jk;
                  bh[mi][i]=jl;       /* bias is positive if real duration
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){                                   * is higher than the multiple of stepm and negative otherwise.
       for (i=1; i<=nlstate;i++){                                   */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            }
           for (cpt=0;cpt<=4;cpt++){            else{
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];              dh[mi][i]=jk+1;
           }              bh[mi][i]=ju;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;            }
         }            if(dh[mi][i]==0){
       }              dh[mi][i]=1; /* At least one step */
     }              bh[mi][i]=ju; /* At least one step */
                  /*  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);*/
 }            }
           } /* end if mle */
         }
 /************** Forecasting ******************/      } /* end wave */
 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){    }
      jmean=sum/k;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   int *popage;    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;   }
   double *popeffectif,*popcount;  
   double ***p3mat;  /*********** Tricode ****************************/
   char fileresf[FILENAMELENGTH];  void tricode(int *Tvar, int **nbcode, int imx)
   {
  agelim=AGESUP;    
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    int Ndum[20],ij=1, k, j, i, maxncov=19;
     int cptcode=0;
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    cptcoveff=0; 
     
      for (k=0; k<maxncov; k++) Ndum[k]=0;
   strcpy(fileresf,"f");    for (k=1; k<=7; k++) ncodemax[k]=0;
   strcat(fileresf,fileres);  
   if((ficresf=fopen(fileresf,"w"))==NULL) {    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     printf("Problem with forecast resultfile: %s\n", fileresf);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   }                                 modality*/ 
   printf("Computing forecasting: result on file '%s' \n", fileresf);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         Ndum[ij]++; /*store the modality */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   if (mobilav==1) {                                         Tvar[j]. If V=sex and male is 0 and 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                                         female is 1, then  cptcode=1.*/
     movingaverage(agedeb, fage, agemin, mobaverage);      }
   }  
       for (i=0; i<=cptcode; i++) {
   stepsize=(int) (stepm+YEARM-1)/YEARM;        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 */
   if (stepm<=12) stepsize=1;      }
    
   agelim=AGESUP;      ij=1; 
        for (i=1; i<=ncodemax[j]; i++) {
   hstepm=1;        for (k=0; k<= maxncov; k++) {
   hstepm=hstepm/stepm;          if (Ndum[k] != 0) {
   yp1=modf(dateintmean,&yp);            nbcode[Tvar[j]][ij]=k; 
   anprojmean=yp;            /* 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; */
   yp2=modf((yp1*12),&yp);            
   mprojmean=yp;            ij++;
   yp1=modf((yp2*30.5),&yp);          }
   jprojmean=yp;          if (ij > ncodemax[j]) break; 
   if(jprojmean==0) jprojmean=1;        }  
   if(mprojmean==0) jprojmean=1;      } 
      }  
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);  
     for (k=0; k< maxncov; k++) Ndum[k]=0;
   for(cptcov=1;cptcov<=i2;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){   for (i=1; i<=ncovmodel-2; i++) { 
       k=k+1;     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
       fprintf(ficresf,"\n#******");     ij=Tvar[i];
       for(j=1;j<=cptcoveff;j++) {     Ndum[ij]++;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   }
       }  
       fprintf(ficresf,"******\n");   ij=1;
       fprintf(ficresf,"# StartingAge FinalAge");   for (i=1; i<= maxncov; i++) {
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);     if((Ndum[i]!=0) && (i<=ncovcol)){
             Tvaraff[ij]=i; /*For printing */
             ij++;
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {     }
         fprintf(ficresf,"\n");   }
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);     
    cptcoveff=ij-1; /*Number of simple covariates*/
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){  }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;  /*********** Health Expectancies ****************/
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  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 )
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    {
            /* Health expectancies */
           for (h=0; h<=nhstepm; h++){    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
             if (h==(int) (calagedate+YEARM*cpt)) {    double age, agelim, hf;
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);    double ***p3mat,***varhe;
             }    double **dnewm,**doldm;
             for(j=1; j<=nlstate+ndeath;j++) {    double *xp;
               kk1=0.;kk2=0;    double **gp, **gm;
               for(i=1; i<=nlstate;i++) {                  double ***gradg, ***trgradg;
                 if (mobilav==1)    int theta;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    xp=vector(1,npar);
                 }    dnewm=matrix(1,nlstate*nlstate,1,npar);
                    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
               }    
               if (h==(int)(calagedate+12*cpt)){    fprintf(ficreseij,"# Health expectancies\n");
                 fprintf(ficresf," %.3f", kk1);    fprintf(ficreseij,"# Age");
                            for(i=1; i<=nlstate;i++)
               }      for(j=1; j<=nlstate;j++)
             }        fprintf(ficreseij," %1d-%1d (SE)",i,j);
           }    fprintf(ficreseij,"\n");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }    if(estepm < stepm){
       }      printf ("Problem %d lower than %d\n",estepm, stepm);
     }    }
   }    else  hstepm=estepm;   
            /* We compute the life expectancy from trapezoids spaced every estepm months
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
   fclose(ficresf);     * we are calculating an estimate of the Life Expectancy assuming a linear 
 }     * progression in between and thus overestimating or underestimating according
 /************** Forecasting ******************/     * to the curvature of the survival function. If, for the same date, we 
 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){     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       * to compare the new estimate of Life expectancy with the same linear 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;     * hypothesis. A more precise result, taking into account a more precise
   int *popage;     * curvature will be obtained if estepm is as small as stepm. */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  
   double *popeffectif,*popcount;    /* For example we decided to compute the life expectancy with the smallest unit */
   double ***p3mat,***tabpop,***tabpopprev;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   char filerespop[FILENAMELENGTH];       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       Look at hpijx to understand the reason of that which relies in memory size
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       and note for a fixed period like estepm months */
   agelim=AGESUP;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;       survival function given by stepm (the optimization length). Unfortunately it
         means that if the survival funtion is printed only each two years of age and if
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);       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.
      */
   strcpy(filerespop,"pop");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   strcat(filerespop,fileres);  
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    agelim=AGESUP;
     printf("Problem with forecast resultfile: %s\n", filerespop);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   }      /* nhstepm age range expressed in number of stepm */
   printf("Computing forecasting: result on file '%s' \n", filerespop);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      /* if (stepm >= YEARM) hstepm=1;*/
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   if (mobilav==1) {      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     movingaverage(agedeb, fage, agemin, mobaverage);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   }      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   if (stepm<=12) stepsize=1;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   agelim=AGESUP;   
    
   hstepm=1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   hstepm=hstepm/stepm;  
        /* Computing Variances of health expectancies */
   if (popforecast==1) {  
     if((ficpop=fopen(popfile,"r"))==NULL) {       for(theta=1; theta <=npar; theta++){
       printf("Problem with population file : %s\n",popfile);exit(0);        for(i=1; i<=npar; i++){ 
     }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     popage=ivector(0,AGESUP);        }
     popeffectif=vector(0,AGESUP);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     popcount=vector(0,AGESUP);    
            cptj=0;
     i=1;          for(j=1; j<= nlstate; j++){
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;          for(i=1; i<=nlstate; i++){
                cptj=cptj+1;
     imx=i;            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   }            }
           }
   for(cptcov=1;cptcov<=i2;cptcov++){        }
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       
       k=k+1;       
       fprintf(ficrespop,"\n#******");        for(i=1; i<=npar; i++) 
       for(j=1;j<=cptcoveff;j++) {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       }        
       fprintf(ficrespop,"******\n");        cptj=0;
       fprintf(ficrespop,"# Age");        for(j=1; j<= nlstate; j++){
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);          for(i=1;i<=nlstate;i++){
       if (popforecast==1)  fprintf(ficrespop," [Population]");            cptj=cptj+1;
                  for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
       for (cpt=0; cpt<=0;cpt++) {  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
                    }
         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(j=1; j<= nlstate*nlstate; j++)
                    for(h=0; h<=nhstepm-1; h++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           oldm=oldms;savm=savms;          }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         } 
             
           for (h=0; h<=nhstepm; h++){  /* End theta */
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
             }  
             for(j=1; j<=nlstate+ndeath;j++) {       for(h=0; h<=nhstepm-1; h++)
               kk1=0.;kk2=0;        for(j=1; j<=nlstate*nlstate;j++)
               for(i=1; i<=nlstate;i++) {                        for(theta=1; theta <=npar; theta++)
                 if (mobilav==1)            trgradg[h][j][theta]=gradg[h][theta][j];
                   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];       for(i=1;i<=nlstate*nlstate;i++)
                 }        for(j=1;j<=nlstate*nlstate;j++)
               }          varhe[i][j][(int)age] =0.;
               if (h==(int)(calagedate+12*cpt)){  
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;       printf("%d|",(int)age);fflush(stdout);
                   /*fprintf(ficrespop," %.3f", kk1);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/       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);
             for(i=1; i<=nlstate;i++){          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
               kk1=0.;          for(i=1;i<=nlstate*nlstate;i++)
                 for(j=1; j<=nlstate;j++){            for(j=1;j<=nlstate*nlstate;j++)
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
                 }        }
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      }
             }      /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        for(j=1; j<=nlstate;j++)
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           }            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            
         }  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
       }  
            }
   /******/  
       fprintf(ficreseij,"%3.0f",age );
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {      cptj=0;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        for(i=1; i<=nlstate;i++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){        for(j=1; j<=nlstate;j++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          cptj++;
           nhstepm = nhstepm/hstepm;          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
                  }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficreseij,"\n");
           oldm=oldms;savm=savms;     
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
           for (h=0; h<=nhstepm; h++){      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
             if (h==(int) (calagedate+YEARM*cpt)) {      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
             }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             for(j=1; j<=nlstate+ndeath;j++) {    }
               kk1=0.;kk2=0;    printf("\n");
               for(i=1; i<=nlstate;i++) {                  fprintf(ficlog,"\n");
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      
               }    free_vector(xp,1,npar);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
             }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
           }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  }
         }  
       }  /************ Variance ******************/
    }  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
   }  {
      /* Variance of health expectancies */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
   if (popforecast==1) {    double **dnewm,**doldm;
     free_ivector(popage,0,AGESUP);    double **dnewmp,**doldmp;
     free_vector(popeffectif,0,AGESUP);    int i, j, nhstepm, hstepm, h, nstepm ;
     free_vector(popcount,0,AGESUP);    int k, cptcode;
   }    double *xp;
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double **gp, **gm;  /* for var eij */
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double ***gradg, ***trgradg; /*for var eij */
   fclose(ficrespop);    double **gradgp, **trgradgp; /* for var p point j */
 }    double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
 /***********************************************/    double ***p3mat;
 /**************** Main Program *****************/    double age,agelim, hf;
 /***********************************************/    double ***mobaverage;
     int theta;
 int main(int argc, char *argv[])    char digit[4];
 {    char digitp[25];
   
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    char fileresprobmorprev[FILENAMELENGTH];
   double agedeb, agefin,hf;  
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    if(popbased==1){
       if(mobilav!=0)
   double fret;        strcpy(digitp,"-populbased-mobilav-");
   double **xi,tmp,delta;      else strcpy(digitp,"-populbased-nomobil-");
     }
   double dum; /* Dummy variable */    else 
   double ***p3mat;      strcpy(digitp,"-stablbased-");
   int *indx;  
   char line[MAXLINE], linepar[MAXLINE];    if (mobilav!=0) {
   char title[MAXLINE];      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
          printf(" Error in movingaverage mobilav=%d\n",mobilav);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];      }
     }
   char filerest[FILENAMELENGTH];  
   char fileregp[FILENAMELENGTH];    strcpy(fileresprobmorprev,"prmorprev"); 
   char popfile[FILENAMELENGTH];    sprintf(digit,"%-d",ij);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   int firstobs=1, lastobs=10;    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   int sdeb, sfin; /* Status at beginning and end */    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   int c,  h , cpt,l;    strcat(fileresprobmorprev,fileres);
   int ju,jl, mi;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   int mobilav=0,popforecast=0;    }
   int hstepm, nhstepm;    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     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);
   double bage, fage, age, agelim, agebase;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   double ftolpl=FTOL;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   double **prlim;      fprintf(ficresprobmorprev," p.%-d SE",j);
   double *severity;      for(i=1; i<=nlstate;i++)
   double ***param; /* Matrix of parameters */        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   double  *p;    }  
   double **matcov; /* Matrix of covariance */    fprintf(ficresprobmorprev,"\n");
   double ***delti3; /* Scale */    fprintf(ficgp,"\n# Routine varevsij");
   double *delti; /* Scale */    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");
   double ***eij, ***vareij;    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   double **varpl; /* Variances of prevalence limits by age */  /*   } */
   double *epj, vepp;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   double kk1, kk2;  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    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");
     for(i=1; i<=nlstate;i++)
   char version[80]="Imach version 0.71, February 2002, INED-EUROREVES ";      for(j=1; j<=nlstate;j++)
   char *alph[]={"a","a","b","c","d","e"}, str[4];        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     fprintf(ficresvij,"\n");
   
   char z[1]="c", occ;    xp=vector(1,npar);
 #include <sys/time.h>    dnewm=matrix(1,nlstate,1,npar);
 #include <time.h>    doldm=matrix(1,nlstate,1,nlstate);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
      doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   /* long total_usecs;  
   struct timeval start_time, end_time;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
      gpp=vector(nlstate+1,nlstate+ndeath);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
   printf("\n%s",version);    if(estepm < stepm){
   if(argc <=1){      printf ("Problem %d lower than %d\n",estepm, stepm);
     printf("\nEnter the parameter file name: ");    }
     scanf("%s",pathtot);    else  hstepm=estepm;   
   }    /* For example we decided to compute the life expectancy with the smallest unit */
   else{    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     strcpy(pathtot,argv[1]);       nhstepm is the number of hstepm from age to agelim 
   }       nstepm is the number of stepm from age to agelin. 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/       Look at hpijx to understand the reason of that which relies in memory size
   /*cygwin_split_path(pathtot,path,optionfile);       and note for a fixed period like k years */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   /* cutv(path,optionfile,pathtot,'\\');*/       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
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);       results. So we changed our mind and took the option of the best precision.
   chdir(path);    */
   replace(pathc,path);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
 /*-------- arguments in the command line --------*/    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   strcpy(fileres,"r");      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   strcat(fileres, optionfilefiname);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   strcat(fileres,".txt");    /* Other files have txt extension */      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
   /*---------arguments file --------*/      gm=matrix(0,nhstepm,1,nlstate);
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  
     printf("Problem with optionfile %s\n",optionfile);      for(theta=1; theta <=npar; theta++){
     goto end;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
   strcpy(filereso,"o");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   strcat(filereso,fileres);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   if((ficparo=fopen(filereso,"w"))==NULL) {  
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        if (popbased==1) {
   }          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
   /* Reads comments: lines beginning with '#' */              prlim[i][i]=probs[(int)age][i][ij];
   while((c=getc(ficpar))=='#' && c!= EOF){          }else{ /* mobilav */ 
     ungetc(c,ficpar);            for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);              prlim[i][i]=mobaverage[(int)age][i][ij];
     puts(line);          }
     fputs(line,ficparo);        }
   }    
   ungetc(c,ficpar);        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
   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);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   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);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   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){        }
     ungetc(c,ficpar);        /* This for computing probability of death (h=1 means
     fgets(line, MAXLINE, ficpar);           computed over hstepm matrices product = hstepm*stepm months) 
     puts(line);           as a weighted average of prlim.
     fputs(line,ficparo);        */
   }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   ungetc(c,ficpar);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
              gpp[j] += prlim[i][i]*p3mat[i][j][1];
            }    
   covar=matrix(0,NCOVMAX,1,n);        /* end probability of death */
   cptcovn=0;  
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
   ncovmodel=2+cptcovn;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     
   /* Read guess parameters */        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);        }
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        for(j=1; j<= nlstate; j++){
     for(i=1; i <=nlstate; i++)          for(h=0; h<=nhstepm; h++){
     for(j=1; j <=nlstate+ndeath-1; j++){            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
       fscanf(ficpar,"%1d%1d",&i1,&j1);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
       fprintf(ficparo,"%1d%1d",i1,j1);          }
       printf("%1d%1d",i,j);        }
       for(k=1; k<=ncovmodel;k++){        /* This for computing probability of death (h=1 means
         fscanf(ficpar," %lf",&param[i][j][k]);           computed over hstepm matrices product = hstepm*stepm months) 
         printf(" %lf",param[i][j][k]);           as a weighted average of prlim.
         fprintf(ficparo," %lf",param[i][j][k]);        */
       }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       fscanf(ficpar,"\n");          for(i=1,gmp[j]=0.; i<= nlstate; i++)
       printf("\n");           gmp[j] += prlim[i][i]*p3mat[i][j][1];
       fprintf(ficparo,"\n");        }    
     }        /* end probability of death */
    
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;        for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
   p=param[1][1];            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
            }
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     ungetc(c,ficpar);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     fgets(line, MAXLINE, ficpar);        }
     puts(line);  
     fputs(line,ficparo);      } /* End theta */
   }  
   ungetc(c,ficpar);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      for(h=0; h<=nhstepm; h++) /* veij */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        for(j=1; j<=nlstate;j++)
   for(i=1; i <=nlstate; i++){          for(theta=1; theta <=npar; theta++)
     for(j=1; j <=nlstate+ndeath-1; j++){            trgradg[h][j][theta]=gradg[h][theta][j];
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       fprintf(ficparo,"%1d%1d",i1,j1);        for(theta=1; theta <=npar; theta++)
       for(k=1; k<=ncovmodel;k++){          trgradgp[j][theta]=gradgp[theta][j];
         fscanf(ficpar,"%le",&delti3[i][j][k]);    
         printf(" %le",delti3[i][j][k]);  
         fprintf(ficparo," %le",delti3[i][j][k]);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       }      for(i=1;i<=nlstate;i++)
       fscanf(ficpar,"\n");        for(j=1;j<=nlstate;j++)
       printf("\n");          vareij[i][j][(int)age] =0.;
       fprintf(ficparo,"\n");  
     }      for(h=0;h<=nhstepm;h++){
   }        for(k=0;k<=nhstepm;k++){
   delti=delti3[1][1];          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   /* Reads comments: lines beginning with '#' */          for(i=1;i<=nlstate;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){            for(j=1;j<=nlstate;j++)
     ungetc(c,ficpar);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     fgets(line, MAXLINE, ficpar);        }
     puts(line);      }
     fputs(line,ficparo);    
   }      /* pptj */
   ungetc(c,ficpar);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
        matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   matcov=matrix(1,npar,1,npar);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   for(i=1; i <=npar; i++){        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     fscanf(ficpar,"%s",&str);          varppt[j][i]=doldmp[j][i];
     printf("%s",str);      /* end ppptj */
     fprintf(ficparo,"%s",str);      /*  x centered again */
     for(j=1; j <=i; j++){      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       fscanf(ficpar," %le",&matcov[i][j]);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
       printf(" %.5le",matcov[i][j]);   
       fprintf(ficparo," %.5le",matcov[i][j]);      if (popbased==1) {
     }        if(mobilav ==0){
     fscanf(ficpar,"\n");          for(i=1; i<=nlstate;i++)
     printf("\n");            prlim[i][i]=probs[(int)age][i][ij];
     fprintf(ficparo,"\n");        }else{ /* mobilav */ 
   }          for(i=1; i<=nlstate;i++)
   for(i=1; i <=npar; i++)            prlim[i][i]=mobaverage[(int)age][i][ij];
     for(j=i+1;j<=npar;j++)        }
       matcov[i][j]=matcov[j][i];      }
                   
   printf("\n");      /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
     /*-------- Rewriting paramater file ----------*/      */
      strcpy(rfileres,"r");    /* "Rparameterfile */      for(j=nlstate+1;j<=nlstate+ndeath;j++){
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
      strcat(rfileres,".");    /* */          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
      strcat(rfileres,optionfilext);    /* Other files have txt extension */      }    
     if((ficres =fopen(rfileres,"w"))==NULL) {      /* end probability of death */
       printf("Problem writing new parameter file: %s\n", fileres);goto end;  
     }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     fprintf(ficres,"#%s\n",version);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
            fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     /*-------- data file ----------*/        for(i=1; i<=nlstate;i++){
     if((fic=fopen(datafile,"r"))==NULL)    {          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
       printf("Problem with datafile: %s\n", datafile);goto end;        }
     }      } 
       fprintf(ficresprobmorprev,"\n");
     n= lastobs;  
     severity = vector(1,maxwav);      fprintf(ficresvij,"%.0f ",age );
     outcome=imatrix(1,maxwav+1,1,n);      for(i=1; i<=nlstate;i++)
     num=ivector(1,n);        for(j=1; j<=nlstate;j++){
     moisnais=vector(1,n);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     annais=vector(1,n);        }
     moisdc=vector(1,n);      fprintf(ficresvij,"\n");
     andc=vector(1,n);      free_matrix(gp,0,nhstepm,1,nlstate);
     agedc=vector(1,n);      free_matrix(gm,0,nhstepm,1,nlstate);
     cod=ivector(1,n);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     weight=vector(1,n);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     mint=matrix(1,maxwav,1,n);    } /* End age */
     anint=matrix(1,maxwav,1,n);    free_vector(gpp,nlstate+1,nlstate+ndeath);
     s=imatrix(1,maxwav+1,1,n);    free_vector(gmp,nlstate+1,nlstate+ndeath);
     adl=imatrix(1,maxwav+1,1,n);        free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     tab=ivector(1,NCOVMAX);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     ncodemax=ivector(1,8);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     i=1;    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     while (fgets(line, MAXLINE, fic) != NULL)    {  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
       if ((i >= firstobs) && (i <=lastobs)) {  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
          /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
         for (j=maxwav;j>=1;j--){    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
           strcpy(line,stra);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
         }    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
          */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    free_vector(xp,1,npar);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         for (j=ncov;j>=1;j--){    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         num[i]=atol(stra);    fclose(ficresprobmorprev);
            fflush(ficgp);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    fflush(fichtm); 
           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;}*/  }  /* end varevsij */
   
         i=i+1;  /************ Variance of prevlim ******************/
       }  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
     }  {
     /* printf("ii=%d", ij);    /* Variance of prevalence limit */
        scanf("%d",i);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   imx=i-1; /* Number of individuals */    double **newm;
     double **dnewm,**doldm;
   /* for (i=1; i<=imx; i++){    int i, j, nhstepm, hstepm;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    int k, cptcode;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    double *xp;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    double *gp, *gm;
     }    double **gradg, **trgradg;
     double age,agelim;
     for (i=1; i<=imx; i++)    int theta;
     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(ficresvpl,"# Standard deviation of stable prevalences \n");
   /* Calculation of the number of parameter from char model*/    fprintf(ficresvpl,"# Age");
   Tvar=ivector(1,15);    for(i=1; i<=nlstate;i++)
   Tprod=ivector(1,15);        fprintf(ficresvpl," %1d-%1d",i,i);
   Tvaraff=ivector(1,15);    fprintf(ficresvpl,"\n");
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);          xp=vector(1,npar);
        dnewm=matrix(1,nlstate,1,npar);
   if (strlen(model) >1){    doldm=matrix(1,nlstate,1,nlstate);
     j=0, j1=0, k1=1, k2=1;    
     j=nbocc(model,'+');    hstepm=1*YEARM; /* Every year of age */
     j1=nbocc(model,'*');    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     cptcovn=j+1;    agelim = AGESUP;
     cptcovprod=j1;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
          nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
          if (stepm >= YEARM) hstepm=1;
     strcpy(modelsav,model);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      gradg=matrix(1,npar,1,nlstate);
       printf("Error. Non available option model=%s ",model);      gp=vector(1,nlstate);
       goto end;      gm=vector(1,nlstate);
     }  
          for(theta=1; theta <=npar; theta++){
     for(i=(j+1); i>=1;i--){        for(i=1; i<=npar; i++){ /* Computes gradient */
       cutv(stra,strb,modelsav,'+');          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        }
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       /*scanf("%d",i);*/        for(i=1;i<=nlstate;i++)
       if (strchr(strb,'*')) {          gp[i] = prlim[i][i];
         cutv(strd,strc,strb,'*');      
         if (strcmp(strc,"age")==0) {        for(i=1; i<=npar; i++) /* Computes gradient */
           cptcovprod--;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           cutv(strb,stre,strd,'V');        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           Tvar[i]=atoi(stre);        for(i=1;i<=nlstate;i++)
           cptcovage++;          gm[i] = prlim[i][i];
             Tage[cptcovage]=i;  
             /*printf("stre=%s ", stre);*/        for(i=1;i<=nlstate;i++)
         }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         else if (strcmp(strd,"age")==0) {      } /* End theta */
           cptcovprod--;  
           cutv(strb,stre,strc,'V');      trgradg =matrix(1,nlstate,1,npar);
           Tvar[i]=atoi(stre);  
           cptcovage++;      for(j=1; j<=nlstate;j++)
           Tage[cptcovage]=i;        for(theta=1; theta <=npar; theta++)
         }          trgradg[j][theta]=gradg[theta][j];
         else {  
           cutv(strb,stre,strc,'V');      for(i=1;i<=nlstate;i++)
           Tvar[i]=ncov+k1;        varpl[i][(int)age] =0.;
           cutv(strb,strc,strd,'V');      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
           Tprod[k1]=i;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
           Tvard[k1][1]=atoi(strc);      for(i=1;i<=nlstate;i++)
           Tvard[k1][2]=atoi(stre);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
           Tvar[cptcovn+k2]=Tvard[k1][1];  
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      fprintf(ficresvpl,"%.0f ",age );
           for (k=1; k<=lastobs;k++)      for(i=1; i<=nlstate;i++)
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
           k1++;      fprintf(ficresvpl,"\n");
           k2=k2+2;      free_vector(gp,1,nlstate);
         }      free_vector(gm,1,nlstate);
       }      free_matrix(gradg,1,npar,1,nlstate);
       else {      free_matrix(trgradg,1,nlstate,1,npar);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    } /* End age */
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');    free_vector(xp,1,npar);
       Tvar[i]=atoi(strc);    free_matrix(doldm,1,nlstate,1,npar);
       }    free_matrix(dnewm,1,nlstate,1,nlstate);
       strcpy(modelsav,stra);    
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  }
         scanf("%d",i);*/  
     }  /************ 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)
    {
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    int i, j=0,  i1, k1, l1, t, tj;
   printf("cptcovprod=%d ", cptcovprod);    int k2, l2, j1,  z1;
   scanf("%d ",i);*/    int k=0,l, cptcode;
     fclose(fic);    int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     /*  if(mle==1){*/    double **dnewm,**doldm;
     if (weightopt != 1) { /* Maximisation without weights*/    double *xp;
       for(i=1;i<=n;i++) weight[i]=1.0;    double *gp, *gm;
     }    double **gradg, **trgradg;
     /*-calculation of age at interview from date of interview and age at death -*/    double **mu;
     agev=matrix(1,maxwav,1,imx);    double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
    for (i=1; i<=imx; i++)    int theta;
      for(m=2; (m<= maxwav); m++)    char fileresprob[FILENAMELENGTH];
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    char fileresprobcov[FILENAMELENGTH];
          anint[m][i]=9999;    char fileresprobcor[FILENAMELENGTH];
          s[m][i]=-1;  
        }    double ***varpij;
      
     for (i=1; i<=imx; i++)  {    strcpy(fileresprob,"prob"); 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    strcat(fileresprob,fileres);
       for(m=1; (m<= maxwav); m++){    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
         if(s[m][i] >0){      printf("Problem with resultfile: %s\n", fileresprob);
           if (s[m][i] == nlstate+1) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
             if(agedc[i]>0)    }
               if(moisdc[i]!=99 && andc[i]!=9999)    strcpy(fileresprobcov,"probcov"); 
               agev[m][i]=agedc[i];    strcat(fileresprobcov,fileres);
             else {    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
               if (andc[i]!=9999){      printf("Problem with resultfile: %s\n", fileresprobcov);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
               agev[m][i]=-1;    }
               }    strcpy(fileresprobcor,"probcor"); 
             }    strcat(fileresprobcor,fileres);
           }    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
           else if(s[m][i] !=9){ /* Should no more exist */      printf("Problem with resultfile: %s\n", fileresprobcor);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
             if(mint[m][i]==99 || anint[m][i]==9999)    }
               agev[m][i]=1;    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
             else if(agev[m][i] <agemin){    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
               agemin=agev[m][i];    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
             }    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
             else if(agev[m][i] >agemax){    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
               agemax=agev[m][i];    
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
             }    fprintf(ficresprob,"# Age");
             /*agev[m][i]=anint[m][i]-annais[i];*/    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
             /*   agev[m][i] = age[i]+2*m;*/    fprintf(ficresprobcov,"# Age");
           }    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
           else { /* =9 */    fprintf(ficresprobcov,"# Age");
             agev[m][i]=1;  
             s[m][i]=-1;  
           }    for(i=1; i<=nlstate;i++)
         }      for(j=1; j<=(nlstate+ndeath);j++){
         else /*= 0 Unknown */        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
           agev[m][i]=1;        fprintf(ficresprobcov," p%1d-%1d ",i,j);
       }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
          }  
     }   /* fprintf(ficresprob,"\n");
     for (i=1; i<=imx; i++)  {    fprintf(ficresprobcov,"\n");
       for(m=1; (m<= maxwav); m++){    fprintf(ficresprobcor,"\n");
         if (s[m][i] > (nlstate+ndeath)) {   */
           printf("Error: Wrong value in nlstate or ndeath\n");     xp=vector(1,npar);
           goto end;    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         }    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
       }    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     }    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     free_vector(severity,1,maxwav);    fprintf(fichtm,"\n");
     free_imatrix(outcome,1,maxwav+1,1,n);  
     free_vector(moisnais,1,n);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);
     free_vector(annais,1,n);    fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\
     /* free_matrix(mint,1,maxwav,1,n);    file %s<br>\n",optionfilehtmcov);
        free_matrix(anint,1,maxwav,1,n);*/    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
     free_vector(moisdc,1,n);  and drawn. It helps understanding how is the covariance between two incidences.\
     free_vector(andc,1,n);   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 \
     wav=ivector(1,imx);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  standard deviations wide on each axis. <br>\
     mw=imatrix(1,lastpass-firstpass+1,1,imx);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
       and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
     /* Concatenates waves */  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  
     cov[1]=1;
     tj=cptcoveff;
       Tcode=ivector(1,100);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    j1=0;
       ncodemax[1]=1;    for(t=1; t<=tj;t++){
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      for(i1=1; i1<=ncodemax[t];i1++){ 
              j1++;
    codtab=imatrix(1,100,1,10);        if  (cptcovn>0) {
    h=0;          fprintf(ficresprob, "\n#********** Variable "); 
    m=pow(2,cptcoveff);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresprob, "**********\n#\n");
    for(k=1;k<=cptcoveff; k++){          fprintf(ficresprobcov, "\n#********** Variable "); 
      for(i=1; i <=(m/pow(2,k));i++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
        for(j=1; j <= ncodemax[k]; j++){          fprintf(ficresprobcov, "**********\n#\n");
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          
            h++;          fprintf(ficgp, "\n#********** Variable "); 
            if (h>m) h=1;codtab[h][k]=j;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
          }          fprintf(ficgp, "**********\n#\n");
        }          
      }          
    }          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
    /*for(i=1; i <=m ;i++){          
      for(k=1; k <=cptcovn; k++){          fprintf(ficresprobcor, "\n#********** Variable ");    
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      }          fprintf(ficresprobcor, "**********\n#");    
      printf("\n");        }
    }        
    scanf("%d",i);*/        for (age=bage; age<=fage; age ++){ 
              cov[2]=age;
    /* Calculates basic frequencies. Computes observed prevalence at single age          for (k=1; k<=cptcovn;k++) {
        and prints on file fileres'p'. */            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++)
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          gp=vector(1,(nlstate)*(nlstate+ndeath));
                gm=vector(1,(nlstate)*(nlstate+ndeath));
     /* 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] */          for(theta=1; theta <=npar; theta++){
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */            for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
     if(mle==1){            
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     }            
                k=0;
     /*--------- results files --------------*/            for(i=1; i<= (nlstate); i++){
     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);              for(j=1; j<=(nlstate+ndeath);j++){
                  k=k+1;
                 gp[k]=pmmij[i][j];
    jk=1;              }
    fprintf(ficres,"# Parameters\n");            }
    printf("# Parameters\n");            
    for(i=1,jk=1; i <=nlstate; i++){            for(i=1; i<=npar; i++)
      for(k=1; k <=(nlstate+ndeath); k++){              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
        if (k != i)      
          {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
            printf("%d%d ",i,k);            k=0;
            fprintf(ficres,"%1d%1d ",i,k);            for(i=1; i<=(nlstate); i++){
            for(j=1; j <=ncovmodel; j++){              for(j=1; j<=(nlstate+ndeath);j++){
              printf("%f ",p[jk]);                k=k+1;
              fprintf(ficres,"%f ",p[jk]);                gm[k]=pmmij[i][j];
              jk++;              }
            }            }
            printf("\n");       
            fprintf(ficres,"\n");            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
          }              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
      }          }
    }  
  if(mle==1){          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     /* Computing hessian and covariance matrix */            for(theta=1; theta <=npar; theta++)
     ftolhess=ftol; /* Usually correct */              trgradg[j][theta]=gradg[theta][j];
     hesscov(matcov, p, npar, delti, ftolhess, func);          
  }          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     fprintf(ficres,"# Scales\n");          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     printf("# Scales\n");          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
      for(i=1,jk=1; i <=nlstate; i++){          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
       for(j=1; j <=nlstate+ndeath; j++){          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         if (j!=i) {          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           fprintf(ficres,"%1d%1d",i,j);  
           printf("%1d%1d",i,j);          pmij(pmmij,cov,ncovmodel,x,nlstate);
           for(k=1; k<=ncovmodel;k++){          
             printf(" %.5e",delti[jk]);          k=0;
             fprintf(ficres," %.5e",delti[jk]);          for(i=1; i<=(nlstate); i++){
             jk++;            for(j=1; j<=(nlstate+ndeath);j++){
           }              k=k+1;
           printf("\n");              mu[k][(int) age]=pmmij[i][j];
           fprintf(ficres,"\n");            }
         }          }
       }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
      }            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                  varpij[i][j][(int)age] = doldm[i][j];
     k=1;  
     fprintf(ficres,"# Covariance\n");          /*printf("\n%d ",(int)age);
     printf("# Covariance\n");            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     for(i=1;i<=npar;i++){            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       /*  if (k>nlstate) k=1;            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       i1=(i-1)/(ncovmodel*nlstate)+1;            }*/
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);  
       printf("%s%d%d",alph[k],i1,tab[i]);*/          fprintf(ficresprob,"\n%d ",(int)age);
       fprintf(ficres,"%3d",i);          fprintf(ficresprobcov,"\n%d ",(int)age);
       printf("%3d",i);          fprintf(ficresprobcor,"\n%d ",(int)age);
       for(j=1; j<=i;j++){  
         fprintf(ficres," %.5e",matcov[i][j]);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
         printf(" %.5e",matcov[i][j]);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       fprintf(ficres,"\n");            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
       printf("\n");            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
       k++;          }
     }          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,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);            }
              }/* end of loop for state */
     if (fage <= 2) {        } /* end of loop for age */
       bage = agemin;  
       fage = agemaxpar;        /* Confidence intervalle of pij  */
     }        /*
              fprintf(ficgp,"\nset noparametric;unset label");
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
            fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     ungetc(c,ficpar);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     fgets(line, MAXLINE, ficpar);        */
     puts(line);  
     fputs(line,ficparo);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   }        first1=1;
   ungetc(c,ficpar);        for (k2=1; k2<=(nlstate);k2++){
            for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);            if(l2==k2) continue;
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            j=(k2-1)*(nlstate+ndeath)+l2;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            for (k1=1; k1<=(nlstate);k1++){
                    for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   while((c=getc(ficpar))=='#' && c!= EOF){                if(l1==k1) continue;
     ungetc(c,ficpar);                i=(k1-1)*(nlstate+ndeath)+l1;
     fgets(line, MAXLINE, ficpar);                if(i<=j) continue;
     puts(line);                for (age=bage; age<=fage; age ++){ 
     fputs(line,ficparo);                  if ((int)age %5==0){
   }                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   ungetc(c,ficpar);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                      cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                    mu2=mu[j][(int) age]/stepm*YEARM;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;                    c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
   fscanf(ficpar,"pop_based=%d\n",&popbased);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   fprintf(ficparo,"pop_based=%d\n",popbased);                      lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   fprintf(ficres,"pop_based=%d\n",popbased);                      /* Eigen vectors */
                      v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   while((c=getc(ficpar))=='#' && c!= EOF){                    /*v21=sqrt(1.-v11*v11); *//* error */
     ungetc(c,ficpar);                    v21=(lc1-v1)/cv12*v11;
     fgets(line, MAXLINE, ficpar);                    v12=-v21;
     puts(line);                    v22=v11;
     fputs(line,ficparo);                    tnalp=v21/v11;
   }                    if(first1==1){
   ungetc(c,ficpar);                      first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
   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(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(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);                    /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
 while((c=getc(ficpar))=='#' && c!= EOF){                    if(first==1){
     ungetc(c,ficpar);                      first=0;
     fgets(line, MAXLINE, ficpar);                      fprintf(ficgp,"\nset parametric;unset label");
     puts(line);                      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);
     fputs(line,ficparo);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   }                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   ungetc(c,ficpar);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
 /*------------ gnuplot -------------*/                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);                      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),\
 /*------------ free_vector  -------------*/                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
  chdir(path);                    }else{
                        first=0;
  free_ivector(wav,1,imx);                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                        fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
  free_ivector(num,1,n);                      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",\
  free_vector(agedc,1,n);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
  /*free_matrix(covar,1,NCOVMAX,1,n);*/                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
  fclose(ficparo);                    }/* if first */
  fclose(ficres);                  } /* age mod 5 */
                 } /* end loop age */
 /*--------- index.htm --------*/                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);              } /*l12 */
             } /* k12 */
            } /*l1 */
   /*--------------- Prevalence limit --------------*/        }/* k1 */
        } /* loop covariates */
   strcpy(filerespl,"pl");    }
   strcat(filerespl,fileres);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    free_vector(xp,1,npar);
   }    fclose(ficresprob);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    fclose(ficresprobcov);
   fprintf(ficrespl,"#Prevalence limit\n");    fclose(ficresprobcor);
   fprintf(ficrespl,"#Age ");    fflush(ficgp);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    fflush(fichtmcov);
   fprintf(ficrespl,"\n");  }
    
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /******************* Printing html file ***********/
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    int lastpass, int stepm, int weightopt, char model[],\
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                    int popforecast, int estepm ,\
   k=0;                    double jprev1, double mprev1,double anprev1, \
   agebase=agemin;                    double jprev2, double mprev2,double anprev2){
   agelim=agemaxpar;    int jj1, k1, i1, cpt;
   ftolpl=1.e-10;    /*char optionfilehtm[FILENAMELENGTH];*/
   i1=cptcoveff;  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
   if (cptcovn < 1){i1=1;}  /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
   /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
   for(cptcov=1;cptcov<=i1;cptcov++){  /*   } */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
         k=k+1;     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
         fprintf(ficrespl,"\n#******");   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
         for(j=1;j<=cptcoveff;j++)   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   - Life expectancies by age and initial health status (estepm=%2d months): \
         fprintf(ficrespl,"******\n");     <a href=\"%s\">%s</a> <br>\n</li>", \
                     jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
         for (age=agebase; age<=agelim; age++){             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
           fprintf(ficrespl,"%.0f",age );             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
           for(i=1; i<=nlstate;i++)  
           fprintf(ficrespl," %.5f", prlim[i][i]);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
           fprintf(ficrespl,"\n");  
         }   m=cptcoveff;
       }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     }  
   fclose(ficrespl);   jj1=0;
    for(k1=1; k1<=m;k1++){
   /*------------- h Pij x at various ages ------------*/     for(i1=1; i1<=ncodemax[k1];i1++){
         jj1++;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);       if (cptcovn > 0) {
   if((ficrespij=fopen(filerespij,"w"))==NULL) {         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;         for (cpt=1; cpt<=cptcoveff;cpt++) 
   }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   printf("Computing pij: result on file '%s' \n", filerespij);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         }
   stepsize=(int) (stepm+YEARM-1)/YEARM;       /* Pij */
   /*if (stepm<=24) stepsize=2;*/       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
   agelim=AGESUP;       /* Quasi-incidences */
   hstepm=stepsize*YEARM; /* Every year of age */       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */   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); 
   k=0;         /* Stable prevalence in each health state */
   for(cptcov=1;cptcov<=i1;cptcov++){         for(cpt=1; cpt<nlstate;cpt++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
       k=k+1;  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
         fprintf(ficrespij,"\n#****** ");         }
         for(j=1;j<=cptcoveff;j++)       for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
         fprintf(ficrespij,"******\n");  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
               }
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  health expectancies in states (1) and (2): %s%d.png<br>\
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     } /* end i1 */
           oldm=oldms;savm=savms;   }/* End k1 */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);     fprintf(fichtm,"</ul>");
           fprintf(ficrespij,"# Age");  
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
               fprintf(ficrespij," %1d-%1d",i,j);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
           fprintf(ficrespij,"\n");   - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
           for (h=0; h<=nhstepm; h++){   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
             for(i=1; i<=nlstate;i++)   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
               for(j=1; j<=nlstate+ndeath;j++)   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
             fprintf(ficrespij,"\n");           rfileres,rfileres,\
           }           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
           fprintf(ficrespij,"\n");           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
         }           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
     }           subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
   }           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/  /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   fclose(ficrespij);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*---------- Forecasting ------------------*/  /*    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); */
   if((stepm == 1) && (model==".")){  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
     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);   m=cptcoveff;
     free_matrix(mint,1,maxwav,1,n);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  
     free_vector(weight,1,n);}   jj1=0;
   else{   for(k1=1; k1<=m;k1++){
     erreur=108;     for(i1=1; i1<=ncodemax[k1];i1++){
     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);       jj1++;
   }       if (cptcovn > 0) {
           fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
   /*---------- Health expectancies and variances ------------*/           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   strcpy(filerest,"t");       }
   strcat(filerest,fileres);       for(cpt=1; cpt<=nlstate;cpt++) {
   if((ficrest=fopen(filerest,"w"))==NULL) {         fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  interval) in state (%d): %s%d%d.png <br>\
   }  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);       }
      } /* end i1 */
    }/* End k1 */
   strcpy(filerese,"e");   fprintf(fichtm,"</ul>");
   strcat(filerese,fileres);   fflush(fichtm);
   if((ficreseij=fopen(filerese,"w"))==NULL) {  }
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  
   }  /******************* Gnuplot file **************/
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
  strcpy(fileresv,"v");    char dirfileres[132],optfileres[132];
   strcat(fileresv,fileres);    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    int ng;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   }  /*     printf("Problem with file %s",optionfilegnuplot); */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){    /*#ifdef windows */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficgp,"cd \"%s\" \n",pathc);
       k=k+1;      /*#endif */
       fprintf(ficrest,"\n#****** ");    m=pow(2,cptcoveff);
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    strcpy(dirfileres,optionfilefiname);
       fprintf(ficrest,"******\n");    strcpy(optfileres,"vpl");
    /* 1eme*/
       fprintf(ficreseij,"\n#****** ");    for (cpt=1; cpt<= nlstate ; cpt ++) {
       for(j=1;j<=cptcoveff;j++)     for (k1=1; k1<= m ; k1 ++) {
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
       fprintf(ficreseij,"******\n");       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
       fprintf(ficresvij,"\n#****** ");  set ylabel \"Probability\" \n\
       for(j=1;j<=cptcoveff;j++)  set ter png small\n\
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  set size 0.65,0.65\n\
       fprintf(ficresvij,"******\n");  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);       for (i=1; i<= nlstate ; i ++) {
       oldm=oldms;savm=savms;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);           else fprintf(ficgp," \%%*lf (\%%*lf)");
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);       }
       oldm=oldms;savm=savms;       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);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);       for (i=1; i<= nlstate ; i ++) {
             if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
         } 
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);       for (i=1; i<= nlstate ; i ++) {
       fprintf(ficrest,"\n");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
       hf=1;       }  
       if (stepm >= YEARM) hf=stepm/YEARM;       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
       epj=vector(1,nlstate+1);     }
       for(age=bage; age <=fage ;age++){    }
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    /*2 eme*/
         if (popbased==1) {    
           for(i=1; i<=nlstate;i++)    for (k1=1; k1<= m ; k1 ++) { 
             prlim[i][i]=probs[(int)age][i][k];      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
         }      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
              
         fprintf(ficrest," %.0f",age);      for (i=1; i<= nlstate+1 ; i ++) {
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){        k=2*i;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];        for (j=1; j<= nlstate+1 ; j ++) {
           }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           epj[nlstate+1] +=epj[j];          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }        }   
         for(i=1, vepp=0.;i <=nlstate;i++)        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
           for(j=1;j <=nlstate;j++)        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
             vepp += vareij[i][j][(int)age];        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));        for (j=1; j<= nlstate+1 ; j ++) {
         for(j=1;j <=nlstate;j++){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }        }   
         fprintf(ficrest,"\n");        fprintf(ficgp,"\" t\"\" w l 0,");
       }        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     }        for (j=1; j<= nlstate+1 ; j ++) {
   }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
   fclose(ficreseij);        }   
   fclose(ficresvij);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
   fclose(ficrest);        else fprintf(ficgp,"\" t\"\" w l 0,");
   fclose(ficpar);      }
   free_vector(epj,1,nlstate+1);    }
      
   /*------- Variance limit prevalence------*/      /*3eme*/
     
   strcpy(fileresvpl,"vpl");    for (k1=1; k1<= m ; k1 ++) { 
   strcat(fileresvpl,fileres);      for (cpt=1; cpt<= nlstate ; cpt ++) {
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        k=2+nlstate*(2*cpt-2);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
     exit(0);        fprintf(ficgp,"set ter png small\n\
   }  set size 0.65,0.65\n\
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   k=0;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
       k=k+1;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       fprintf(ficresvpl,"\n#****** ");          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       for(j=1;j<=cptcoveff;j++)          
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        */
       fprintf(ficresvpl,"******\n");        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);
       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);      }
     }    }
  }    
     /* CV preval stable (period) */
   fclose(ficresvpl);    for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
   /*---------- End : free ----------------*/        k=3;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  set ter png small\nset size 0.65,0.65\n\
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  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);
          
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        for (i=1; i< nlstate ; i ++)
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);          fprintf(ficgp,"+$%d",k+i+1);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        
          l=3+(nlstate+ndeath)*cpt;
   free_matrix(matcov,1,npar,1,npar);        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
   free_vector(delti,1,npar);        for (i=1; i< nlstate ; i ++) {
   free_matrix(agev,1,maxwav,1,imx);          l=3+(nlstate+ndeath)*cpt;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);          fprintf(ficgp,"+$%d",l+i+1);
         }
   if(erreur >0)        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
     printf("End of Imach with error %d\n",erreur);      } 
   else   printf("End of Imach\n");    }  
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    
      /* proba elementaires */
   /* 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);*/    for(i=1,jk=1; i <=nlstate; i++){
   /*printf("Total time was %d uSec.\n", total_usecs);*/      for(k=1; k <=(nlstate+ndeath); k++){
   /*------ End -----------*/        if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
  end:            jk++; 
 #ifdef windows            fprintf(ficgp,"\n");
   /* chdir(pathcd);*/          }
 #endif        }
  /*system("wgnuplot graph.plt");*/      }
  /*system("../gp37mgw/wgnuplot graph.plt");*/     }
  /*system("cd ../gp37mgw");*/  
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
  strcpy(plotcmd,GNUPLOTPROGRAM);       for(jk=1; jk <=m; jk++) {
  strcat(plotcmd," ");         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
  strcat(plotcmd,optionfilegnuplot);         if (ng==2)
  system(plotcmd);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
 #ifdef windows           fprintf(ficgp,"\nset title \"Probability\"\n");
   while (z[0] != 'q') {         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
     chdir(path);         i=1;
     printf("\nType e to edit output files, c to start again, and q for exiting: ");         for(k2=1; k2<=nlstate; k2++) {
     scanf("%s",z);           k3=i;
     if (z[0] == 'c') system("./imach");           for(k=1; k<=(nlstate+ndeath); k++) {
     else if (z[0] == 'e') {             if (k != k2){
       chdir(path);               if(ng==2)
       system(optionfilehtm);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
     }               else
     else if (z[0] == 'q') exit(0);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
   }               ij=1;
 #endif               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 of prwizard */
   
   
   /***********************************************/
   /**************** 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, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     /*  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]; 
     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;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     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;
    
     /*   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(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",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 */
    
     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);
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     /* 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);
   
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     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);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     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 paramater 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);
       
     /*-------- 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); 
   
     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);
     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 */
     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*/
     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);
     
   
     jk=1;
     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");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     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.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     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);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,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);
   
     /*---------- 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 ----------------*/
     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);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     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 warnings %d\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,GNUPLOTPROGRAM);
     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') 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.1.94


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