Diff for /imach/src/imach.c between versions 1.52 and 1.93

version 1.52, 2002/07/19 18:49:30 version 1.93, 2003/06/25 16:33:55
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.93  2003/06/25 16:33:55  brouard
      (Module): On windows (cygwin) function asctime_r doesn't
   This program computes Healthy Life Expectancies from    exist so I changed back to asctime which exists.
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    (Module): Version 0.96b
   first survey ("cross") where individuals from different ages are  
   interviewed on their health status or degree of disability (in the    Revision 1.92  2003/06/25 16:30:45  brouard
   case of a health survey which is our main interest) -2- at least a    (Module): On windows (cygwin) function asctime_r doesn't
   second wave of interviews ("longitudinal") which measure each change    exist so I changed back to asctime which exists.
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.91  2003/06/25 15:30:29  brouard
   model. More health states you consider, more time is necessary to reach the    * imach.c (Repository): Duplicated warning errors corrected.
   Maximum Likelihood of the parameters involved in the model.  The    (Repository): Elapsed time after each iteration is now output. It
   simplest model is the multinomial logistic model where pij is the    helps to forecast when convergence will be reached. Elapsed time
   probability to be observed in state j at the second wave    is stamped in powell.  We created a new html file for the graphs
   conditional to be observed in state i at the first wave. Therefore    concerning matrix of covariance. It has extension -cov.htm.
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    Revision 1.90  2003/06/24 12:34:15  brouard
   complex model than "constant and age", you should modify the program    (Module): Some bugs corrected for windows. Also, when
   where the markup *Covariates have to be included here again* invites    mle=-1 a template is output in file "or"mypar.txt with the design
   you to do it.  More covariates you add, slower the    of the covariance matrix to be input.
   convergence.  
     Revision 1.89  2003/06/24 12:30:52  brouard
   The advantage of this computer programme, compared to a simple    (Module): Some bugs corrected for windows. Also, when
   multinomial logistic model, is clear when the delay between waves is not    mle=-1 a template is output in file "or"mypar.txt with the design
   identical for each individual. Also, if a individual missed an    of the covariance matrix to be input.
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.88  2003/06/23 17:54:56  brouard
     * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   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 1.87  2003/06/18 12:26:01  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    Version 0.96
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.86  2003/06/17 20:04:08  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    (Module): Change position of html and gnuplot routines and added
   and the contribution of each individual to the likelihood is simply    routine fileappend.
   hPijx.  
     Revision 1.85  2003/06/17 13:12:43  brouard
   Also this programme outputs the covariance matrix of the parameters but also    * imach.c (Repository): Check when date of death was earlier that
   of the life expectancies. It also computes the prevalence limits.    current date of interview. It may happen when the death was just
      prior to the death. In this case, dh was negative and likelihood
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    was wrong (infinity). We still send an "Error" but patch by
            Institut national d'études démographiques, Paris.    assuming that the date of death was just one stepm after the
   This software have been partly granted by Euro-REVES, a concerted action    interview.
   from the European Union.    (Repository): Because some people have very long ID (first column)
   It is copyrighted identically to a GNU software product, ie programme and    we changed int to long in num[] and we added a new lvector for
   software can be distributed freely for non commercial use. Latest version    memory allocation. But we also truncated to 8 characters (left
   can be accessed at http://euroreves.ined.fr/imach .    truncation)
   **********************************************************************/    (Repository): No more line truncation errors.
    
 #include <math.h>    Revision 1.84  2003/06/13 21:44:43  brouard
 #include <stdio.h>    * imach.c (Repository): Replace "freqsummary" at a correct
 #include <stdlib.h>    place. It differs from routine "prevalence" which may be called
 #include <unistd.h>    many times. Probs is memory consuming and must be used with
     parcimony.
 #define MAXLINE 256    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #define GNUPLOTPROGRAM "gnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.83  2003/06/10 13:39:11  lievre
 #define FILENAMELENGTH 80    *** empty log message ***
 /*#define DEBUG*/  
 #define windows    Revision 1.82  2003/06/05 15:57:20  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Add log in  imach.c and  fullversion number is now printed.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
   */
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  /*
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */     Interpolated Markov Chain
   
 #define NINTERVMAX 8    Short summary of the programme:
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    This program computes Healthy Life Expectancies from
 #define NCOVMAX 8 /* Maximum number of covariates */    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #define MAXN 20000    first survey ("cross") where individuals from different ages are
 #define YEARM 12. /* Number of months per year */    interviewed on their health status or degree of disability (in the
 #define AGESUP 130    case of a health survey which is our main interest) -2- at least a
 #define AGEBASE 40    second wave of interviews ("longitudinal") which measure each change
 #ifdef windows    (if any) in individual health status.  Health expectancies are
 #define DIRSEPARATOR '\\'    computed from the time spent in each health state according to a
 #define ODIRSEPARATOR '/'    model. More health states you consider, more time is necessary to reach the
 #else    Maximum Likelihood of the parameters involved in the model.  The
 #define DIRSEPARATOR '/'    simplest model is the multinomial logistic model where pij is the
 #define ODIRSEPARATOR '\\'    probability to be observed in state j at the second wave
 #endif    conditional to be observed in state i at the first wave. Therefore
     the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";    'age' is age and 'sex' is a covariate. If you want to have a more
 int erreur; /* Error number */    complex model than "constant and age", you should modify the program
 int nvar;    where the markup *Covariates have to be included here again* invites
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    you to do it.  More covariates you add, slower the
 int npar=NPARMAX;    convergence.
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    The advantage of this computer programme, compared to a simple
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    multinomial logistic model, is clear when the delay between waves is not
 int popbased=0;    identical for each individual. Also, if a individual missed an
     intermediate interview, the information is lost, but taken into
 int *wav; /* Number of waves for this individuual 0 is possible */    account using an interpolation or extrapolation.  
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    hPijx is the probability to be observed in state i at age x+h
 int mle, weightopt;    conditional to the observed state i at age x. The delay 'h' can be
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    split into an exact number (nh*stepm) of unobserved intermediate
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    states. This elementary transition (by month, quarter,
 double jmean; /* Mean space between 2 waves */    semester or year) is modelled as a multinomial logistic.  The hPx
 double **oldm, **newm, **savm; /* Working pointers to matrices */    matrix is simply the matrix product of nh*stepm elementary matrices
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    and the contribution of each individual to the likelihood is simply
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    hPijx.
 FILE *ficlog;  
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    Also this programme outputs the covariance matrix of the parameters but also
 FILE *ficresprobmorprev;    of the life expectancies. It also computes the stable prevalence. 
 FILE *fichtm; /* Html File */    
 FILE *ficreseij;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 char filerese[FILENAMELENGTH];             Institut national d'études démographiques, Paris.
 FILE  *ficresvij;    This software have been partly granted by Euro-REVES, a concerted action
 char fileresv[FILENAMELENGTH];    from the European Union.
 FILE  *ficresvpl;    It is copyrighted identically to a GNU software product, ie programme and
 char fileresvpl[FILENAMELENGTH];    software can be distributed freely for non commercial use. Latest version
 char title[MAXLINE];    can be accessed at http://euroreves.ined.fr/imach .
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    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
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    
 char filelog[FILENAMELENGTH]; /* Log file */    **********************************************************************/
 char filerest[FILENAMELENGTH];  /*
 char fileregp[FILENAMELENGTH];    main
 char popfile[FILENAMELENGTH];    read parameterfile
     read datafile
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    concatwav
     freqsummary
 #define NR_END 1    if (mle >= 1)
 #define FREE_ARG char*      mlikeli
 #define FTOL 1.0e-10    print results files
     if mle==1 
 #define NRANSI       computes hessian
 #define ITMAX 200    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 #define TOL 2.0e-4    open gnuplot file
     open html file
 #define CGOLD 0.3819660    stable prevalence
 #define ZEPS 1.0e-10     for age prevalim()
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    h Pij x
     variance of p varprob
 #define GOLD 1.618034    forecasting if prevfcast==1 prevforecast call prevalence()
 #define GLIMIT 100.0    health expectancies
 #define TINY 1.0e-20    Variance-covariance of DFLE
     prevalence()
 static double maxarg1,maxarg2;     movingaverage()
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    varevsij() 
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    if popbased==1 varevsij(,popbased)
      total life expectancies
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Variance of stable prevalence
 #define rint(a) floor(a+0.5)   end
   */
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
    
 int imx;  #include <math.h>
 int stepm;  #include <stdio.h>
 /* Stepm, step in month: minimum step interpolation*/  #include <stdlib.h>
   #include <unistd.h>
 int estepm;  
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  #include <sys/time.h>
   #include <time.h>
 int m,nb;  #include "timeval.h"
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define MAXLINE 256
 double **pmmij, ***probs, ***mobaverage;  #define GNUPLOTPROGRAM "gnuplot"
 double dateintmean=0;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
 double *weight;  /*#define DEBUG*/
 int **s; /* Status */  /*#define windows*/
 double *agedc, **covar, idx;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 double ftolhess; /* Tolerance for computing hessian */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 /**************** split *************************/  #define NINTERVMAX 8
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 {  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
    char *s;                             /* pointer */  #define NCOVMAX 8 /* Maximum number of covariates */
    int  l1, l2;                         /* length counters */  #define MAXN 20000
   #define YEARM 12. /* Number of months per year */
    l1 = strlen( path );                 /* length of path */  #define AGESUP 130
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define AGEBASE 40
    s= strrchr( path, DIRSEPARATOR );            /* find last / */  #ifdef unix
    if ( s == NULL ) {                   /* no directory, so use current */  #define DIRSEPARATOR '/'
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)  #define ODIRSEPARATOR '\\'
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/  #else
 #if     defined(__bsd__)                /* get current working directory */  #define DIRSEPARATOR '\\'
       extern char       *getwd( );  #define ODIRSEPARATOR '/'
   #endif
       if ( getwd( dirc ) == NULL ) {  
 #else  /* $Id$ */
       extern char       *getcwd( );  /* $State$ */
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  char version[]="Imach version 0.96b, June 2003, INED-EUROREVES ";
 #endif  char fullversion[]="$Revision$ $Date$"; 
          return( GLOCK_ERROR_GETCWD );  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
       }  int nvar;
       strcpy( name, path );             /* we've got it */  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
    } else {                             /* strip direcotry from path */  int npar=NPARMAX;
       s++;                              /* after this, the filename */  int nlstate=2; /* Number of live states */
       l2 = strlen( s );                 /* length of filename */  int ndeath=1; /* Number of dead states */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       strcpy( name, s );                /* save file name */  int popbased=0;
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */  int *wav; /* Number of waves for this individuual 0 is possible */
    }  int maxwav; /* Maxim number of waves */
    l1 = strlen( dirc );                 /* length of directory */  int jmin, jmax; /* min, max spacing between 2 waves */
 #ifdef windows  int gipmx, gsw; /* Global variables on the number of contributions 
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }                     to the likelihood and the sum of weights (done by funcone)*/
 #else  int mle, weightopt;
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #endif  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
    s = strrchr( name, '.' );            /* find last / */  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
    s++;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
    strcpy(ext,s);                       /* save extension */  double jmean; /* Mean space between 2 waves */
    l1= strlen( name);  double **oldm, **newm, **savm; /* Working pointers to matrices */
    l2= strlen( s)+1;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
    strncpy( finame, name, l1-l2);  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
    finame[l1-l2]= 0;  FILE *ficlog, *ficrespow;
    return( 0 );                         /* we're done */  int globpr; /* Global variable for printing or not */
 }  double fretone; /* Only one call to likelihood */
   long ipmx; /* Number of contributions */
   double sw; /* Sum of weights */
 /******************************************/  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   FILE *ficresilk;
 void replace(char *s, char*t)  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 {  FILE *ficresprobmorprev;
   int i;  FILE *fichtm, *fichtmcov; /* Html File */
   int lg=20;  FILE *ficreseij;
   i=0;  char filerese[FILENAMELENGTH];
   lg=strlen(t);  FILE  *ficresvij;
   for(i=0; i<= lg; i++) {  char fileresv[FILENAMELENGTH];
     (s[i] = t[i]);  FILE  *ficresvpl;
     if (t[i]== '\\') s[i]='/';  char fileresvpl[FILENAMELENGTH];
   }  char title[MAXLINE];
 }  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 int nbocc(char *s, char occ)  char tmpout[FILENAMELENGTH]; 
 {  char command[FILENAMELENGTH];
   int i,j=0;  int  outcmd=0;
   int lg=20;  
   i=0;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   lg=strlen(s);  char lfileres[FILENAMELENGTH];
   for(i=0; i<= lg; i++) {  char filelog[FILENAMELENGTH]; /* Log file */
   if  (s[i] == occ ) j++;  char filerest[FILENAMELENGTH];
   }  char fileregp[FILENAMELENGTH];
   return j;  char popfile[FILENAMELENGTH];
 }  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 void cutv(char *u,char *v, char*t, char occ)  
 {  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   /* cuts string t into u and v where u is ended by char occ excluding it  struct timezone tzp;
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)  extern int gettimeofday();
      gives u="abcedf" and v="ghi2j" */  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   int i,lg,j,p=0;  long time_value;
   i=0;  extern long time();
   for(j=0; j<=strlen(t)-1; j++) {  char strcurr[80], strfor[80];
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }  #define NR_END 1
   #define FREE_ARG char*
   lg=strlen(t);  #define FTOL 1.0e-10
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);  #define NRANSI 
   }  #define ITMAX 200 
      u[p]='\0';  
   #define TOL 2.0e-4 
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);  #define CGOLD 0.3819660 
   }  #define ZEPS 1.0e-10 
 }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
 /********************** nrerror ********************/  #define GOLD 1.618034 
   #define GLIMIT 100.0 
 void nrerror(char error_text[])  #define TINY 1.0e-20 
 {  
   fprintf(stderr,"ERREUR ...\n");  static double maxarg1,maxarg2;
   fprintf(stderr,"%s\n",error_text);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   exit(1);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 }    
 /*********************** vector *******************/  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 double *vector(int nl, int nh)  #define rint(a) floor(a+0.5)
 {  
   double *v;  static double sqrarg;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   if (!v) nrerror("allocation failure in vector");  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   return v-nl+NR_END;  
 }  int imx; 
   int stepm;
 /************************ free vector ******************/  /* Stepm, step in month: minimum step interpolation*/
 void free_vector(double*v, int nl, int nh)  
 {  int estepm;
   free((FREE_ARG)(v+nl-NR_END));  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 }  
   int m,nb;
 /************************ivector *******************************/  long *num;
 int *ivector(long nl,long nh)  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   int *v;  double **pmmij, ***probs;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  double dateintmean=0;
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;  double *weight;
 }  int **s; /* Status */
   double *agedc, **covar, idx;
 /******************free ivector **************************/  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 void free_ivector(int *v, long nl, long nh)  
 {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   free((FREE_ARG)(v+nl-NR_END));  double ftolhess; /* Tolerance for computing hessian */
 }  
   /**************** split *************************/
 /******************* imatrix *******************************/  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 int **imatrix(long nrl, long nrh, long ncl, long nch)  {
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    char  *ss;                            /* pointer */
 {    int   l1, l2;                         /* length counters */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;    l1 = strlen(path );                   /* length of path */
      if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   /* allocate pointers to rows */    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    if ( ss == NULL ) {                   /* no directory, so use current */
   if (!m) nrerror("allocation failure 1 in matrix()");      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   m += NR_END;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   m -= nrl;      /* get current working directory */
        /*    extern  char* getcwd ( char *buf , int len);*/
        if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   /* allocate rows and set pointers to them */        return( GLOCK_ERROR_GETCWD );
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));      }
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      strcpy( name, path );               /* we've got it */
   m[nrl] += NR_END;    } else {                              /* strip direcotry from path */
   m[nrl] -= ncl;      ss++;                               /* after this, the filename */
        l2 = strlen( ss );                  /* length of filename */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
        strcpy( name, ss );         /* save file name */
   /* return pointer to array of pointers to rows */      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   return m;      dirc[l1-l2] = 0;                    /* add zero */
 }    }
     l1 = strlen( dirc );                  /* length of directory */
 /****************** free_imatrix *************************/    /*#ifdef windows
 void free_imatrix(m,nrl,nrh,ncl,nch)    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
       int **m;  #else
       long nch,ncl,nrh,nrl;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
      /* free an int matrix allocated by imatrix() */  #endif
 {    */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    ss = strrchr( name, '.' );            /* find last / */
   free((FREE_ARG) (m+nrl-NR_END));    ss++;
 }    strcpy(ext,ss);                       /* save extension */
     l1= strlen( name);
 /******************* matrix *******************************/    l2= strlen(ss)+1;
 double **matrix(long nrl, long nrh, long ncl, long nch)    strncpy( finame, name, l1-l2);
 {    finame[l1-l2]= 0;
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    return( 0 );                          /* we're done */
   double **m;  }
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  /******************************************/
   m += NR_END;  
   m -= nrl;  void replace_back_to_slash(char *s, char*t)
   {
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    int i;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    int lg=0;
   m[nrl] += NR_END;    i=0;
   m[nrl] -= ncl;    lg=strlen(t);
     for(i=0; i<= lg; i++) {
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;      (s[i] = t[i]);
   return m;      if (t[i]== '\\') s[i]='/';
 }    }
   }
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  int nbocc(char *s, char occ)
 {  {
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    int i,j=0;
   free((FREE_ARG)(m+nrl-NR_END));    int lg=20;
 }    i=0;
     lg=strlen(s);
 /******************* ma3x *******************************/    for(i=0; i<= lg; i++) {
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    if  (s[i] == occ ) j++;
 {    }
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    return j;
   double ***m;  }
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  void cutv(char *u,char *v, char*t, char occ)
   if (!m) nrerror("allocation failure 1 in matrix()");  {
   m += NR_END;    /* cuts string t into u and v where u is ended by char occ excluding it
   m -= nrl;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
        gives u="abcedf" and v="ghi2j" */
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    int i,lg,j,p=0;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    i=0;
   m[nrl] += NR_END;    for(j=0; j<=strlen(t)-1; j++) {
   m[nrl] -= ncl;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
     lg=strlen(t);
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    for(j=0; j<p; j++) {
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");      (u[j] = t[j]);
   m[nrl][ncl] += NR_END;    }
   m[nrl][ncl] -= nll;       u[p]='\0';
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;     for(j=0; j<= lg; j++) {
        if (j>=(p+1))(v[j-p-1] = t[j]);
   for (i=nrl+1; i<=nrh; i++) {    }
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  }
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  /********************** nrerror ********************/
   }  
   return m;  void nrerror(char error_text[])
 }  {
     fprintf(stderr,"ERREUR ...\n");
 /*************************free ma3x ************************/    fprintf(stderr,"%s\n",error_text);
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    exit(EXIT_FAILURE);
 {  }
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  /*********************** vector *******************/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  double *vector(int nl, int nh)
   free((FREE_ARG)(m+nrl-NR_END));  {
 }    double *v;
     v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 /***************** f1dim *************************/    if (!v) nrerror("allocation failure in vector");
 extern int ncom;    return v-nl+NR_END;
 extern double *pcom,*xicom;  }
 extern double (*nrfunc)(double []);  
    /************************ free vector ******************/
 double f1dim(double x)  void free_vector(double*v, int nl, int nh)
 {  {
   int j;    free((FREE_ARG)(v+nl-NR_END));
   double f;  }
   double *xt;  
    /************************ivector *******************************/
   xt=vector(1,ncom);  int *ivector(long nl,long nh)
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  {
   f=(*nrfunc)(xt);    int *v;
   free_vector(xt,1,ncom);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   return f;    if (!v) nrerror("allocation failure in ivector");
 }    return v-nl+NR_END;
   }
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  /******************free ivector **************************/
 {  void free_ivector(int *v, long nl, long nh)
   int iter;  {
   double a,b,d,etemp;    free((FREE_ARG)(v+nl-NR_END));
   double fu,fv,fw,fx;  }
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;  /************************lvector *******************************/
   double e=0.0;  long *lvector(long nl,long nh)
    {
   a=(ax < cx ? ax : cx);    long *v;
   b=(ax > cx ? ax : cx);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   x=w=v=bx;    if (!v) nrerror("allocation failure in ivector");
   fw=fv=fx=(*f)(x);    return v-nl+NR_END;
   for (iter=1;iter<=ITMAX;iter++) {  }
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  /******************free lvector **************************/
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  void free_lvector(long *v, long nl, long nh)
     printf(".");fflush(stdout);  {
     fprintf(ficlog,".");fflush(ficlog);    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);  
     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);  /******************* imatrix *******************************/
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  int **imatrix(long nrl, long nrh, long ncl, long nch) 
 #endif       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  { 
       *xmin=x;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       return fx;    int **m; 
     }    
     ftemp=fu;    /* allocate pointers to rows */ 
     if (fabs(e) > tol1) {    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       r=(x-w)*(fx-fv);    if (!m) nrerror("allocation failure 1 in matrix()"); 
       q=(x-v)*(fx-fw);    m += NR_END; 
       p=(x-v)*q-(x-w)*r;    m -= nrl; 
       q=2.0*(q-r);    
       if (q > 0.0) p = -p;    
       q=fabs(q);    /* allocate rows and set pointers to them */ 
       etemp=e;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       e=d;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    m[nrl] += NR_END; 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    m[nrl] -= ncl; 
       else {    
         d=p/q;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
         u=x+d;    
         if (u-a < tol2 || b-u < tol2)    /* return pointer to array of pointers to rows */ 
           d=SIGN(tol1,xm-x);    return m; 
       }  } 
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  /****************** free_imatrix *************************/
     }  void free_imatrix(m,nrl,nrh,ncl,nch)
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));        int **m;
     fu=(*f)(u);        long nch,ncl,nrh,nrl; 
     if (fu <= fx) {       /* free an int matrix allocated by imatrix() */ 
       if (u >= x) a=x; else b=x;  { 
       SHFT(v,w,x,u)    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         SHFT(fv,fw,fx,fu)    free((FREE_ARG) (m+nrl-NR_END)); 
         } else {  } 
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  /******************* matrix *******************************/
             v=w;  double **matrix(long nrl, long nrh, long ncl, long nch)
             w=u;  {
             fv=fw;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
             fw=fu;    double **m;
           } else if (fu <= fv || v == x || v == w) {  
             v=u;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
             fv=fu;    if (!m) nrerror("allocation failure 1 in matrix()");
           }    m += NR_END;
         }    m -= nrl;
   }  
   nrerror("Too many iterations in brent");    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   *xmin=x;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   return fx;    m[nrl] += NR_END;
 }    m[nrl] -= ncl;
   
 /****************** mnbrak ***********************/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
             double (*func)(double))     */
 {  }
   double ulim,u,r,q, dum;  
   double fu;  /*************************free matrix ************************/
    void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   *fa=(*func)(*ax);  {
   *fb=(*func)(*bx);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   if (*fb > *fa) {    free((FREE_ARG)(m+nrl-NR_END));
     SHFT(dum,*ax,*bx,dum)  }
       SHFT(dum,*fb,*fa,dum)  
       }  /******************* ma3x *******************************/
   *cx=(*bx)+GOLD*(*bx-*ax);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   *fc=(*func)(*cx);  {
   while (*fb > *fc) {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     r=(*bx-*ax)*(*fb-*fc);    double ***m;
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    if (!m) nrerror("allocation failure 1 in matrix()");
     ulim=(*bx)+GLIMIT*(*cx-*bx);    m += NR_END;
     if ((*bx-u)*(u-*cx) > 0.0) {    m -= nrl;
       fu=(*func)(u);  
     } else if ((*cx-u)*(u-ulim) > 0.0) {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       fu=(*func)(u);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       if (fu < *fc) {    m[nrl] += NR_END;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    m[nrl] -= ncl;
           SHFT(*fb,*fc,fu,(*func)(u))  
           }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       fu=(*func)(u);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     } else {    m[nrl][ncl] += NR_END;
       u=(*cx)+GOLD*(*cx-*bx);    m[nrl][ncl] -= nll;
       fu=(*func)(u);    for (j=ncl+1; j<=nch; j++) 
     }      m[nrl][j]=m[nrl][j-1]+nlay;
     SHFT(*ax,*bx,*cx,u)    
       SHFT(*fa,*fb,*fc,fu)    for (i=nrl+1; i<=nrh; i++) {
       }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 }      for (j=ncl+1; j<=nch; j++) 
         m[i][j]=m[i][j-1]+nlay;
 /*************** linmin ************************/    }
     return m; 
 int ncom;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 double *pcom,*xicom;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 double (*nrfunc)(double []);    */
    }
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {  /*************************free ma3x ************************/
   double brent(double ax, double bx, double cx,  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
                double (*f)(double), double tol, double *xmin);  {
   double f1dim(double x);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    free((FREE_ARG)(m[nrl]+ncl-NR_END));
               double *fc, double (*func)(double));    free((FREE_ARG)(m+nrl-NR_END));
   int j;  }
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  /***************** f1dim *************************/
    extern int ncom; 
   ncom=n;  extern double *pcom,*xicom;
   pcom=vector(1,n);  extern double (*nrfunc)(double []); 
   xicom=vector(1,n);   
   nrfunc=func;  double f1dim(double x) 
   for (j=1;j<=n;j++) {  { 
     pcom[j]=p[j];    int j; 
     xicom[j]=xi[j];    double f;
   }    double *xt; 
   ax=0.0;   
   xx=1.0;    xt=vector(1,ncom); 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    f=(*nrfunc)(xt); 
 #ifdef DEBUG    free_vector(xt,1,ncom); 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    return f; 
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  } 
 #endif  
   for (j=1;j<=n;j++) {  /*****************brent *************************/
     xi[j] *= xmin;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     p[j] += xi[j];  { 
   }    int iter; 
   free_vector(xicom,1,n);    double a,b,d,etemp;
   free_vector(pcom,1,n);    double fu,fv,fw,fx;
 }    double ftemp;
     double p,q,r,tol1,tol2,u,v,w,x,xm; 
 /*************** powell ************************/    double e=0.0; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,   
             double (*func)(double []))    a=(ax < cx ? ax : cx); 
 {    b=(ax > cx ? ax : cx); 
   void linmin(double p[], double xi[], int n, double *fret,    x=w=v=bx; 
               double (*func)(double []));    fw=fv=fx=(*f)(x); 
   int i,ibig,j;    for (iter=1;iter<=ITMAX;iter++) { 
   double del,t,*pt,*ptt,*xit;      xm=0.5*(a+b); 
   double fp,fptt;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   double *xits;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   pt=vector(1,n);      printf(".");fflush(stdout);
   ptt=vector(1,n);      fprintf(ficlog,".");fflush(ficlog);
   xit=vector(1,n);  #ifdef DEBUG
   xits=vector(1,n);      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);
   *fret=(*func)(p);      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   for (j=1;j<=n;j++) pt[j]=p[j];      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   for (*iter=1;;++(*iter)) {  #endif
     fp=(*fret);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     ibig=0;        *xmin=x; 
     del=0.0;        return fx; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      } 
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      ftemp=fu;
     for (i=1;i<=n;i++)      if (fabs(e) > tol1) { 
       printf(" %d %.12f",i, p[i]);        r=(x-w)*(fx-fv); 
     fprintf(ficlog," %d %.12f",i, p[i]);        q=(x-v)*(fx-fw); 
     printf("\n");        p=(x-v)*q-(x-w)*r; 
     fprintf(ficlog,"\n");        q=2.0*(q-r); 
     for (i=1;i<=n;i++) {        if (q > 0.0) p = -p; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];        q=fabs(q); 
       fptt=(*fret);        etemp=e; 
 #ifdef DEBUG        e=d; 
       printf("fret=%lf \n",*fret);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       fprintf(ficlog,"fret=%lf \n",*fret);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 #endif        else { 
       printf("%d",i);fflush(stdout);          d=p/q; 
       fprintf(ficlog,"%d",i);fflush(ficlog);          u=x+d; 
       linmin(p,xit,n,fret,func);          if (u-a < tol2 || b-u < tol2) 
       if (fabs(fptt-(*fret)) > del) {            d=SIGN(tol1,xm-x); 
         del=fabs(fptt-(*fret));        } 
         ibig=i;      } else { 
       }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 #ifdef DEBUG      } 
       printf("%d %.12e",i,(*fret));      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       fprintf(ficlog,"%d %.12e",i,(*fret));      fu=(*f)(u); 
       for (j=1;j<=n;j++) {      if (fu <= fx) { 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);        if (u >= x) a=x; else b=x; 
         printf(" x(%d)=%.12e",j,xit[j]);        SHFT(v,w,x,u) 
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);          SHFT(fv,fw,fx,fu) 
       }          } else { 
       for(j=1;j<=n;j++) {            if (u < x) a=u; else b=u; 
         printf(" p=%.12e",p[j]);            if (fu <= fw || w == x) { 
         fprintf(ficlog," p=%.12e",p[j]);              v=w; 
       }              w=u; 
       printf("\n");              fv=fw; 
       fprintf(ficlog,"\n");              fw=fu; 
 #endif            } else if (fu <= fv || v == x || v == w) { 
     }              v=u; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {              fv=fu; 
 #ifdef DEBUG            } 
       int k[2],l;          } 
       k[0]=1;    } 
       k[1]=-1;    nrerror("Too many iterations in brent"); 
       printf("Max: %.12e",(*func)(p));    *xmin=x; 
       fprintf(ficlog,"Max: %.12e",(*func)(p));    return fx; 
       for (j=1;j<=n;j++) {  } 
         printf(" %.12e",p[j]);  
         fprintf(ficlog," %.12e",p[j]);  /****************** mnbrak ***********************/
       }  
       printf("\n");  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       fprintf(ficlog,"\n");              double (*func)(double)) 
       for(l=0;l<=1;l++) {  { 
         for (j=1;j<=n;j++) {    double ulim,u,r,q, dum;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    double fu; 
           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]);    *fa=(*func)(*ax); 
         }    *fb=(*func)(*bx); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    if (*fb > *fa) { 
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));      SHFT(dum,*ax,*bx,dum) 
       }        SHFT(dum,*fb,*fa,dum) 
 #endif        } 
     *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
       free_vector(xit,1,n);    while (*fb > *fc) { 
       free_vector(xits,1,n);      r=(*bx-*ax)*(*fb-*fc); 
       free_vector(ptt,1,n);      q=(*bx-*cx)*(*fb-*fa); 
       free_vector(pt,1,n);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       return;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     }      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");      if ((*bx-u)*(u-*cx) > 0.0) { 
     for (j=1;j<=n;j++) {        fu=(*func)(u); 
       ptt[j]=2.0*p[j]-pt[j];      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       xit[j]=p[j]-pt[j];        fu=(*func)(u); 
       pt[j]=p[j];        if (fu < *fc) { 
     }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     fptt=(*func)(ptt);            SHFT(*fb,*fc,fu,(*func)(u)) 
     if (fptt < fp) {            } 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       if (t < 0.0) {        u=ulim; 
         linmin(p,xit,n,fret,func);        fu=(*func)(u); 
         for (j=1;j<=n;j++) {      } else { 
           xi[j][ibig]=xi[j][n];        u=(*cx)+GOLD*(*cx-*bx); 
           xi[j][n]=xit[j];        fu=(*func)(u); 
         }      } 
 #ifdef DEBUG      SHFT(*ax,*bx,*cx,u) 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        SHFT(*fa,*fb,*fc,fu) 
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        } 
         for(j=1;j<=n;j++){  } 
           printf(" %.12e",xit[j]);  
           fprintf(ficlog," %.12e",xit[j]);  /*************** linmin ************************/
         }  
         printf("\n");  int ncom; 
         fprintf(ficlog,"\n");  double *pcom,*xicom;
 #endif  double (*nrfunc)(double []); 
       }   
     }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   }  { 
 }    double brent(double ax, double bx, double cx, 
                  double (*f)(double), double tol, double *xmin); 
 /**** Prevalence limit ****************/    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)                double *fc, double (*func)(double)); 
 {    int j; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    double xx,xmin,bx,ax; 
      matrix by transitions matrix until convergence is reached */    double fx,fb,fa;
    
   int i, ii,j,k;    ncom=n; 
   double min, max, maxmin, maxmax,sumnew=0.;    pcom=vector(1,n); 
   double **matprod2();    xicom=vector(1,n); 
   double **out, cov[NCOVMAX], **pmij();    nrfunc=func; 
   double **newm;    for (j=1;j<=n;j++) { 
   double agefin, delaymax=50 ; /* Max number of years to converge */      pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
   for (ii=1;ii<=nlstate+ndeath;ii++)    } 
     for (j=1;j<=nlstate+ndeath;j++){    ax=0.0; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    xx=1.0; 
     }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
    cov[1]=1.;  #ifdef DEBUG
      printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  #endif
     newm=savm;    for (j=1;j<=n;j++) { 
     /* Covariates have to be included here again */      xi[j] *= xmin; 
      cov[2]=agefin;      p[j] += xi[j]; 
      } 
       for (k=1; k<=cptcovn;k++) {    free_vector(xicom,1,n); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    free_vector(pcom,1,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]]);*/  } 
       }  
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  char *asc_diff_time(long time_sec, char ascdiff[])
       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]]];    long sec_left, days, hours, minutes;
     days = (time_sec) / (60*60*24);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    sec_left = (time_sec) % (60*60*24);
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    hours = (sec_left) / (60*60) ;
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    sec_left = (sec_left) %(60*60);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    minutes = (sec_left) /60;
     sec_left = (sec_left) % (60);
     savm=oldm;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     oldm=newm;    return ascdiff;
     maxmax=0.;  }
     for(j=1;j<=nlstate;j++){  
       min=1.;  /*************** powell ************************/
       max=0.;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       for(i=1; i<=nlstate; i++) {              double (*func)(double [])) 
         sumnew=0;  { 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    void linmin(double p[], double xi[], int n, double *fret, 
         prlim[i][j]= newm[i][j]/(1-sumnew);                double (*func)(double [])); 
         max=FMAX(max,prlim[i][j]);    int i,ibig,j; 
         min=FMIN(min,prlim[i][j]);    double del,t,*pt,*ptt,*xit;
       }    double fp,fptt;
       maxmin=max-min;    double *xits;
       maxmax=FMAX(maxmax,maxmin);    int niterf, itmp;
     }  
     if(maxmax < ftolpl){    pt=vector(1,n); 
       return prlim;    ptt=vector(1,n); 
     }    xit=vector(1,n); 
   }    xits=vector(1,n); 
 }    *fret=(*func)(p); 
     for (j=1;j<=n;j++) pt[j]=p[j]; 
 /*************** transition probabilities ***************/    for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      ibig=0; 
 {      del=0.0; 
   double s1, s2;      last_time=curr_time;
   /*double t34;*/      (void) gettimeofday(&curr_time,&tzp);
   int i,j,j1, nc, ii, jj;      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);
     for(i=1; i<= nlstate; i++){      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
     for(j=1; j<i;j++){      for (i=1;i<=n;i++) {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        printf(" %d %.12f",i, p[i]);
         /*s2 += param[i][j][nc]*cov[nc];*/        fprintf(ficlog," %d %.12lf",i, p[i]);
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        fprintf(ficrespow," %.12lf", p[i]);
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      }
       }      printf("\n");
       ps[i][j]=s2;      fprintf(ficlog,"\n");
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      fprintf(ficrespow,"\n");fflush(ficrespow);
     }      if(*iter <=3){
     for(j=i+1; j<=nlstate+ndeath;j++){        tm = *localtime(&curr_time.tv_sec);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        strcpy(strcurr,asctime(&tmf));
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /*       asctime_r(&tm,strcurr); */
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        forecast_time=curr_time;
       }        itmp = strlen(strcurr);
       ps[i][j]=s2;        if(strcurr[itmp-1]=='\n')
     }          strcurr[itmp-1]='\0';
   }        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     /*ps[3][2]=1;*/        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         for(niterf=10;niterf<=30;niterf+=10){
   for(i=1; i<= nlstate; i++){          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
      s1=0;          tmf = *localtime(&forecast_time.tv_sec);
     for(j=1; j<i; j++)  /*      asctime_r(&tmf,strfor); */
       s1+=exp(ps[i][j]);          strcpy(strfor,asctime(&tmf));
     for(j=i+1; j<=nlstate+ndeath; j++)          itmp = strlen(strfor);
       s1+=exp(ps[i][j]);          if(strfor[itmp-1]=='\n')
     ps[i][i]=1./(s1+1.);          strfor[itmp-1]='\0';
     for(j=1; j<i; j++)          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);
       ps[i][j]= exp(ps[i][j])*ps[i][i];          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);
     for(j=i+1; j<=nlstate+ndeath; j++)        }
       ps[i][j]= exp(ps[i][j])*ps[i][i];      }
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      for (i=1;i<=n;i++) { 
   } /* end i */        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         fptt=(*fret); 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  #ifdef DEBUG
     for(jj=1; jj<= nlstate+ndeath; jj++){        printf("fret=%lf \n",*fret);
       ps[ii][jj]=0;        fprintf(ficlog,"fret=%lf \n",*fret);
       ps[ii][ii]=1;  #endif
     }        printf("%d",i);fflush(stdout);
   }        fprintf(ficlog,"%d",i);fflush(ficlog);
         linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){          del=fabs(fptt-(*fret)); 
     for(jj=1; jj<= nlstate+ndeath; jj++){          ibig=i; 
      printf("%lf ",ps[ii][jj]);        } 
    }  #ifdef DEBUG
     printf("\n ");        printf("%d %.12e",i,(*fret));
     }        fprintf(ficlog,"%d %.12e",i,(*fret));
     printf("\n ");printf("%lf ",cov[2]);*/        for (j=1;j<=n;j++) {
 /*          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          printf(" x(%d)=%.12e",j,xit[j]);
   goto end;*/          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     return ps;        }
 }        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
 /**************** Product of 2 matrices ******************/          fprintf(ficlog," p=%.12e",p[j]);
         }
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        printf("\n");
 {        fprintf(ficlog,"\n");
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  #endif
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      } 
   /* in, b, out are matrice of pointers which should have been initialized      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
      before: only the contents of out is modified. The function returns  #ifdef DEBUG
      a pointer to pointers identical to out */        int k[2],l;
   long i, j, k;        k[0]=1;
   for(i=nrl; i<= nrh; i++)        k[1]=-1;
     for(k=ncolol; k<=ncoloh; k++)        printf("Max: %.12e",(*func)(p));
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        fprintf(ficlog,"Max: %.12e",(*func)(p));
         out[i][k] +=in[i][j]*b[j][k];        for (j=1;j<=n;j++) {
           printf(" %.12e",p[j]);
   return out;          fprintf(ficlog," %.12e",p[j]);
 }        }
         printf("\n");
         fprintf(ficlog,"\n");
 /************* Higher Matrix Product ***************/        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )            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]);
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
      duration (i.e. until          }
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
      (typically every 2 years instead of every month which is too big).        }
      Model is determined by parameters x and covariates have to be  #endif
      included manually here.  
   
      */        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
   int i, j, d, h, k;        free_vector(ptt,1,n); 
   double **out, cov[NCOVMAX];        free_vector(pt,1,n); 
   double **newm;        return; 
       } 
   /* Hstepm could be zero and should return the unit matrix */      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   for (i=1;i<=nlstate+ndeath;i++)      for (j=1;j<=n;j++) { 
     for (j=1;j<=nlstate+ndeath;j++){        ptt[j]=2.0*p[j]-pt[j]; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);        xit[j]=p[j]-pt[j]; 
       po[i][j][0]=(i==j ? 1.0 : 0.0);        pt[j]=p[j]; 
     }      } 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      fptt=(*func)(ptt); 
   for(h=1; h <=nhstepm; h++){      if (fptt < fp) { 
     for(d=1; d <=hstepm; d++){        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       newm=savm;        if (t < 0.0) { 
       /* Covariates have to be included here again */          linmin(p,xit,n,fret,func); 
       cov[1]=1.;          for (j=1;j<=n;j++) { 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;            xi[j][ibig]=xi[j][n]; 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];            xi[j][n]=xit[j]; 
       for (k=1; k<=cptcovage;k++)          }
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  #ifdef DEBUG
       for (k=1; k<=cptcovprod;k++)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/            fprintf(ficlog," %.12e",xit[j]);
       /*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,          printf("\n");
                    pmij(pmmij,cov,ncovmodel,x,nlstate));          fprintf(ficlog,"\n");
       savm=oldm;  #endif
       oldm=newm;        }
     }      } 
     for(i=1; i<=nlstate+ndeath; i++)    } 
       for(j=1;j<=nlstate+ndeath;j++) {  } 
         po[i][j][h]=newm[i][j];  
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  /**** Prevalence limit (stable prevalence)  ****************/
          */  
       }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   } /* end h */  {
   return po;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
 }       matrix by transitions matrix until convergence is reached */
   
     int i, ii,j,k;
 /*************** log-likelihood *************/    double min, max, maxmin, maxmax,sumnew=0.;
 double func( double *x)    double **matprod2();
 {    double **out, cov[NCOVMAX], **pmij();
   int i, ii, j, k, mi, d, kk;    double **newm;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    double agefin, delaymax=50 ; /* Max number of years to converge */
   double **out;  
   double sw; /* Sum of weights */    for (ii=1;ii<=nlstate+ndeath;ii++)
   double lli; /* Individual log likelihood */      for (j=1;j<=nlstate+ndeath;j++){
   long ipmx;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /*extern weight */      }
   /* We are differentiating ll according to initial status */  
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/     cov[1]=1.;
   /*for(i=1;i<imx;i++)   
     printf(" %d\n",s[4][i]);   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   */    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   cov[1]=1.;      newm=savm;
       /* Covariates have to be included here again */
   for(k=1; k<=nlstate; k++) ll[k]=0.;       cov[2]=agefin;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        for (k=1; k<=cptcovn;k++) {
     for(mi=1; mi<= wav[i]-1; mi++){          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for (ii=1;ii<=nlstate+ndeath;ii++)          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        }
       for(d=0; d<dh[mi][i]; d++){        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         newm=savm;        for (k=1; k<=cptcovprod;k++)
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         for (kk=1; kk<=cptcovage;kk++) {  
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        /*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]);*/
                /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
         savm=oldm;      savm=oldm;
         oldm=newm;      oldm=newm;
              maxmax=0.;
              for(j=1;j<=nlstate;j++){
       } /* end mult */        min=1.;
              max=0.;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        for(i=1; i<=nlstate; i++) {
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/          sumnew=0;
       ipmx +=1;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       sw += weight[i];          prlim[i][j]= newm[i][j]/(1-sumnew);
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          max=FMAX(max,prlim[i][j]);
     } /* end of wave */          min=FMIN(min,prlim[i][j]);
   } /* end of individual */        }
         maxmin=max-min;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        maxmax=FMAX(maxmax,maxmin);
   /* 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(maxmax < ftolpl){
   return -l;        return prlim;
 }      }
     }
   }
 /*********** Maximum Likelihood Estimation ***************/  
   /*************** transition probabilities ***************/ 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   int i,j, iter;  {
   double **xi,*delti;    double s1, s2;
   double fret;    /*double t34;*/
   xi=matrix(1,npar,1,npar);    int i,j,j1, nc, ii, jj;
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)      for(i=1; i<= nlstate; i++){
       xi[i][j]=(i==j ? 1.0 : 0.0);      for(j=1; j<i;j++){
   printf("Powell\n");  fprintf(ficlog,"Powell\n");        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   powell(p,xi,npar,ftol,&iter,&fret,func);          /*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("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
   fprintf(ficlog,"#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));        ps[i][j]=s2;
         /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
 }      }
       for(j=i+1; j<=nlstate+ndeath;j++){
 /**** Computes Hessian and covariance matrix ***/        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          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);*/
   double  **a,**y,*x,pd;        }
   double **hess;        ps[i][j]=s2;
   int i, j,jk;      }
   int *indx;    }
       /*ps[3][2]=1;*/
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);    for(i=1; i<= nlstate; i++){
   void lubksb(double **a, int npar, int *indx, double b[]) ;       s1=0;
   void ludcmp(double **a, int npar, int *indx, double *d) ;      for(j=1; j<i; j++)
         s1+=exp(ps[i][j]);
   hess=matrix(1,npar,1,npar);      for(j=i+1; j<=nlstate+ndeath; j++)
         s1+=exp(ps[i][j]);
   printf("\nCalculation of the hessian matrix. Wait...\n");      ps[i][i]=1./(s1+1.);
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");      for(j=1; j<i; j++)
   for (i=1;i<=npar;i++){        ps[i][j]= exp(ps[i][j])*ps[i][i];
     printf("%d",i);fflush(stdout);      for(j=i+1; j<=nlstate+ndeath; j++)
     fprintf(ficlog,"%d",i);fflush(ficlog);        ps[i][j]= exp(ps[i][j])*ps[i][i];
     hess[i][i]=hessii(p,ftolhess,i,delti);      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     /*printf(" %f ",p[i]);*/    } /* end i */
     /*printf(" %lf ",hess[i][i]);*/  
   }    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
        for(jj=1; jj<= nlstate+ndeath; jj++){
   for (i=1;i<=npar;i++) {        ps[ii][jj]=0;
     for (j=1;j<=npar;j++)  {        ps[ii][ii]=1;
       if (j>i) {      }
         printf(".%d%d",i,j);fflush(stdout);    }
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);  
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];        /*   for(ii=1; ii<= nlstate+ndeath; ii++){
         /*printf(" %lf ",hess[i][j]);*/      for(jj=1; jj<= nlstate+ndeath; jj++){
       }       printf("%lf ",ps[ii][jj]);
     }     }
   }      printf("\n ");
   printf("\n");      }
   fprintf(ficlog,"\n");      printf("\n ");printf("%lf ",cov[2]);*/
   /*
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");    goto end;*/
        return ps;
   a=matrix(1,npar,1,npar);  }
   y=matrix(1,npar,1,npar);  
   x=vector(1,npar);  /**************** Product of 2 matrices ******************/
   indx=ivector(1,npar);  
   for (i=1;i<=npar;i++)  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  {
   ludcmp(a,npar,indx,&pd);    /* 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(...) */
   for (j=1;j<=npar;j++) {    /* in, b, out are matrice of pointers which should have been initialized 
     for (i=1;i<=npar;i++) x[i]=0;       before: only the contents of out is modified. The function returns
     x[j]=1;       a pointer to pointers identical to out */
     lubksb(a,npar,indx,x);    long i, j, k;
     for (i=1;i<=npar;i++){    for(i=nrl; i<= nrh; i++)
       matcov[i][j]=x[i];      for(k=ncolol; k<=ncoloh; k++)
     }        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   }          out[i][k] +=in[i][j]*b[j][k];
   
   printf("\n#Hessian matrix#\n");    return out;
   fprintf(ficlog,"\n#Hessian matrix#\n");  }
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);  /************* Higher Matrix Product ***************/
       fprintf(ficlog,"%.3e ",hess[i][j]);  
     }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     printf("\n");  {
     fprintf(ficlog,"\n");    /* Computes the transition matrix starting at age 'age' over 
   }       'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   /* Recompute Inverse */       nhstepm*hstepm matrices. 
   for (i=1;i<=npar;i++)       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];       (typically every 2 years instead of every month which is too big 
   ludcmp(a,npar,indx,&pd);       for the memory).
        Model is determined by parameters x and covariates have to be 
   /*  printf("\n#Hessian matrix recomputed#\n");       included manually here. 
   
   for (j=1;j<=npar;j++) {       */
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;    int i, j, d, h, k;
     lubksb(a,npar,indx,x);    double **out, cov[NCOVMAX];
     for (i=1;i<=npar;i++){    double **newm;
       y[i][j]=x[i];  
       printf("%.3e ",y[i][j]);    /* Hstepm could be zero and should return the unit matrix */
       fprintf(ficlog,"%.3e ",y[i][j]);    for (i=1;i<=nlstate+ndeath;i++)
     }      for (j=1;j<=nlstate+ndeath;j++){
     printf("\n");        oldm[i][j]=(i==j ? 1.0 : 0.0);
     fprintf(ficlog,"\n");        po[i][j][0]=(i==j ? 1.0 : 0.0);
   }      }
   */    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=1; h <=nhstepm; h++){
   free_matrix(a,1,npar,1,npar);      for(d=1; d <=hstepm; d++){
   free_matrix(y,1,npar,1,npar);        newm=savm;
   free_vector(x,1,npar);        /* Covariates have to be included here again */
   free_ivector(indx,1,npar);        cov[1]=1.;
   free_matrix(hess,1,npar,1,npar);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
 }          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
 /*************** hessian matrix ****************/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 double hessii( double x[], double delta, int theta, double delti[])  
 {  
   int i;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   int l=1, lmax=20;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   double k1,k2;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   double p2[NPARMAX+1];                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   double res;        savm=oldm;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        oldm=newm;
   double fx;      }
   int k=0,kmax=10;      for(i=1; i<=nlstate+ndeath; i++)
   double l1;        for(j=1;j<=nlstate+ndeath;j++) {
           po[i][j][h]=newm[i][j];
   fx=func(x);          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   for (i=1;i<=npar;i++) p2[i]=x[i];           */
   for(l=0 ; l <=lmax; l++){        }
     l1=pow(10,l);    } /* end h */
     delts=delt;    return po;
     for(k=1 ; k <kmax; k=k+1){  }
       delt = delta*(l1*k);  
       p2[theta]=x[theta] +delt;  
       k1=func(p2)-fx;  /*************** log-likelihood *************/
       p2[theta]=x[theta]-delt;  double func( double *x)
       k2=func(p2)-fx;  {
       /*res= (k1-2.0*fx+k2)/delt/delt; */    int i, ii, j, k, mi, d, kk;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    double l, ll[NLSTATEMAX], cov[NCOVMAX];
          double **out;
 #ifdef DEBUG    double sw; /* Sum of weights */
       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);    double lli; /* Individual log likelihood */
       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);    int s1, s2;
 #endif    double bbh, survp;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    long ipmx;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    /*extern weight */
         k=kmax;    /* We are differentiating ll according to initial status */
       }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    /*for(i=1;i<imx;i++) 
         k=kmax; l=lmax*10.;      printf(" %d\n",s[4][i]);
       }    */
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    cov[1]=1.;
         delts=delt;  
       }    for(k=1; k<=nlstate; k++) ll[k]=0.;
     }  
   }    if(mle==1){
   delti[theta]=delts;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   return res;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
 }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
 double hessij( double x[], double delti[], int thetai,int thetaj)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i;            }
   int l=1, l1, lmax=20;          for(d=0; d<dh[mi][i]; d++){
   double k1,k2,k3,k4,res,fx;            newm=savm;
   double p2[NPARMAX+1];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int k;            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   fx=func(x);            }
   for (k=1; k<=2; k++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for (i=1;i<=npar;i++) p2[i]=x[i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     p2[thetai]=x[thetai]+delti[thetai]/k;            savm=oldm;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            oldm=newm;
     k1=func(p2)-fx;          } /* end mult */
          
     p2[thetai]=x[thetai]+delti[thetai]/k;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          /* But now since version 0.9 we anticipate for bias and large stepm.
     k2=func(p2)-fx;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
             * (in months) between two waves is not a multiple of stepm, we rounded to 
     p2[thetai]=x[thetai]-delti[thetai]/k;           * the nearest (and in case of equal distance, to the lowest) interval but now
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     k3=func(p2)-fx;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
             * probability in order to take into account the bias as a fraction of the way
     p2[thetai]=x[thetai]-delti[thetai]/k;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * -stepm/2 to stepm/2 .
     k4=func(p2)-fx;           * For stepm=1 the results are the same as for previous versions of Imach.
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */           * For stepm > 1 the results are less biased than in previous versions. 
 #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);          s1=s[mw[mi][i]][i];
     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);          s2=s[mw[mi+1][i]][i];
 #endif          bbh=(double)bh[mi][i]/(double)stepm; 
   }          /* bias is positive if real duration
   return res;           * is higher than the multiple of stepm and negative otherwise.
 }           */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 /************** Inverse of matrix **************/          if( s2 > nlstate){ 
 void ludcmp(double **a, int n, int *indx, double *d)            /* i.e. if s2 is a death state and if the date of death is known then the contribution
 {               to the likelihood is the probability to die between last step unit time and current 
   int i,imax,j,k;               step unit time, which is also the differences between probability to die before dh 
   double big,dum,sum,temp;               and probability to die before dh-stepm . 
   double *vv;               In version up to 0.92 likelihood was computed
            as if date of death was unknown. Death was treated as any other
   vv=vector(1,n);          health state: the date of the interview describes the actual state
   *d=1.0;          and not the date of a change in health state. The former idea was
   for (i=1;i<=n;i++) {          to consider that at each interview the state was recorded
     big=0.0;          (healthy, disable or death) and IMaCh was corrected; but when we
     for (j=1;j<=n;j++)          introduced the exact date of death then we should have modified
       if ((temp=fabs(a[i][j])) > big) big=temp;          the contribution of an exact death to the likelihood. This new
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          contribution is smaller and very dependent of the step unit
     vv[i]=1.0/big;          stepm. It is no more the probability to die between last interview
   }          and month of death but the probability to survive from last
   for (j=1;j<=n;j++) {          interview up to one month before death multiplied by the
     for (i=1;i<j;i++) {          probability to die within a month. Thanks to Chris
       sum=a[i][j];          Jackson for correcting this bug.  Former versions increased
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          mortality artificially. The bad side is that we add another loop
       a[i][j]=sum;          which slows down the processing. The difference can be up to 10%
     }          lower mortality.
     big=0.0;            */
     for (i=j;i<=n;i++) {            lli=log(out[s1][s2] - savm[s1][s2]);
       sum=a[i][j];          }else{
       for (k=1;k<j;k++)            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         sum -= a[i][k]*a[k][j];            /*  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 */
       a[i][j]=sum;          } 
       if ( (dum=vv[i]*fabs(sum)) >= big) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         big=dum;          /*if(lli ==000.0)*/
         imax=i;          /*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];
     if (j != imax) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for (k=1;k<=n;k++) {        } /* end of wave */
         dum=a[imax][k];      } /* end of individual */
         a[imax][k]=a[j][k];    }  else if(mle==2){
         a[j][k]=dum;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       *d = -(*d);        for(mi=1; mi<= wav[i]-1; mi++){
       vv[imax]=vv[j];          for (ii=1;ii<=nlstate+ndeath;ii++)
     }            for (j=1;j<=nlstate+ndeath;j++){
     indx[j]=imax;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (a[j][j] == 0.0) a[j][j]=TINY;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (j != n) {            }
       dum=1.0/(a[j][j]);          for(d=0; d<=dh[mi][i]; d++){
       for (i=j+1;i<=n;i++) a[i][j] *= dum;            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   }            for (kk=1; kk<=cptcovage;kk++) {
   free_vector(vv,1,n);  /* Doesn't work */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 ;            }
 }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 void lubksb(double **a, int n, int *indx, double b[])            savm=oldm;
 {            oldm=newm;
   int i,ii=0,ip,j;          } /* end mult */
   double sum;        
            /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   for (i=1;i<=n;i++) {          /* But now since version 0.9 we anticipate for bias and large stepm.
     ip=indx[i];           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     sum=b[ip];           * (in months) between two waves is not a multiple of stepm, we rounded to 
     b[ip]=b[i];           * the nearest (and in case of equal distance, to the lowest) interval but now
     if (ii)           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     else if (sum) ii=i;           * probability in order to take into account the bias as a fraction of the way
     b[i]=sum;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   }           * -stepm/2 to stepm/2 .
   for (i=n;i>=1;i--) {           * For stepm=1 the results are the same as for previous versions of Imach.
     sum=b[i];           * For stepm > 1 the results are less biased than in previous versions. 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];           */
     b[i]=sum/a[i][i];          s1=s[mw[mi][i]][i];
   }          s2=s[mw[mi+1][i]][i];
 }          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias is positive if real duration
 /************ Frequencies ********************/           * is higher than the multiple of stepm and negative otherwise.
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)           */
 {  /* Some frequencies */          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
            /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
   int first;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double ***freq; /* Frequencies */          /*if(lli ==000.0)*/
   double *pp;          /*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); */
   double pos, k2, dateintsum=0,k2cpt=0;          ipmx +=1;
   FILE *ficresp;          sw += weight[i];
   char fileresp[FILENAMELENGTH];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
   pp=vector(1,nlstate);      } /* end of individual */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    }  else if(mle==3){  /* exponential inter-extrapolation */
   strcpy(fileresp,"p");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   strcat(fileresp,fileres);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   if((ficresp=fopen(fileresp,"w"))==NULL) {        for(mi=1; mi<= wav[i]-1; mi++){
     printf("Problem with prevalence resultfile: %s\n", fileresp);          for (ii=1;ii<=nlstate+ndeath;ii++)
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);            for (j=1;j<=nlstate+ndeath;j++){
     exit(0);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            }
   j1=0;          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
   j=cptcoveff;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   first=1;            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for(k1=1; k1<=j;k1++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(i1=1; i1<=ncodemax[k1];i1++){            savm=oldm;
       j1++;            oldm=newm;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          } /* end mult */
         scanf("%d", i);*/        
       for (i=-1; i<=nlstate+ndeath; i++)            /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         for (jk=-1; jk<=nlstate+ndeath; jk++)            /* But now since version 0.9 we anticipate for bias and large stepm.
           for(m=agemin; m <= agemax+3; m++)           * If stepm is larger than one month (smallest stepm) and if the exact delay 
             freq[i][jk][m]=0;           * (in months) between two waves is not a multiple of stepm, we rounded to 
                 * the nearest (and in case of equal distance, to the lowest) interval but now
       dateintsum=0;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       k2cpt=0;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
       for (i=1; i<=imx; i++) {           * probability in order to take into account the bias as a fraction of the way
         bool=1;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
         if  (cptcovn>0) {           * -stepm/2 to stepm/2 .
           for (z1=1; z1<=cptcoveff; z1++)           * For stepm=1 the results are the same as for previous versions of Imach.
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])           * For stepm > 1 the results are less biased than in previous versions. 
               bool=0;           */
         }          s1=s[mw[mi][i]][i];
         if (bool==1) {          s2=s[mw[mi+1][i]][i];
           for(m=firstpass; m<=lastpass; m++){          bbh=(double)bh[mi][i]/(double)stepm; 
             k2=anint[m][i]+(mint[m][i]/12.);          /* bias is positive if real duration
             if ((k2>=dateprev1) && (k2<=dateprev2)) {           * is higher than the multiple of stepm and negative otherwise.
               if(agev[m][i]==0) agev[m][i]=agemax+1;           */
               if(agev[m][i]==1) agev[m][i]=agemax+2;          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
               if (m<lastpass) {          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 */
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          /*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;
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          sw += weight[i];
                 dateintsum=dateintsum+k2;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                 k2cpt++;        } /* end of wave */
               }      } /* end of individual */
             }    }else if (mle==4){  /* ml=4 no inter-extrapolation */
           }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       }        for(mi=1; mi<= wav[i]-1; mi++){
                  for (ii=1;ii<=nlstate+ndeath;ii++)
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       if  (cptcovn>0) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficresp, "\n#********** Variable ");            }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          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=1; i<=nlstate;i++)            for (kk=1; kk<=cptcovage;kk++) {
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       fprintf(ficresp, "\n");            }
                
       for(i=(int)agemin; i <= (int)agemax+3; i++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         if(i==(int)agemax+3){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           fprintf(ficlog,"Total");            savm=oldm;
         }else{            oldm=newm;
           if(first==1){          } /* end mult */
             first=0;        
             printf("See log file for details...\n");          s1=s[mw[mi][i]][i];
           }          s2=s[mw[mi+1][i]][i];
           fprintf(ficlog,"Age %d", i);          if( s2 > nlstate){ 
         }            lli=log(out[s1][s2] - savm[s1][s2]);
         for(jk=1; jk <=nlstate ; jk++){          }else{
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
             pp[jk] += freq[jk][m][i];          }
         }          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]); */
           if(pp[jk]>=1.e-10){        } /* end of wave */
             if(first==1){      } /* end of individual */
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
             }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           }else{        for(mi=1; mi<= wav[i]-1; mi++){
             if(first==1)          for (ii=1;ii<=nlstate+ndeath;ii++)
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            for (j=1;j<=nlstate+ndeath;j++){
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            }
           for(d=0; d<dh[mi][i]; d++){
         for(jk=1; jk <=nlstate ; jk++){            newm=savm;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             pp[jk] += freq[jk][m][i];            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
         for(jk=1,pos=0; jk <=nlstate ; jk++)          
           pos += pp[jk];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for(jk=1; jk <=nlstate ; jk++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           if(pos>=1.e-5){            savm=oldm;
             if(first==1)            oldm=newm;
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          } /* end mult */
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        
           }else{          s1=s[mw[mi][i]][i];
             if(first==1)          s2=s[mw[mi+1][i]][i];
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          ipmx +=1;
           }          sw += weight[i];
           if( i <= (int) agemax){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             if(pos>=1.e-5){          /*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]);*/
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        } /* end of wave */
               probs[i][jk][j1]= pp[jk]/pos;      } /* end of individual */
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    } /* End of if */
             }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
             else    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           }    return -l;
         }  }
          
         for(jk=-1; jk <=nlstate+ndeath; jk++)  /*************** log-likelihood *************/
           for(m=-1; m <=nlstate+ndeath; m++)  double funcone( double *x)
             if(freq[jk][m][i] !=0 ) {  {
             if(first==1)    /* Same as likeli but slower because of a lot of printf and if */
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    int i, ii, j, k, mi, d, kk;
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
             }    double **out;
         if(i <= (int) agemax)    double lli; /* Individual log likelihood */
           fprintf(ficresp,"\n");    double llt;
         if(first==1)    int s1, s2;
           printf("Others in log...\n");    double bbh, survp;
         fprintf(ficlog,"\n");    /*extern weight */
       }    /* We are differentiating ll according to initial status */
     }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   }    /*for(i=1;i<imx;i++) 
   dateintmean=dateintsum/k2cpt;      printf(" %d\n",s[4][i]);
      */
   fclose(ficresp);    cov[1]=1.;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);    for(k=1; k<=nlstate; k++) ll[k]=0.;
    
   /* End of Freq */    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 }      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
 /************ Prevalence ********************/        for (ii=1;ii<=nlstate+ndeath;ii++)
 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)          for (j=1;j<=nlstate+ndeath;j++){
 {  /* Some frequencies */            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          }
   double ***freq; /* Frequencies */        for(d=0; d<dh[mi][i]; d++){
   double *pp;          newm=savm;
   double pos, k2;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {
   pp=vector(1,nlstate);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   j1=0;          savm=oldm;
            oldm=newm;
   j=cptcoveff;        } /* end mult */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        
          s1=s[mw[mi][i]][i];
   for(k1=1; k1<=j;k1++){        s2=s[mw[mi+1][i]][i];
     for(i1=1; i1<=ncodemax[k1];i1++){        bbh=(double)bh[mi][i]/(double)stepm; 
       j1++;        /* bias is positive if real duration
               * is higher than the multiple of stepm and negative otherwise.
       for (i=-1; i<=nlstate+ndeath; i++)           */
         for (jk=-1; jk<=nlstate+ndeath; jk++)          if( s2 > nlstate && (mle <5) ){  /* Jackson */
           for(m=agemin; m <= agemax+3; m++)          lli=log(out[s1][s2] - savm[s1][s2]);
             freq[i][jk][m]=0;        } else if (mle==1){
                lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       for (i=1; i<=imx; i++) {        } else if(mle==2){
         bool=1;          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  (cptcovn>0) {        } else if(mle==3){  /* exponential inter-extrapolation */
           for (z1=1; z1<=cptcoveff; z1++)          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 */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        } else if (mle==4){  /* mle=4 no inter-extrapolation */
               bool=0;          lli=log(out[s1][s2]); /* Original formula */
         }        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
         if (bool==1) {          lli=log(out[s1][s2]); /* Original formula */
           for(m=firstpass; m<=lastpass; m++){        } /* End of if */
             k2=anint[m][i]+(mint[m][i]/12.);        ipmx +=1;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        sw += weight[i];
               if(agev[m][i]==0) agev[m][i]=agemax+1;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
               if(agev[m][i]==1) agev[m][i]=agemax+2;  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
               if (m<lastpass) {        if(globpr){
                 if (calagedate>0)          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];   %10.6f %10.6f %10.6f ", \
                 else                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
               }            llt +=ll[k]*gipmx/gsw;
             }            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }          }
         }          fprintf(ficresilk," %10.6f\n", -llt);
       }        }
       for(i=(int)agemin; i <= (int)agemax+3; i++){      } /* end of wave */
         for(jk=1; jk <=nlstate ; jk++){    } /* end of individual */
           for(m=-1, 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 */
         for(jk=1; jk <=nlstate ; jk++){    if(globpr==0){ /* First time we count the contributions and weights */
           for(m=-1, pos=0; m <=0 ; m++)      gipmx=ipmx;
             pos += freq[jk][m][i];      gsw=sw;
         }    }
            return -l;
         for(jk=1; jk <=nlstate ; jk++){  }
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
             pp[jk] += freq[jk][m][i];  char *subdirf(char fileres[])
         }  {
            /* Caution optionfilefiname is hidden */
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    strcpy(tmpout,optionfilefiname);
            strcat(tmpout,"/"); /* Add to the right */
         for(jk=1; jk <=nlstate ; jk++){        strcat(tmpout,fileres);
           if( i <= (int) agemax){    return tmpout;
             if(pos>=1.e-5){  }
               probs[i][jk][j1]= pp[jk]/pos;  
             }  char *subdirf2(char fileres[], char *preop)
           }  {
         }/* end jk */    
       }/* end i */    strcpy(tmpout,optionfilefiname);
     } /* end i1 */    strcat(tmpout,"/");
   } /* end k1 */    strcat(tmpout,preop);
     strcat(tmpout,fileres);
      return tmpout;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  }
   free_vector(pp,1,nlstate);  char *subdirf3(char fileres[], char *preop, char *preop2)
    {
 }  /* End of Freq */    
     strcpy(tmpout,optionfilefiname);
 /************* Waves Concatenation ***************/    strcat(tmpout,"/");
     strcat(tmpout,preop);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    strcat(tmpout,preop2);
 {    strcat(tmpout,fileres);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    return tmpout;
      Death is a valid wave (if date is known).  }
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
      and mw[mi+1][i]. dh depends on stepm.  {
      */    /* This routine should help understanding what is done with 
        the selection of individuals/waves and
   int i, mi, m;       to check the exact contribution to the likelihood.
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;       Plotting could be done.
      double sum=0., jmean=0.;*/     */
   int first;    int k;
   int j, k=0,jk, ju, jl;  
   double sum=0.;    if(*globpri !=0){ /* Just counts and sums, no printings */
   first=0;      strcpy(fileresilk,"ilk"); 
   jmin=1e+5;      strcat(fileresilk,fileres);
   jmax=-1;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   jmean=0.;        printf("Problem with resultfile: %s\n", fileresilk);
   for(i=1; i<=imx; i++){        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     mi=0;      }
     m=firstpass;      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");
     while(s[m][i] <= nlstate){      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       if(s[m][i]>=1)      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
         mw[++mi][i]=m;      for(k=1; k<=nlstate; k++) 
       if(m >=lastpass)        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
         break;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       else    }
         m++;  
     }/* end while */    *fretone=(*funcone)(p);
     if (s[m][i] > nlstate){    if(*globpri !=0){
       mi++;     /* Death is another wave */      fclose(ficresilk);
       /* if(mi==0)  never been interviewed correctly before death */      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
          /* Only death is a correct wave */      fflush(fichtm); 
       mw[mi][i]=m;    } 
     }    return;
   }
     wav[i]=mi;  
     if(mi==0){  
       if(first==0){  /*********** Maximum Likelihood Estimation ***************/
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);  
         first=1;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       }  {
       if(first==1){    int i,j, iter;
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);    double **xi;
       }    double fret;
     } /* end mi==0 */    double fretone; /* Only one call to likelihood */
   }    char filerespow[FILENAMELENGTH];
     xi=matrix(1,npar,1,npar);
   for(i=1; i<=imx; i++){    for (i=1;i<=npar;i++)
     for(mi=1; mi<wav[i];mi++){      for (j=1;j<=npar;j++)
       if (stepm <=0)        xi[i][j]=(i==j ? 1.0 : 0.0);
         dh[mi][i]=1;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       else{    strcpy(filerespow,"pow"); 
         if (s[mw[mi+1][i]][i] > nlstate) {    strcat(filerespow,fileres);
           if (agedc[i] < 2*AGESUP) {    if((ficrespow=fopen(filerespow,"w"))==NULL) {
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      printf("Problem with resultfile: %s\n", filerespow);
           if(j==0) j=1;  /* Survives at least one month after exam */      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
           k=k+1;    }
           if (j >= jmax) jmax=j;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
           if (j <= jmin) jmin=j;    for (i=1;i<=nlstate;i++)
           sum=sum+j;      for(j=1;j<=nlstate+ndeath;j++)
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
           }    fprintf(ficrespow,"\n");
         }  
         else{    powell(p,xi,npar,ftol,&iter,&fret,func);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  
           k=k+1;    fclose(ficrespow);
           if (j >= jmax) jmax=j;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
           else if (j <= jmin)jmin=j;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           sum=sum+j;  
         }  }
         jk= j/stepm;  
         jl= j -jk*stepm;  /**** Computes Hessian and covariance matrix ***/
         ju= j -(jk+1)*stepm;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
         if(jl <= -ju)  {
           dh[mi][i]=jk;    double  **a,**y,*x,pd;
         else    double **hess;
           dh[mi][i]=jk+1;    int i, j,jk;
         if(dh[mi][i]==0)    int *indx;
           dh[mi][i]=1; /* At least one step */  
       }    double hessii(double p[], double delta, int theta, double delti[]);
     }    double hessij(double p[], double delti[], int i, int j);
   }    void lubksb(double **a, int npar, int *indx, double b[]) ;
   jmean=sum/k;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    hess=matrix(1,npar,1,npar);
  }  
     printf("\nCalculation of the hessian matrix. Wait...\n");
 /*********** Tricode ****************************/    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
 void tricode(int *Tvar, int **nbcode, int imx)    for (i=1;i<=npar;i++){
 {      printf("%d",i);fflush(stdout);
   int Ndum[20],ij=1, k, j, i;      fprintf(ficlog,"%d",i);fflush(ficlog);
   int cptcode=0;      hess[i][i]=hessii(p,ftolhess,i,delti);
   cptcoveff=0;      /*printf(" %f ",p[i]);*/
        /*printf(" %lf ",hess[i][i]);*/
   for (k=0; k<19; k++) Ndum[k]=0;    }
   for (k=1; k<=7; k++) ncodemax[k]=0;    
     for (i=1;i<=npar;i++) {
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      for (j=1;j<=npar;j++)  {
     for (i=1; i<=imx; i++) {        if (j>i) { 
       ij=(int)(covar[Tvar[j]][i]);          printf(".%d%d",i,j);fflush(stdout);
       Ndum[ij]++;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          hess[i][j]=hessij(p,delti,i,j);
       if (ij > cptcode) cptcode=ij;          hess[j][i]=hess[i][j];    
     }          /*printf(" %lf ",hess[i][j]);*/
         }
     for (i=0; i<=cptcode; i++) {      }
       if(Ndum[i]!=0) ncodemax[j]++;    }
     }    printf("\n");
     ij=1;    fprintf(ficlog,"\n");
   
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     for (i=1; i<=ncodemax[j]; i++) {    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       for (k=0; k<=19; k++) {    
         if (Ndum[k] != 0) {    a=matrix(1,npar,1,npar);
           nbcode[Tvar[j]][ij]=k;    y=matrix(1,npar,1,npar);
              x=vector(1,npar);
           ij++;    indx=ivector(1,npar);
         }    for (i=1;i<=npar;i++)
         if (ij > ncodemax[j]) break;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       }      ludcmp(a,npar,indx,&pd);
     }  
   }      for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
  for (k=0; k<19; k++) Ndum[k]=0;      x[j]=1;
       lubksb(a,npar,indx,x);
  for (i=1; i<=ncovmodel-2; i++) {      for (i=1;i<=npar;i++){ 
    ij=Tvar[i];        matcov[i][j]=x[i];
    Ndum[ij]++;      }
  }    }
   
  ij=1;    printf("\n#Hessian matrix#\n");
  for (i=1; i<=10; i++) {    fprintf(ficlog,"\n#Hessian matrix#\n");
    if((Ndum[i]!=0) && (i<=ncovcol)){    for (i=1;i<=npar;i++) { 
      Tvaraff[ij]=i;      for (j=1;j<=npar;j++) { 
      ij++;        printf("%.3e ",hess[i][j]);
    }        fprintf(ficlog,"%.3e ",hess[i][j]);
  }      }
        printf("\n");
  cptcoveff=ij-1;      fprintf(ficlog,"\n");
 }    }
   
 /*********** Health Expectancies ****************/    /* Recompute Inverse */
     for (i=1;i<=npar;i++)
 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 )      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
 {  
   /* Health expectancies */    /*  printf("\n#Hessian matrix recomputed#\n");
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;  
   double age, agelim, hf;    for (j=1;j<=npar;j++) {
   double ***p3mat,***varhe;      for (i=1;i<=npar;i++) x[i]=0;
   double **dnewm,**doldm;      x[j]=1;
   double *xp;      lubksb(a,npar,indx,x);
   double **gp, **gm;      for (i=1;i<=npar;i++){ 
   double ***gradg, ***trgradg;        y[i][j]=x[i];
   int theta;        printf("%.3e ",y[i][j]);
         fprintf(ficlog,"%.3e ",y[i][j]);
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);      }
   xp=vector(1,npar);      printf("\n");
   dnewm=matrix(1,nlstate*2,1,npar);      fprintf(ficlog,"\n");
   doldm=matrix(1,nlstate*2,1,nlstate*2);    }
      */
   fprintf(ficreseij,"# Health expectancies\n");  
   fprintf(ficreseij,"# Age");    free_matrix(a,1,npar,1,npar);
   for(i=1; i<=nlstate;i++)    free_matrix(y,1,npar,1,npar);
     for(j=1; j<=nlstate;j++)    free_vector(x,1,npar);
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    free_ivector(indx,1,npar);
   fprintf(ficreseij,"\n");    free_matrix(hess,1,npar,1,npar);
   
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);  }
   }  
   else  hstepm=estepm;    /*************** hessian matrix ****************/
   /* We compute the life expectancy from trapezoids spaced every estepm months  double hessii( double x[], double delta, int theta, double delti[])
    * 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    int i;
    * we are calculating an estimate of the Life Expectancy assuming a linear    int l=1, lmax=20;
    * progression inbetween and thus overestimating or underestimating according    double k1,k2;
    * to the curvature of the survival function. If, for the same date, we    double p2[NPARMAX+1];
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    double res;
    * to compare the new estimate of Life expectancy with the same linear    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
    * hypothesis. A more precise result, taking into account a more precise    double fx;
    * curvature will be obtained if estepm is as small as stepm. */    int k=0,kmax=10;
     double l1;
   /* For example we decided to compute the life expectancy with the smallest unit */  
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    fx=func(x);
      nhstepm is the number of hstepm from age to agelim    for (i=1;i<=npar;i++) p2[i]=x[i];
      nstepm is the number of stepm from age to agelin.    for(l=0 ; l <=lmax; l++){
      Look at hpijx to understand the reason of that which relies in memory size      l1=pow(10,l);
      and note for a fixed period like estepm months */      delts=delt;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      for(k=1 ; k <kmax; k=k+1){
      survival function given by stepm (the optimization length). Unfortunately it        delt = delta*(l1*k);
      means that if the survival funtion is printed only each two years of age and if        p2[theta]=x[theta] +delt;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        k1=func(p2)-fx;
      results. So we changed our mind and took the option of the best precision.        p2[theta]=x[theta]-delt;
   */        k2=func(p2)-fx;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   agelim=AGESUP;        
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  #ifdef DEBUG
     /* nhstepm age range expressed in number of stepm */        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);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);        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);
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */  #endif
     /* if (stepm >= YEARM) hstepm=1;*/        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          k=kmax;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);        }
     gp=matrix(0,nhstepm,1,nlstate*2);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     gm=matrix(0,nhstepm,1,nlstate*2);          k=kmax; l=lmax*10.;
         }
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          delts=delt;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          }
        }
     }
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    delti[theta]=delts;
     return res; 
     /* Computing Variances of health expectancies */    
   }
      for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){  double hessij( double x[], double delti[], int thetai,int thetaj)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  {
       }    int i;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      int l=1, l1, lmax=20;
      double k1,k2,k3,k4,res,fx;
       cptj=0;    double p2[NPARMAX+1];
       for(j=1; j<= nlstate; j++){    int k;
         for(i=1; i<=nlstate; i++){  
           cptj=cptj+1;    fx=func(x);
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    for (k=1; k<=2; k++) {
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      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;
          
            p2[thetai]=x[thetai]+delti[thetai]/k;
       for(i=1; i<=npar; i++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      k2=func(p2)-fx;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      
            p2[thetai]=x[thetai]-delti[thetai]/k;
       cptj=0;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       for(j=1; j<= nlstate; j++){      k3=func(p2)-fx;
         for(i=1;i<=nlstate;i++){    
           cptj=cptj+1;      p2[thetai]=x[thetai]-delti[thetai]/k;
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      k4=func(p2)-fx;
           }      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         }  #ifdef DEBUG
       }      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       for(j=1; j<= nlstate*2; j++)      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         for(h=0; h<=nhstepm-1; h++){  #endif
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    }
         }    return res;
      }  }
      
 /* End theta */  /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);  { 
     int i,imax,j,k; 
      for(h=0; h<=nhstepm-1; h++)    double big,dum,sum,temp; 
       for(j=1; j<=nlstate*2;j++)    double *vv; 
         for(theta=1; theta <=npar; theta++)   
           trgradg[h][j][theta]=gradg[h][theta][j];    vv=vector(1,n); 
          *d=1.0; 
     for (i=1;i<=n;i++) { 
      for(i=1;i<=nlstate*2;i++)      big=0.0; 
       for(j=1;j<=nlstate*2;j++)      for (j=1;j<=n;j++) 
         varhe[i][j][(int)age] =0.;        if ((temp=fabs(a[i][j])) > big) big=temp; 
       if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
      printf("%d|",(int)age);fflush(stdout);      vv[i]=1.0/big; 
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);    } 
      for(h=0;h<=nhstepm-1;h++){    for (j=1;j<=n;j++) { 
       for(k=0;k<=nhstepm-1;k++){      for (i=1;i<j;i++) { 
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);        sum=a[i][j]; 
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         for(i=1;i<=nlstate*2;i++)        a[i][j]=sum; 
           for(j=1;j<=nlstate*2;j++)      } 
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;      big=0.0; 
       }      for (i=j;i<=n;i++) { 
     }        sum=a[i][j]; 
     /* Computing expectancies */        for (k=1;k<j;k++) 
     for(i=1; i<=nlstate;i++)          sum -= a[i][k]*a[k][j]; 
       for(j=1; j<=nlstate;j++)        a[i][j]=sum; 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;          big=dum; 
                    imax=i; 
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/        } 
       } 
         }      if (j != imax) { 
         for (k=1;k<=n;k++) { 
     fprintf(ficreseij,"%3.0f",age );          dum=a[imax][k]; 
     cptj=0;          a[imax][k]=a[j][k]; 
     for(i=1; i<=nlstate;i++)          a[j][k]=dum; 
       for(j=1; j<=nlstate;j++){        } 
         cptj++;        *d = -(*d); 
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );        vv[imax]=vv[j]; 
       }      } 
     fprintf(ficreseij,"\n");      indx[j]=imax; 
          if (a[j][j] == 0.0) a[j][j]=TINY; 
     free_matrix(gm,0,nhstepm,1,nlstate*2);      if (j != n) { 
     free_matrix(gp,0,nhstepm,1,nlstate*2);        dum=1.0/(a[j][j]); 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);      } 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    } 
   }    free_vector(vv,1,n);  /* Doesn't work */
   printf("\n");  ;
   fprintf(ficlog,"\n");  } 
   
   free_vector(xp,1,npar);  void lubksb(double **a, int n, int *indx, double b[]) 
   free_matrix(dnewm,1,nlstate*2,1,npar);  { 
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);    int i,ii=0,ip,j; 
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);    double sum; 
 }   
     for (i=1;i<=n;i++) { 
 /************ Variance ******************/      ip=indx[i]; 
 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)      sum=b[ip]; 
 {      b[ip]=b[i]; 
   /* Variance of health expectancies */      if (ii) 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   /* double **newm;*/      else if (sum) ii=i; 
   double **dnewm,**doldm;      b[i]=sum; 
   double **dnewmp,**doldmp;    } 
   int i, j, nhstepm, hstepm, h, nstepm ;    for (i=n;i>=1;i--) { 
   int k, cptcode;      sum=b[i]; 
   double *xp;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   double **gp, **gm;  /* for var eij */      b[i]=sum/a[i][i]; 
   double ***gradg, ***trgradg; /*for var eij */    } 
   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 */  /************ Frequencies ********************/
   double ***p3mat;  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 age,agelim, hf;  {  /* Some frequencies */
   int theta;    
   char digit[4];    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   char digitp[16];    int first;
     double ***freq; /* Frequencies */
   char fileresprobmorprev[FILENAMELENGTH];    double *pp, **prop;
     double pos,posprop, k2, dateintsum=0,k2cpt=0;
   if(popbased==1)    FILE *ficresp;
     strcpy(digitp,"-populbased-");    char fileresp[FILENAMELENGTH];
   else    
     strcpy(digitp,"-stablbased-");    pp=vector(1,nlstate);
     prop=matrix(1,nlstate,iagemin,iagemax+3);
   strcpy(fileresprobmorprev,"prmorprev");    strcpy(fileresp,"p");
   sprintf(digit,"%-d",ij);    strcat(fileresp,fileres);
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/    if((ficresp=fopen(fileresp,"w"))==NULL) {
   strcat(fileresprobmorprev,digit); /* Tvar to be done */      printf("Problem with prevalence resultfile: %s\n", fileresp);
   strcat(fileresprobmorprev,digitp); /* Popbased or not */      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   strcat(fileresprobmorprev,fileres);      exit(0);
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {    }
     printf("Problem with resultfile: %s\n", fileresprobmorprev);    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);    j1=0;
   }    
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    j=cptcoveff;
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");  
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);    first=1;
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){  
     fprintf(ficresprobmorprev," p.%-d SE",j);    for(k1=1; k1<=j;k1++){
     for(i=1; i<=nlstate;i++)      for(i1=1; i1<=ncodemax[k1];i1++){
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);        j1++;
   }          /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   fprintf(ficresprobmorprev,"\n");          scanf("%d", i);*/
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {        for (i=-1; i<=nlstate+ndeath; i++)  
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);            for(m=iagemin; m <= iagemax+3; m++)
     exit(0);              freq[i][jk][m]=0;
   }  
   else{      for (i=1; i<=nlstate; i++)  
     fprintf(ficgp,"\n# Routine varevsij");        for(m=iagemin; m <= iagemax+3; m++)
   }          prop[i][m]=0;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {        
     printf("Problem with html file: %s\n", optionfilehtm);        dateintsum=0;
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);        k2cpt=0;
     exit(0);        for (i=1; i<=imx; i++) {
   }          bool=1;
   else{          if  (cptcovn>0) {
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");            for (z1=1; z1<=cptcoveff; z1++) 
   }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);                bool=0;
           }
   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");          if (bool==1){
   fprintf(ficresvij,"# Age");            for(m=firstpass; m<=lastpass; m++){
   for(i=1; i<=nlstate;i++)              k2=anint[m][i]+(mint[m][i]/12.);
     for(j=1; j<=nlstate;j++)              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   fprintf(ficresvij,"\n");                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];
   xp=vector(1,npar);                if (m<lastpass) {
   dnewm=matrix(1,nlstate,1,npar);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   doldm=matrix(1,nlstate,1,nlstate);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);                }
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);                  dateintsum=dateintsum+k2;
   gpp=vector(nlstate+1,nlstate+ndeath);                  k2cpt++;
   gmp=vector(nlstate+1,nlstate+ndeath);                }
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/                /*}*/
              }
   if(estepm < stepm){          }
     printf ("Problem %d lower than %d\n",estepm, stepm);        }
   }         
   else  hstepm=estepm;          /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   /* For example we decided to compute the life expectancy with the smallest unit */  
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        if  (cptcovn>0) {
      nhstepm is the number of hstepm from age to agelim          fprintf(ficresp, "\n#********** Variable "); 
      nstepm is the number of stepm from age to agelin.          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      Look at hpijx to understand the reason of that which relies in memory size          fprintf(ficresp, "**********\n#");
      and note for a fixed period like k years */        }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        for(i=1; i<=nlstate;i++) 
      survival function given by stepm (the optimization length). Unfortunately it          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
      means that if the survival funtion is printed only each two years of age and if        fprintf(ficresp, "\n");
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        
      results. So we changed our mind and took the option of the best precision.        for(i=iagemin; i <= iagemax+3; i++){
   */          if(i==iagemax+3){
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            fprintf(ficlog,"Total");
   agelim = AGESUP;          }else{
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            if(first==1){
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              first=0;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */              printf("See log file for details...\n");
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);            fprintf(ficlog,"Age %d", i);
     gp=matrix(0,nhstepm,1,nlstate);          }
     gm=matrix(0,nhstepm,1,nlstate);          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
     for(theta=1; theta <=npar; theta++){          }
       for(i=1; i<=npar; i++){ /* Computes gradient */          for(jk=1; jk <=nlstate ; jk++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            for(m=-1, pos=0; m <=0 ; m++)
       }              pos += freq[jk][m][i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              if(pp[jk]>=1.e-10){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       if (popbased==1) {              }
         for(i=1; i<=nlstate;i++)              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           prlim[i][i]=probs[(int)age][i][ij];            }else{
       }              if(first==1)
                  printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       for(j=1; j<= nlstate; j++){              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         for(h=0; h<=nhstepm; h++){            }
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          }
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }          for(jk=1; jk <=nlstate ; jk++){
       }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       /* This for computing forces of mortality (h=1)as a weighted average */              pp[jk] += freq[jk][m][i];
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){          }       
         for(i=1; i<= nlstate; i++)          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
           gpp[j] += prlim[i][i]*p3mat[i][j][1];            pos += pp[jk];
       }                posprop += prop[jk][i];
       /* end force of mortality */          }
           for(jk=1; jk <=nlstate ; jk++){
       for(i=1; i<=npar; i++) /* Computes gradient */            if(pos>=1.e-5){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              if(first==1)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                  printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
              }else{
       if (popbased==1) {              if(first==1)
         for(i=1; i<=nlstate;i++)                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           prlim[i][i]=probs[(int)age][i][ij];              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       }            }
             if( i <= iagemax){
       for(j=1; j<= nlstate; j++){              if(pos>=1.e-5){
         for(h=0; h<=nhstepm; h++){                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)                /*probs[i][jk][j1]= pp[jk]/pos;*/
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
         }              }
       }              else
       /* This for computing force of mortality (h=1)as a weighted average */                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){            }
         for(i=1; i<= nlstate; i++)          }
           gmp[j] += prlim[i][i]*p3mat[i][j][1];          
       }              for(jk=-1; jk <=nlstate+ndeath; jk++)
       /* end force of mortality */            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
       for(j=1; j<= nlstate; j++) /* vareij */              if(first==1)
         for(h=0; h<=nhstepm; h++){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
         }              }
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */          if(i <= iagemax)
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];            fprintf(ficresp,"\n");
       }          if(first==1)
             printf("Others in log...\n");
     } /* End theta */          fprintf(ficlog,"\n");
         }
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */      }
     }
     for(h=0; h<=nhstepm; h++) /* veij */    dateintmean=dateintsum/k2cpt; 
       for(j=1; j<=nlstate;j++)   
         for(theta=1; theta <=npar; theta++)    fclose(ficresp);
           trgradg[h][j][theta]=gradg[h][theta][j];    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       for(theta=1; theta <=npar; theta++)    /* End of Freq */
         trgradgp[j][theta]=gradgp[theta][j];  }
   
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  /************ Prevalence ********************/
     for(i=1;i<=nlstate;i++)  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)
       for(j=1;j<=nlstate;j++)  {  
         vareij[i][j][(int)age] =0.;    /* 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).
     for(h=0;h<=nhstepm;h++){       We still use firstpass and lastpass as another selection.
       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]);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
         for(i=1;i<=nlstate;i++)    double ***freq; /* Frequencies */
           for(j=1;j<=nlstate;j++)    double *pp, **prop;
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    double pos,posprop; 
       }    double  y2; /* in fractional years */
     }    int iagemin, iagemax;
   
     /* pptj */    iagemin= (int) agemin;
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);    iagemax= (int) agemax;
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);    /*pp=vector(1,nlstate);*/
     for(j=nlstate+1;j<=nlstate+ndeath;j++)    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       for(i=nlstate+1;i<=nlstate+ndeath;i++)    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
         varppt[j][i]=doldmp[j][i];    j1=0;
     /* end ppptj */    
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);      j=cptcoveff;
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      
     if (popbased==1) {    for(k1=1; k1<=j;k1++){
       for(i=1; i<=nlstate;i++)      for(i1=1; i1<=ncodemax[k1];i1++){
         prlim[i][i]=probs[(int)age][i][ij];        j1++;
     }        
            for (i=1; i<=nlstate; i++)  
     /* This for computing force of mortality (h=1)as a weighted average */          for(m=iagemin; m <= iagemax+3; m++)
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){            prop[i][m]=0.0;
       for(i=1; i<= nlstate; i++)       
         gmp[j] += prlim[i][i]*p3mat[i][j][1];        for (i=1; i<=imx; i++) { /* Each individual */
     }              bool=1;
     /* end force of mortality */          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){                bool=0;
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));          } 
       for(i=1; i<=nlstate;i++){          if (bool==1) { 
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       }              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     }              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     fprintf(ficresprobmorprev,"\n");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
     fprintf(ficresvij,"%.0f ",age );                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
     for(i=1; i<=nlstate;i++)                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       for(j=1; j<=nlstate;j++){                  /*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]]);*/
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       }                  prop[s[m][i]][iagemax+3] += weight[i]; 
     fprintf(ficresvij,"\n");                } 
     free_matrix(gp,0,nhstepm,1,nlstate);              }
     free_matrix(gm,0,nhstepm,1,nlstate);            } /* end selection of waves */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          }
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(i=iagemin; i <= iagemax+3; i++){  
   } /* End age */          
   free_vector(gpp,nlstate+1,nlstate+ndeath);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   free_vector(gmp,nlstate+1,nlstate+ndeath);            posprop += prop[jk][i]; 
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);          } 
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/  
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");          for(jk=1; jk <=nlstate ; jk++){     
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */            if( i <=  iagemax){ 
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");              if(posprop>=1.e-5){ 
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);                probs[i][jk][j1]= prop[jk][i]/posprop;
   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);            } 
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);          }/* end jk */ 
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);        }/* end i */ 
   /*  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);      } /* end i1 */
 */    } /* end k1 */
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);    
     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   free_vector(xp,1,npar);    /*free_vector(pp,1,nlstate);*/
   free_matrix(doldm,1,nlstate,1,nlstate);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   free_matrix(dnewm,1,nlstate,1,npar);  }  /* End of prevalence */
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);  
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);  /************* Waves Concatenation ***************/
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);  
   fclose(ficresprobmorprev);  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)
   fclose(ficgp);  {
   fclose(fichtm);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        Death is a valid wave (if date is known).
 }       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]
 /************ Variance of prevlim ******************/       and mw[mi+1][i]. dh depends on stepm.
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)       */
 {  
   /* Variance of prevalence limit */    int i, mi, m;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   double **newm;       double sum=0., jmean=0.;*/
   double **dnewm,**doldm;    int first;
   int i, j, nhstepm, hstepm;    int j, k=0,jk, ju, jl;
   int k, cptcode;    double sum=0.;
   double *xp;    first=0;
   double *gp, *gm;    jmin=1e+5;
   double **gradg, **trgradg;    jmax=-1;
   double age,agelim;    jmean=0.;
   int theta;    for(i=1; i<=imx; i++){
          mi=0;
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");      m=firstpass;
   fprintf(ficresvpl,"# Age");      while(s[m][i] <= nlstate){
   for(i=1; i<=nlstate;i++)        if(s[m][i]>=1)
       fprintf(ficresvpl," %1d-%1d",i,i);          mw[++mi][i]=m;
   fprintf(ficresvpl,"\n");        if(m >=lastpass)
           break;
   xp=vector(1,npar);        else
   dnewm=matrix(1,nlstate,1,npar);          m++;
   doldm=matrix(1,nlstate,1,nlstate);      }/* end while */
        if (s[m][i] > nlstate){
   hstepm=1*YEARM; /* Every year of age */        mi++;     /* Death is another wave */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        /* if(mi==0)  never been interviewed correctly before death */
   agelim = AGESUP;           /* Only death is a correct wave */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        mw[mi][i]=m;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      }
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      wav[i]=mi;
     gradg=matrix(1,npar,1,nlstate);      if(mi==0){
     gp=vector(1,nlstate);        nbwarn++;
     gm=vector(1,nlstate);        if(first==0){
           printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     for(theta=1; theta <=npar; theta++){          first=1;
       for(i=1; i<=npar; i++){ /* Computes gradient */        }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        if(first==1){
       }          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        }
       for(i=1;i<=nlstate;i++)      } /* end mi==0 */
         gp[i] = prlim[i][i];    } /* End individuals */
      
       for(i=1; i<=npar; i++) /* Computes gradient */    for(i=1; i<=imx; i++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for(mi=1; mi<wav[i];mi++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        if (stepm <=0)
       for(i=1;i<=nlstate;i++)          dh[mi][i]=1;
         gm[i] = prlim[i][i];        else{
           if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       for(i=1;i<=nlstate;i++)            if (agedc[i] < 2*AGESUP) {
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     } /* End theta */              if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
     trgradg =matrix(1,nlstate,1,npar);                nberr++;
                 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]);
     for(j=1; j<=nlstate;j++)                j=1; /* Temporary Dangerous patch */
       for(theta=1; theta <=npar; theta++)                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);
         trgradg[j][theta]=gradg[theta][j];                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);
     for(i=1;i<=nlstate;i++)              }
       varpl[i][(int)age] =0.;              k=k+1;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);              if (j >= jmax) jmax=j;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);              if (j <= jmin) jmin=j;
     for(i=1;i<=nlstate;i++)              sum=sum+j;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     fprintf(ficresvpl,"%.0f ",age );            }
     for(i=1; i<=nlstate;i++)          }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          else{
     fprintf(ficresvpl,"\n");            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     free_vector(gp,1,nlstate);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     free_vector(gm,1,nlstate);            k=k+1;
     free_matrix(gradg,1,npar,1,nlstate);            if (j >= jmax) jmax=j;
     free_matrix(trgradg,1,nlstate,1,npar);            else if (j <= jmin)jmin=j;
   } /* End age */            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
   free_vector(xp,1,npar);            if(j<0){
   free_matrix(doldm,1,nlstate,1,npar);              nberr++;
   free_matrix(dnewm,1,nlstate,1,nlstate);              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
 }            }
             sum=sum+j;
 /************ 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)          jk= j/stepm;
 {          jl= j -jk*stepm;
   int i, j=0,  i1, k1, l1, t, tj;          ju= j -(jk+1)*stepm;
   int k2, l2, j1,  z1;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   int k=0,l, cptcode;            if(jl==0){
   int first=1, first1;              dh[mi][i]=jk;
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;              bh[mi][i]=0;
   double **dnewm,**doldm;            }else{ /* We want a negative bias in order to only have interpolation ie
   double *xp;                    * at the price of an extra matrix product in likelihood */
   double *gp, *gm;              dh[mi][i]=jk+1;
   double **gradg, **trgradg;              bh[mi][i]=ju;
   double **mu;            }
   double age,agelim, cov[NCOVMAX];          }else{
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */            if(jl <= -ju){
   int theta;              dh[mi][i]=jk;
   char fileresprob[FILENAMELENGTH];              bh[mi][i]=jl;       /* bias is positive if real duration
   char fileresprobcov[FILENAMELENGTH];                                   * is higher than the multiple of stepm and negative otherwise.
   char fileresprobcor[FILENAMELENGTH];                                   */
             }
   double ***varpij;            else{
               dh[mi][i]=jk+1;
   strcpy(fileresprob,"prob");              bh[mi][i]=ju;
   strcat(fileresprob,fileres);            }
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {            if(dh[mi][i]==0){
     printf("Problem with resultfile: %s\n", fileresprob);              dh[mi][i]=1; /* At least one step */
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);              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);*/
   strcpy(fileresprobcov,"probcov");            }
   strcat(fileresprobcov,fileres);          } /* end if mle */
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {        }
     printf("Problem with resultfile: %s\n", fileresprobcov);      } /* end wave */
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);    }
   }    jmean=sum/k;
   strcpy(fileresprobcor,"probcor");    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   strcat(fileresprobcor,fileres);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {   }
     printf("Problem with resultfile: %s\n", fileresprobcor);  
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);  /*********** Tricode ****************************/
   }  void tricode(int *Tvar, int **nbcode, int imx)
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);  {
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    int Ndum[20],ij=1, k, j, i, maxncov=19;
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    int cptcode=0;
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    cptcoveff=0; 
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);   
      for (k=0; k<maxncov; k++) Ndum[k]=0;
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    for (k=1; k<=7; k++) ncodemax[k]=0;
   fprintf(ficresprob,"# Age");  
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   fprintf(ficresprobcov,"# Age");      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");                                 modality*/ 
   fprintf(ficresprobcov,"# Age");        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         Ndum[ij]++; /*store the modality */
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   for(i=1; i<=nlstate;i++)        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     for(j=1; j<=(nlstate+ndeath);j++){                                         Tvar[j]. If V=sex and male is 0 and 
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);                                         female is 1, then  cptcode=1.*/
       fprintf(ficresprobcov," p%1d-%1d ",i,j);      }
       fprintf(ficresprobcor," p%1d-%1d ",i,j);  
     }        for (i=0; i<=cptcode; i++) {
   fprintf(ficresprob,"\n");        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
   fprintf(ficresprobcov,"\n");      }
   fprintf(ficresprobcor,"\n");  
   xp=vector(1,npar);      ij=1; 
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);      for (i=1; i<=ncodemax[j]; i++) {
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));        for (k=0; k<= maxncov; k++) {
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);          if (Ndum[k] != 0) {
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);            nbcode[Tvar[j]][ij]=k; 
   first=1;            /* 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; */
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {            
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);            ij++;
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);          }
     exit(0);          if (ij > ncodemax[j]) break; 
   }        }  
   else{      } 
     fprintf(ficgp,"\n# Routine varprob");    }  
   }  
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {   for (k=0; k< maxncov; k++) Ndum[k]=0;
     printf("Problem with html file: %s\n", optionfilehtm);  
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);   for (i=1; i<=ncovmodel-2; i++) { 
     exit(0);     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   }     ij=Tvar[i];
   else{     Ndum[ij]++;
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");   }
     fprintf(fichtm,"\n");  
    ij=1;
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");   for (i=1; i<= maxncov; i++) {
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");     if((Ndum[i]!=0) && (i<=ncovcol)){
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");       Tvaraff[ij]=i; /*For printing */
        ij++;
   }     }
    }
     
   cov[1]=1;   cptcoveff=ij-1; /*Number of simple covariates*/
   tj=cptcoveff;  }
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}  
   j1=0;  /*********** Health Expectancies ****************/
   for(t=1; t<=tj;t++){  
     for(i1=1; i1<=ncodemax[t];i1++){  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 )
       j1++;  
        {
       if  (cptcovn>0) {    /* Health expectancies */
         fprintf(ficresprob, "\n#********** Variable ");    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double age, agelim, hf;
         fprintf(ficresprob, "**********\n#");    double ***p3mat,***varhe;
         fprintf(ficresprobcov, "\n#********** Variable ");    double **dnewm,**doldm;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double *xp;
         fprintf(ficresprobcov, "**********\n#");    double **gp, **gm;
            double ***gradg, ***trgradg;
         fprintf(ficgp, "\n#********** Variable ");    int theta;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficgp, "**********\n#");    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
            xp=vector(1,npar);
            dnewm=matrix(1,nlstate*nlstate,1,npar);
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
         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\">");    fprintf(ficreseij,"# Health expectancies\n");
            fprintf(ficreseij,"# Age");
         fprintf(ficresprobcor, "\n#********** Variable ");        for(i=1; i<=nlstate;i++)
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      for(j=1; j<=nlstate;j++)
         fprintf(ficgp, "**********\n#");            fprintf(ficreseij," %1d-%1d (SE)",i,j);
       }    fprintf(ficreseij,"\n");
        
       for (age=bage; age<=fage; age ++){    if(estepm < stepm){
         cov[2]=age;      printf ("Problem %d lower than %d\n",estepm, stepm);
         for (k=1; k<=cptcovn;k++) {    }
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    else  hstepm=estepm;   
         }    /* We compute the life expectancy from trapezoids spaced every estepm months
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];     * This is mainly to measure the difference between two models: for example
         for (k=1; k<=cptcovprod;k++)     * if stepm=24 months pijx are given only every 2 years and by summing them
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];     * we are calculating an estimate of the Life Expectancy assuming a linear 
             * progression in between and thus overestimating or underestimating according
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));     * to the curvature of the survival function. If, for the same date, we 
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         gp=vector(1,(nlstate)*(nlstate+ndeath));     * to compare the new estimate of Life expectancy with the same linear 
         gm=vector(1,(nlstate)*(nlstate+ndeath));     * hypothesis. A more precise result, taking into account a more precise
         * curvature will be obtained if estepm is as small as stepm. */
         for(theta=1; theta <=npar; theta++){  
           for(i=1; i<=npar; i++)    /* For example we decided to compute the life expectancy with the smallest unit */
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                 nhstepm is the number of hstepm from age to agelim 
           pmij(pmmij,cov,ncovmodel,xp,nlstate);       nstepm is the number of stepm from age to agelin. 
                 Look at hpijx to understand the reason of that which relies in memory size
           k=0;       and note for a fixed period like estepm months */
           for(i=1; i<= (nlstate); i++){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
             for(j=1; j<=(nlstate+ndeath);j++){       survival function given by stepm (the optimization length). Unfortunately it
               k=k+1;       means that if the survival funtion is printed only each two years of age and if
               gp[k]=pmmij[i][j];       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.
           }    */
              hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           for(i=1; i<=npar; i++)  
             xp[i] = x[i] - (i==theta ?delti[theta]:0);    agelim=AGESUP;
        for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      /* nhstepm age range expressed in number of stepm */
           k=0;      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
           for(i=1; i<=(nlstate); i++){      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
             for(j=1; j<=(nlstate+ndeath);j++){      /* if (stepm >= YEARM) hstepm=1;*/
               k=k+1;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
               gm[k]=pmmij[i][j];      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
           }      gp=matrix(0,nhstepm,1,nlstate*nlstate);
            gm=matrix(0,nhstepm,1,nlstate*nlstate);
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)  
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        /* 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(j=1; j<=(nlstate)*(nlstate+ndeath);j++)   
           for(theta=1; theta <=npar; theta++)  
             trgradg[j][theta]=gradg[theta][j];      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
          
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);      /* Computing Variances of health expectancies */
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);  
               for(theta=1; theta <=npar; theta++){
         pmij(pmmij,cov,ncovmodel,x,nlstate);        for(i=1; i<=npar; i++){ 
                  xp[i] = x[i] + (i==theta ?delti[theta]:0);
         k=0;        }
         for(i=1; i<=(nlstate); i++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           for(j=1; j<=(nlstate+ndeath);j++){    
             k=k+1;        cptj=0;
             mu[k][(int) age]=pmmij[i][j];        for(j=1; j<= nlstate; j++){
           }          for(i=1; i<=nlstate; i++){
         }            cptj=cptj+1;
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             varpij[i][j][(int)age] = doldm[i][j];            }
           }
         /*printf("\n%d ",(int)age);        }
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){       
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));       
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        for(i=1; i<=npar; i++) 
      }*/          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         fprintf(ficresprob,"\n%d ",(int)age);        
         fprintf(ficresprobcov,"\n%d ",(int)age);        cptj=0;
         fprintf(ficresprobcor,"\n%d ",(int)age);        for(j=1; j<= nlstate; j++){
           for(i=1;i<=nlstate;i++){
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)            cptj=cptj+1;
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){  
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);            }
         }          }
         i=0;        }
         for (k=1; k<=(nlstate);k++){        for(j=1; j<= nlstate*nlstate; j++)
           for (l=1; l<=(nlstate+ndeath);l++){          for(h=0; h<=nhstepm-1; h++){
             i=i++;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);          }
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);       } 
             for (j=1; j<=i;j++){     
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);  /* End theta */
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));  
             }       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
           }  
         }/* end of loop for state */       for(h=0; h<=nhstepm-1; h++)
       } /* end of loop for age */        for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
       /* Confidence intervalle of pij  */            trgradg[h][j][theta]=gradg[h][theta][j];
       /*       
       fprintf(ficgp,"\nset noparametric;unset label");  
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");       for(i=1;i<=nlstate*nlstate;i++)
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");        for(j=1;j<=nlstate*nlstate;j++)
       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);          varhe[i][j][(int)age] =0.;
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);  
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);       printf("%d|",(int)age);fflush(stdout);
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       */       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       first1=1;          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       for (k2=1; k2<=(nlstate);k2++){          for(i=1;i<=nlstate*nlstate;i++)
         for (l2=1; l2<=(nlstate+ndeath);l2++){            for(j=1;j<=nlstate*nlstate;j++)
           if(l2==k2) continue;              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
           j=(k2-1)*(nlstate+ndeath)+l2;        }
           for (k1=1; k1<=(nlstate);k1++){      }
             for (l1=1; l1<=(nlstate+ndeath);l1++){      /* Computing expectancies */
               if(l1==k1) continue;      for(i=1; i<=nlstate;i++)
               i=(k1-1)*(nlstate+ndeath)+l1;        for(j=1; j<=nlstate;j++)
               if(i<=j) continue;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
               for (age=bage; age<=fage; age ++){            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
                 if ((int)age %5==0){            
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;  /* 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]);*/
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;  
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;          }
                   mu1=mu[i][(int) age]/stepm*YEARM ;  
                   mu2=mu[j][(int) age]/stepm*YEARM;      fprintf(ficreseij,"%3.0f",age );
                   c12=cv12/sqrt(v1*v2);      cptj=0;
                   /* Computing eigen value of matrix of covariance */      for(i=1; i<=nlstate;i++)
                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;        for(j=1; j<=nlstate;j++){
                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;          cptj++;
                   /* Eigen vectors */          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));        }
                   /*v21=sqrt(1.-v11*v11); *//* error */      fprintf(ficreseij,"\n");
                   v21=(lc1-v1)/cv12*v11;     
                   v12=-v21;      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
                   v22=v11;      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
                   tnalp=v21/v11;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
                   if(first1==1){      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
                     first1=0;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                     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);    }
                   }    printf("\n");
                   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(ficlog,"\n");
                   /*printf(fignu*/  
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */    free_vector(xp,1,npar);
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
                   if(first==1){    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
                     first=0;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
                     fprintf(ficgp,"\nset parametric;unset label");  }
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);  
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");  /************ Variance ******************/
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);  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)
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);  {
                     fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);    /* Variance of health expectancies */
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);    /* double **newm;*/
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);    double **dnewm,**doldm;
                     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",\    double **dnewmp,**doldmp;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\    int i, j, nhstepm, hstepm, h, nstepm ;
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));    int k, cptcode;
                   }else{    double *xp;
                     first=0;    double **gp, **gm;  /* for var eij */
                     fprintf(fichtm," %d (%.3f),",(int) age, c12);    double ***gradg, ***trgradg; /*for var eij */
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);    double **gradgp, **trgradgp; /* for var p point j */
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);    double *gpp, *gmp; /* for var p point j */
                     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",\    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\    double ***p3mat;
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));    double age,agelim, hf;
                   }/* if first */    double ***mobaverage;
                 } /* age mod 5 */    int theta;
               } /* end loop age */    char digit[4];
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);    char digitp[25];
               first=1;  
             } /*l12 */    char fileresprobmorprev[FILENAMELENGTH];
           } /* k12 */  
         } /*l1 */    if(popbased==1){
       }/* k1 */      if(mobilav!=0)
     } /* loop covariates */        strcpy(digitp,"-populbased-mobilav-");
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);      else strcpy(digitp,"-populbased-nomobil-");
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    }
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    else 
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);      strcpy(digitp,"-stablbased-");
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    if (mobilav!=0) {
   }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_vector(xp,1,npar);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   fclose(ficresprob);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   fclose(ficresprobcov);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   fclose(ficresprobcor);      }
   fclose(ficgp);    }
   fclose(fichtm);  
 }    strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
 /******************* Printing html file ***********/    strcat(fileresprobmorprev,digit); /* Tvar to be done */
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
                   int lastpass, int stepm, int weightopt, char model[],\    strcat(fileresprobmorprev,fileres);
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
                   int popforecast, int estepm ,\      printf("Problem with resultfile: %s\n", fileresprobmorprev);
                   double jprev1, double mprev1,double anprev1, \      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
                   double jprev2, double mprev2,double anprev2){    }
   int jj1, k1, i1, cpt;    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   /*char optionfilehtm[FILENAMELENGTH];*/    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {    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);
     printf("Problem with %s \n",optionfilehtm), exit(0);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   }      fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n    }  
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    fprintf(ficresprobmorprev,"\n");
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n    fprintf(ficgp,"\n# Routine varevsij");
  - Life expectancies by age and initial health status (estepm=%2d months):    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");
    <a href=\"e%s\">e%s</a> <br>\n</li>", \    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);  /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");  
     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");
  m=cptcoveff;    fprintf(ficresvij,"# Age");
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
  jj1=0;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
  for(k1=1; k1<=m;k1++){    fprintf(ficresvij,"\n");
    for(i1=1; i1<=ncodemax[k1];i1++){  
      jj1++;    xp=vector(1,npar);
      if (cptcovn > 0) {    dnewm=matrix(1,nlstate,1,npar);
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    doldm=matrix(1,nlstate,1,nlstate);
        for (cpt=1; cpt<=cptcoveff;cpt++)    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  
      }    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
      /* Pij */    gpp=vector(nlstate+1,nlstate+ndeath);
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>    gmp=vector(nlstate+1,nlstate+ndeath);
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      /* Quasi-incidences */    
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>    if(estepm < stepm){
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      printf ("Problem %d lower than %d\n",estepm, stepm);
        /* Stable prevalence in each health state */    }
        for(cpt=1; cpt<nlstate;cpt++){    else  hstepm=estepm;   
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    /* For example we decided to compute the life expectancy with the smallest unit */
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        }       nhstepm is the number of hstepm from age to agelim 
      for(cpt=1; cpt<=nlstate;cpt++) {       nstepm is the number of stepm from age to agelin. 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>       Look at hpijx to understand the reason of that which relies in memory size
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);       and note for a fixed period like k years */
      }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
      fprintf(fichtm,"\n<br>- Total life expectancy by age and       survival function given by stepm (the optimization length). Unfortunately it
 health expectancies in states (1) and (2): e%s%d.png<br>       means that if the survival funtion is printed every two years of age and if
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
    } /* end i1 */       results. So we changed our mind and took the option of the best precision.
  }/* End k1 */    */
  fprintf(fichtm,"</ul>");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n      gp=matrix(0,nhstepm,1,nlstate);
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n      gm=matrix(0,nhstepm,1,nlstate);
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n  
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);  
       for(theta=1; theta <=npar; theta++){
  if(popforecast==1) fprintf(fichtm,"\n        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n          xp[i] = x[i] + (i==theta ?delti[theta]:0);
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n        }
         <br>",fileres,fileres,fileres,fileres);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
  else        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    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);  
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");        if (popbased==1) {
           if(mobilav ==0){
  m=cptcoveff;            for(i=1; i<=nlstate;i++)
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
  jj1=0;            for(i=1; i<=nlstate;i++)
  for(k1=1; k1<=m;k1++){              prlim[i][i]=mobaverage[(int)age][i][ij];
    for(i1=1; i1<=ncodemax[k1];i1++){          }
      jj1++;        }
      if (cptcovn > 0) {    
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        for(j=1; j<= nlstate; j++){
        for (cpt=1; cpt<=cptcoveff;cpt++)          for(h=0; h<=nhstepm; h++){
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
      }          }
      for(cpt=1; cpt<=nlstate;cpt++) {        }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        /* This for computing probability of death (h=1 means
 interval) in state (%d): v%s%d%d.png <br>           computed over hstepm matrices product = hstepm*stepm months) 
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);             as a weighted average of prlim.
      }        */
    } /* end i1 */        for(j=nlstate+1;j<=nlstate+ndeath;j++){
  }/* End k1 */          for(i=1,gpp[j]=0.; i<= nlstate; i++)
  fprintf(fichtm,"</ul>");            gpp[j] += prlim[i][i]*p3mat[i][j][1];
 fclose(fichtm);        }    
 }        /* end probability of death */
   
 /******************* Gnuplot file **************/        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   int ng;   
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {        if (popbased==1) {
     printf("Problem with file %s",optionfilegnuplot);          if(mobilav ==0){
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);            for(i=1; i<=nlstate;i++)
   }              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
 #ifdef windows            for(i=1; i<=nlstate;i++)
     fprintf(ficgp,"cd \"%s\" \n",pathc);              prlim[i][i]=mobaverage[(int)age][i][ij];
 #endif          }
 m=pow(2,cptcoveff);        }
    
  /* 1eme*/        for(j=1; j<= nlstate; j++){
   for (cpt=1; cpt<= nlstate ; cpt ++) {          for(h=0; h<=nhstepm; h++){
    for (k1=1; k1<= m ; k1 ++) {            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
 #ifdef windows          }
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        }
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);        /* This for computing probability of death (h=1 means
 #endif           computed over hstepm matrices product = hstepm*stepm months) 
 #ifdef unix           as a weighted average of prlim.
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
 #endif          for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
 for (i=1; i<= nlstate ; i ++) {        }    
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        /* end probability of death */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }        for(j=1; j<= nlstate; j++) /* vareij */
     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(h=0; h<=nhstepm; h++){
     for (i=1; i<= nlstate ; i ++) {            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
      for (i=1; i<= nlstate ; i ++) {        }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");      } /* End theta */
 }    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
 #ifdef unix  
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");      for(h=0; h<=nhstepm; h++) /* veij */
 #endif        for(j=1; j<=nlstate;j++)
    }          for(theta=1; theta <=npar; theta++)
   }            trgradg[h][j][theta]=gradg[h][theta][j];
   /*2 eme*/  
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   for (k1=1; k1<= m ; k1 ++) {        for(theta=1; theta <=npar; theta++)
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);          trgradgp[j][theta]=gradgp[theta][j];
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);    
      
     for (i=1; i<= nlstate+1 ; i ++) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       k=2*i;      for(i=1;i<=nlstate;i++)
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        for(j=1;j<=nlstate;j++)
       for (j=1; j<= nlstate+1 ; j ++) {          vareij[i][j][(int)age] =0.;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(h=0;h<=nhstepm;h++){
 }          for(k=0;k<=nhstepm;k++){
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          for(i=1;i<=nlstate;i++)
       for (j=1; j<= nlstate+1 ; j ++) {            for(j=1;j<=nlstate;j++)
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }        }
       fprintf(ficgp,"\" t\"\" w l 0,");    
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      /* pptj */
       for (j=1; j<= nlstate+1 ; j ++) {      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(j=nlstate+1;j<=nlstate+ndeath;j++)
 }          for(i=nlstate+1;i<=nlstate+ndeath;i++)
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          varppt[j][i]=doldmp[j][i];
       else fprintf(ficgp,"\" t\"\" w l 0,");      /* end ppptj */
     }      /*  x centered again */
   }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
        prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   /*3eme*/   
       if (popbased==1) {
   for (k1=1; k1<= m ; k1 ++) {        if(mobilav ==0){
     for (cpt=1; cpt<= nlstate ; cpt ++) {          for(i=1; i<=nlstate;i++)
       k=2+nlstate*(2*cpt-2);            prlim[i][i]=probs[(int)age][i][ij];
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        }else{ /* mobilav */ 
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);          for(i=1; i<=nlstate;i++)
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);            prlim[i][i]=mobaverage[(int)age][i][ij];
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        }
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      }
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);               
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      /* This for computing probability of death (h=1 means
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
 */      */
       for (i=1; i< nlstate ; i ++) {      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }      }    
     }      /* end probability of death */
   }  
        fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   /* CV preval stat */      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     for (k1=1; k1<= m ; k1 ++) {        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     for (cpt=1; cpt<nlstate ; cpt ++) {        for(i=1; i<=nlstate;i++){
       k=3;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        }
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);      } 
       fprintf(ficresprobmorprev,"\n");
       for (i=1; i< nlstate ; i ++)  
         fprintf(ficgp,"+$%d",k+i+1);      fprintf(ficresvij,"%.0f ",age );
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      for(i=1; i<=nlstate;i++)
              for(j=1; j<=nlstate;j++){
       l=3+(nlstate+ndeath)*cpt;          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        }
       for (i=1; i< nlstate ; i ++) {      fprintf(ficresvij,"\n");
         l=3+(nlstate+ndeath)*cpt;      free_matrix(gp,0,nhstepm,1,nlstate);
         fprintf(ficgp,"+$%d",l+i+1);      free_matrix(gm,0,nhstepm,1,nlstate);
       }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }      } /* End age */
      free_vector(gpp,nlstate+1,nlstate+ndeath);
   /* proba elementaires */    free_vector(gmp,nlstate+1,nlstate+ndeath);
    for(i=1,jk=1; i <=nlstate; i++){    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     for(k=1; k <=(nlstate+ndeath); k++){    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       if (k != i) {    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
         for(j=1; j <=ncovmodel; j++){    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
           jk++;  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
           fprintf(ficgp,"\n");  /*   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); */
       }    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
    }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/    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);
      for(jk=1; jk <=m; jk++) {    /*  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);
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);  */
        if (ng==2)  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
        else  
          fprintf(ficgp,"\nset title \"Probability\"\n");    free_vector(xp,1,npar);
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    free_matrix(doldm,1,nlstate,1,nlstate);
        i=1;    free_matrix(dnewm,1,nlstate,1,npar);
        for(k2=1; k2<=nlstate; k2++) {    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
          k3=i;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
          for(k=1; k<=(nlstate+ndeath); k++) {    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
            if (k != k2){    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
              if(ng==2)    fclose(ficresprobmorprev);
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);    fflush(ficgp);
              else    fflush(fichtm); 
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  }  /* end varevsij */
              ij=1;  
              for(j=3; j <=ncovmodel; j++) {  /************ Variance of prevlim ******************/
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  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)
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  {
                  ij++;    /* Variance of prevalence limit */
                }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
                else    double **newm;
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    double **dnewm,**doldm;
              }    int i, j, nhstepm, hstepm;
              fprintf(ficgp,")/(1");    int k, cptcode;
                  double *xp;
              for(k1=1; k1 <=nlstate; k1++){      double *gp, *gm;
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    double **gradg, **trgradg;
                ij=1;    double age,agelim;
                for(j=3; j <=ncovmodel; j++){    int theta;
                  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]]]);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
                    ij++;    fprintf(ficresvpl,"# Age");
                  }    for(i=1; i<=nlstate;i++)
                  else        fprintf(ficresvpl," %1d-%1d",i,i);
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    fprintf(ficresvpl,"\n");
                }  
                fprintf(ficgp,")");    xp=vector(1,npar);
              }    dnewm=matrix(1,nlstate,1,npar);
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);    doldm=matrix(1,nlstate,1,nlstate);
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    
              i=i+ncovmodel;    hstepm=1*YEARM; /* Every year of age */
            }    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
          } /* end k */    agelim = AGESUP;
        } /* end k2 */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
      } /* end jk */      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
    } /* end ng */      if (stepm >= YEARM) hstepm=1;
    fclose(ficgp);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
 }  /* end gnuplot */      gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
 /*************** Moving average **************/  
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
   int i, cpt, cptcod;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)        }
       for (i=1; i<=nlstate;i++)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        for(i=1;i<=nlstate;i++)
           mobaverage[(int)agedeb][i][cptcod]=0.;          gp[i] = prlim[i][i];
          
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){        for(i=1; i<=npar; i++) /* Computes gradient */
       for (i=1; i<=nlstate;i++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           for (cpt=0;cpt<=4;cpt++){        for(i=1;i<=nlstate;i++)
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          gm[i] = prlim[i][i];
           }  
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        for(i=1;i<=nlstate;i++)
         }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       }      } /* End theta */
     }  
          trgradg =matrix(1,nlstate,1,npar);
 }  
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
 /************** Forecasting ******************/          trgradg[j][theta]=gradg[theta][j];
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){  
        for(i=1;i<=nlstate;i++)
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        varpl[i][(int)age] =0.;
   int *popage;      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   double *popeffectif,*popcount;      for(i=1;i<=nlstate;i++)
   double ***p3mat;        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   char fileresf[FILENAMELENGTH];  
       fprintf(ficresvpl,"%.0f ",age );
  agelim=AGESUP;      for(i=1; i<=nlstate;i++)
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      free_vector(gp,1,nlstate);
        free_vector(gm,1,nlstate);
        free_matrix(gradg,1,npar,1,nlstate);
   strcpy(fileresf,"f");      free_matrix(trgradg,1,nlstate,1,npar);
   strcat(fileresf,fileres);    } /* End age */
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);    free_vector(xp,1,npar);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);    free_matrix(doldm,1,nlstate,1,npar);
   }    free_matrix(dnewm,1,nlstate,1,nlstate);
   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;  /************ 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)
   if (mobilav==1) {  {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int i, j=0,  i1, k1, l1, t, tj;
     movingaverage(agedeb, fage, ageminpar, mobaverage);    int k2, l2, j1,  z1;
   }    int k=0,l, cptcode;
     int first=1, first1;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   if (stepm<=12) stepsize=1;    double **dnewm,**doldm;
      double *xp;
   agelim=AGESUP;    double *gp, *gm;
      double **gradg, **trgradg;
   hstepm=1;    double **mu;
   hstepm=hstepm/stepm;    double age,agelim, cov[NCOVMAX];
   yp1=modf(dateintmean,&yp);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   anprojmean=yp;    int theta;
   yp2=modf((yp1*12),&yp);    char fileresprob[FILENAMELENGTH];
   mprojmean=yp;    char fileresprobcov[FILENAMELENGTH];
   yp1=modf((yp2*30.5),&yp);    char fileresprobcor[FILENAMELENGTH];
   jprojmean=yp;  
   if(jprojmean==0) jprojmean=1;    double ***varpij;
   if(mprojmean==0) jprojmean=1;  
      strcpy(fileresprob,"prob"); 
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    strcat(fileresprob,fileres);
      if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   for(cptcov=1;cptcov<=i2;cptcov++){      printf("Problem with resultfile: %s\n", fileresprob);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
       k=k+1;    }
       fprintf(ficresf,"\n#******");    strcpy(fileresprobcov,"probcov"); 
       for(j=1;j<=cptcoveff;j++) {    strcat(fileresprobcov,fileres);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       }      printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficresf,"******\n");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficresf,"# StartingAge FinalAge");    }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    strcpy(fileresprobcor,"probcor"); 
          strcat(fileresprobcor,fileres);
          if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      printf("Problem with resultfile: %s\n", fileresprobcor);
         fprintf(ficresf,"\n");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           nhstepm = nhstepm/hstepm;    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);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           oldm=oldms;savm=savms;    
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
            fprintf(ficresprob,"# Age");
           for (h=0; h<=nhstepm; h++){    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
             if (h==(int) (calagedate+YEARM*cpt)) {    fprintf(ficresprobcov,"# Age");
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
             }    fprintf(ficresprobcov,"# Age");
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                  for(i=1; i<=nlstate;i++)
                 if (mobilav==1)      for(j=1; j<=(nlstate+ndeath);j++){
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
                 else {        fprintf(ficresprobcov," p%1d-%1d ",i,j);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        fprintf(ficresprobcor," p%1d-%1d ",i,j);
                 }      }  
                   /* fprintf(ficresprob,"\n");
               }    fprintf(ficresprobcov,"\n");
               if (h==(int)(calagedate+12*cpt)){    fprintf(ficresprobcor,"\n");
                 fprintf(ficresf," %.3f", kk1);   */
                           xp=vector(1,npar);
               }    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);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
         }    first=1;
       }    fprintf(ficgp,"\n# Routine varprob");
     }    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   }    fprintf(fichtm,"\n");
          
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\
   fclose(ficresf);    file %s<br>\n",optionfilehtmcov);
 }    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
 /************** Forecasting ******************/  and drawn. It helps understanding how is the covariance between two incidences.\
 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){   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. \
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   int *popage;  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  standard deviations wide on each axis. <br>\
   double *popeffectif,*popcount;   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
   double ***p3mat,***tabpop,***tabpopprev;   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   char filerespop[FILENAMELENGTH];  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    cov[1]=1;
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    tj=cptcoveff;
   agelim=AGESUP;    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    j1=0;
      for(t=1; t<=tj;t++){
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      for(i1=1; i1<=ncodemax[t];i1++){ 
          j1++;
          if  (cptcovn>0) {
   strcpy(filerespop,"pop");          fprintf(ficresprob, "\n#********** Variable "); 
   strcat(filerespop,fileres);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {          fprintf(ficresprob, "**********\n#\n");
     printf("Problem with forecast resultfile: %s\n", filerespop);          fprintf(ficresprobcov, "\n#********** Variable "); 
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(ficresprobcov, "**********\n#\n");
   printf("Computing forecasting: result on file '%s' \n", filerespop);          
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);          fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          fprintf(ficgp, "**********\n#\n");
           
   if (mobilav==1) {          
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     movingaverage(agedeb, fage, ageminpar, mobaverage);          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\">");
           
   stepsize=(int) (stepm+YEARM-1)/YEARM;          fprintf(ficresprobcor, "\n#********** Variable ");    
   if (stepm<=12) stepsize=1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresprobcor, "**********\n#");    
   agelim=AGESUP;        }
          
   hstepm=1;        for (age=bage; age<=fage; age ++){ 
   hstepm=hstepm/stepm;          cov[2]=age;
            for (k=1; k<=cptcovn;k++) {
   if (popforecast==1) {            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     if((ficpop=fopen(popfile,"r"))==NULL) {          }
       printf("Problem with population file : %s\n",popfile);exit(0);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);          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]]];
     popage=ivector(0,AGESUP);          
     popeffectif=vector(0,AGESUP);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     popcount=vector(0,AGESUP);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
              gp=vector(1,(nlstate)*(nlstate+ndeath));
     i=1;            gm=vector(1,(nlstate)*(nlstate+ndeath));
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;      
              for(theta=1; theta <=npar; theta++){
     imx=i;            for(i=1; i<=npar; i++)
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   }            
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
   for(cptcov=1;cptcov<=i2;cptcov++){            
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            k=0;
       k=k+1;            for(i=1; i<= (nlstate); i++){
       fprintf(ficrespop,"\n#******");              for(j=1; j<=(nlstate+ndeath);j++){
       for(j=1;j<=cptcoveff;j++) {                k=k+1;
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                gp[k]=pmmij[i][j];
       }              }
       fprintf(ficrespop,"******\n");            }
       fprintf(ficrespop,"# Age");            
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);            for(i=1; i<=npar; i++)
       if (popforecast==1)  fprintf(ficrespop," [Population]");              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
            
       for (cpt=0; cpt<=0;cpt++) {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);              k=0;
                    for(i=1; i<=(nlstate); i++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){              for(j=1; j<=(nlstate+ndeath);j++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                k=k+1;
           nhstepm = nhstepm/hstepm;                gm[k]=pmmij[i][j];
                        }
           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(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
                      gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           for (h=0; h<=nhstepm; h++){          }
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             }            for(theta=1; theta <=npar; theta++)
             for(j=1; j<=nlstate+ndeath;j++) {              trgradg[j][theta]=gradg[theta][j];
               kk1=0.;kk2=0;          
               for(i=1; i<=nlstate;i++) {                        matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
                 if (mobilav==1)          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
                 else {          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                 }          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
               }  
               if (h==(int)(calagedate+12*cpt)){          pmij(pmmij,cov,ncovmodel,x,nlstate);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          
                   /*fprintf(ficrespop," %.3f", kk1);          k=0;
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/          for(i=1; i<=(nlstate); i++){
               }            for(j=1; j<=(nlstate+ndeath);j++){
             }              k=k+1;
             for(i=1; i<=nlstate;i++){              mu[k][(int) age]=pmmij[i][j];
               kk1=0.;            }
                 for(j=1; j<=nlstate;j++){          }
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
                 }            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];              varpij[i][j][(int)age] = doldm[i][j];
             }  
           /*printf("\n%d ",(int)age);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
           }            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }*/
         }  
       }          fprintf(ficresprob,"\n%d ",(int)age);
            fprintf(ficresprobcov,"\n%d ",(int)age);
   /******/          fprintf(ficresprobcor,"\n%d ",(int)age);
   
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);              fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
           nhstepm = nhstepm/hstepm;            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
                    }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          i=0;
           oldm=oldms;savm=savms;          for (k=1; k<=(nlstate);k++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              for (l=1; l<=(nlstate+ndeath);l++){ 
           for (h=0; h<=nhstepm; h++){              i=i++;
             if (h==(int) (calagedate+YEARM*cpt)) {              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
             }              for (j=1; j<=i;j++){
             for(j=1; j<=nlstate+ndeath;j++) {                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
               kk1=0.;kk2=0;                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               for(i=1; i<=nlstate;i++) {                            }
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                }
               }          }/* end of loop for state */
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);        } /* end of loop for age */
             }  
           }        /* Confidence intervalle of pij  */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /*
         }          fprintf(ficgp,"\nset noparametric;unset label");
       }          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
    }          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   }          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);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   if (popforecast==1) {        */
     free_ivector(popage,0,AGESUP);  
     free_vector(popeffectif,0,AGESUP);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     free_vector(popcount,0,AGESUP);        first1=1;
   }        for (k2=1; k2<=(nlstate);k2++){
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            if(l2==k2) continue;
   fclose(ficrespop);            j=(k2-1)*(nlstate+ndeath)+l2;
 }            for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
 /***********************************************/                if(l1==k1) continue;
 /**************** Main Program *****************/                i=(k1-1)*(nlstate+ndeath)+l1;
 /***********************************************/                if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
 int main(int argc, char *argv[])                  if ((int)age %5==0){
 {                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   double agedeb, agefin,hf;                    mu1=mu[i][(int) age]/stepm*YEARM ;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;                    mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
   double fret;                    /* Computing eigen value of matrix of covariance */
   double **xi,tmp,delta;                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   double dum; /* Dummy variable */                    /* Eigen vectors */
   double ***p3mat;                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   int *indx;                    /*v21=sqrt(1.-v11*v11); *//* error */
   char line[MAXLINE], linepar[MAXLINE];                    v21=(lc1-v1)/cv12*v11;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];                    v12=-v21;
   int firstobs=1, lastobs=10;                    v22=v11;
   int sdeb, sfin; /* Status at beginning and end */                    tnalp=v21/v11;
   int c,  h , cpt,l;                    if(first1==1){
   int ju,jl, mi;                      first1=0;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;                      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);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;                    }
   int mobilav=0,popforecast=0;                    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);
   int hstepm, nhstepm;                    /*printf(fignu*/
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   double bage, fage, age, agelim, agebase;                    if(first==1){
   double ftolpl=FTOL;                      first=0;
   double **prlim;                      fprintf(ficgp,"\nset parametric;unset label");
   double *severity;                      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);
   double ***param; /* Matrix of parameters */                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   double  *p;                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   double **matcov; /* Matrix of covariance */   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   double ***delti3; /* Scale */  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
   double *delti; /* Scale */                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
   double ***eij, ***vareij;                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   double **varpl; /* Variances of prevalence limits by age */                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   double *epj, vepp;                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
   double kk1, kk2;                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                        fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   char *alph[]={"a","a","b","c","d","e"}, str[4];                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
   char z[1]="c", occ;                      first=0;
 #include <sys/time.h>                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
 #include <time.h>                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                        fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   /* long total_usecs;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   struct timeval start_time, end_time;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                      }/* if first */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */                  } /* age mod 5 */
   getcwd(pathcd, size);                } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   printf("\n%s",version);                first=1;
   if(argc <=1){              } /*l12 */
     printf("\nEnter the parameter file name: ");            } /* k12 */
     scanf("%s",pathtot);          } /*l1 */
   }        }/* k1 */
   else{      } /* loop covariates */
     strcpy(pathtot,argv[1]);    }
   }    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   /*cygwin_split_path(pathtot,path,optionfile);    free_vector(xp,1,npar);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    fclose(ficresprob);
   /* cutv(path,optionfile,pathtot,'\\');*/    fclose(ficresprobcov);
     fclose(ficresprobcor);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    fflush(ficgp);
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    fflush(fichtmcov);
   chdir(path);  }
   replace(pathc,path);  
   
 /*-------- arguments in the command line --------*/  /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   /* Log file */                    int lastpass, int stepm, int weightopt, char model[],\
   strcat(filelog, optionfilefiname);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   strcat(filelog,".log");    /* */                    int popforecast, int estepm ,\
   if((ficlog=fopen(filelog,"w"))==NULL)    {                    double jprev1, double mprev1,double anprev1, \
     printf("Problem with logfile %s\n",filelog);                    double jprev2, double mprev2,double anprev2){
     goto end;    int jj1, k1, i1, cpt;
   }    /*char optionfilehtm[FILENAMELENGTH];*/
   fprintf(ficlog,"Log filename:%s\n",filelog);  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
   fprintf(ficlog,"\n%s",version);  /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
   fprintf(ficlog,"\nEnter the parameter file name: ");  /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  /*   } */
   fflush(ficlog);  
      fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
   /* */   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
   strcpy(fileres,"r");   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
   strcat(fileres, optionfilefiname);   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
   strcat(fileres,".txt");    /* Other files have txt extension */   - Life expectancies by age and initial health status (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>", \
   /*---------arguments file --------*/             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
   if((ficpar=fopen(optionfile,"r"))==NULL)    {             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
     printf("Problem with optionfile %s\n",optionfile);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);  
     goto end;  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   }  
    m=cptcoveff;
   strcpy(filereso,"o");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   strcat(filereso,fileres);  
   if((ficparo=fopen(filereso,"w"))==NULL) {   jj1=0;
     printf("Problem with Output resultfile: %s\n", filereso);   for(k1=1; k1<=m;k1++){
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);     for(i1=1; i1<=ncodemax[k1];i1++){
     goto end;       jj1++;
   }       if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   /* Reads comments: lines beginning with '#' */         for (cpt=1; cpt<=cptcoveff;cpt++) 
   while((c=getc(ficpar))=='#' && c!= EOF){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     ungetc(c,ficpar);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     fgets(line, MAXLINE, ficpar);       }
     puts(line);       /* Pij */
     fputs(line,ficparo);       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);     
   ungetc(c,ficpar);       /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   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);   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   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);  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
   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);         /* Stable prevalence in each health state */
 while((c=getc(ficpar))=='#' && c!= EOF){         for(cpt=1; cpt<nlstate;cpt++){
     ungetc(c,ficpar);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
     fgets(line, MAXLINE, ficpar);  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
     puts(line);         }
     fputs(line,ficparo);       for(cpt=1; cpt<=nlstate;cpt++) {
   }          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   ungetc(c,ficpar);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
         }
           fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   covar=matrix(0,NCOVMAX,1,n);  health expectancies in states (1) and (2): %s%d.png<br>\
   cptcovn=0;  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;     } /* end i1 */
    }/* End k1 */
   ncovmodel=2+cptcovn;   fprintf(fichtm,"</ul>");
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
    
   /* Read guess parameters */   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
   /* Reads comments: lines beginning with '#' */   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
   while((c=getc(ficpar))=='#' && c!= EOF){   - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
     ungetc(c,ficpar);   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
     fgets(line, MAXLINE, ficpar);   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
     puts(line);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
     fputs(line,ficparo);   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
   }   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
   ungetc(c,ficpar);           rfileres,rfileres,\
             subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
     for(i=1; i <=nlstate; i++)           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
     for(j=1; j <=nlstate+ndeath-1; j++){           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
       fscanf(ficpar,"%1d%1d",&i1,&j1);           subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
       fprintf(ficparo,"%1d%1d",i1,j1);           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
       if(mle==1)  
         printf("%1d%1d",i,j);  /*  if(popforecast==1) fprintf(fichtm,"\n */
       fprintf(ficlog,"%1d%1d",i,j);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
       for(k=1; k<=ncovmodel;k++){  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
         fscanf(ficpar," %lf",&param[i][j][k]);  /*      <br>",fileres,fileres,fileres,fileres); */
         if(mle==1){  /*  else  */
           printf(" %lf",param[i][j][k]);  /*    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); */
           fprintf(ficlog," %lf",param[i][j][k]);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
         }  
         else   m=cptcoveff;
           fprintf(ficlog," %lf",param[i][j][k]);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
         fprintf(ficparo," %lf",param[i][j][k]);  
       }   jj1=0;
       fscanf(ficpar,"\n");   for(k1=1; k1<=m;k1++){
       if(mle==1)     for(i1=1; i1<=ncodemax[k1];i1++){
         printf("\n");       jj1++;
       fprintf(ficlog,"\n");       if (cptcovn > 0) {
       fprintf(ficparo,"\n");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     }         for (cpt=1; cpt<=cptcoveff;cpt++) 
             fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
   p=param[1][1];       for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
   /* Reads comments: lines beginning with '#' */  interval) in state (%d): %s%d%d.png <br>\
   while((c=getc(ficpar))=='#' && c!= EOF){  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
     ungetc(c,ficpar);       }
     fgets(line, MAXLINE, ficpar);     } /* end i1 */
     puts(line);   }/* End k1 */
     fputs(line,ficparo);   fprintf(fichtm,"</ul>");
   }   fflush(fichtm);
   ungetc(c,ficpar);  }
   
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  /******************* Gnuplot file **************/
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   for(i=1; i <=nlstate; i++){  
     for(j=1; j <=nlstate+ndeath-1; j++){    char dirfileres[132],optfileres[132];
       fscanf(ficpar,"%1d%1d",&i1,&j1);    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
       printf("%1d%1d",i,j);    int ng;
       fprintf(ficparo,"%1d%1d",i1,j1);  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
       for(k=1; k<=ncovmodel;k++){  /*     printf("Problem with file %s",optionfilegnuplot); */
         fscanf(ficpar,"%le",&delti3[i][j][k]);  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
         printf(" %le",delti3[i][j][k]);  /*   } */
         fprintf(ficparo," %le",delti3[i][j][k]);  
       }    /*#ifdef windows */
       fscanf(ficpar,"\n");    fprintf(ficgp,"cd \"%s\" \n",pathc);
       printf("\n");      /*#endif */
       fprintf(ficparo,"\n");    m=pow(2,cptcoveff);
     }  
   }    strcpy(dirfileres,optionfilefiname);
   delti=delti3[1][1];    strcpy(optfileres,"vpl");
     /* 1eme*/
   /* Reads comments: lines beginning with '#' */    for (cpt=1; cpt<= nlstate ; cpt ++) {
   while((c=getc(ficpar))=='#' && c!= EOF){     for (k1=1; k1<= m ; k1 ++) {
     ungetc(c,ficpar);       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
     fgets(line, MAXLINE, ficpar);       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
     puts(line);       fprintf(ficgp,"set xlabel \"Age\" \n\
     fputs(line,ficparo);  set ylabel \"Probability\" \n\
   }  set ter png small\n\
   ungetc(c,ficpar);  set size 0.65,0.65\n\
    plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   matcov=matrix(1,npar,1,npar);  
   for(i=1; i <=npar; i++){       for (i=1; i<= nlstate ; i ++) {
     fscanf(ficpar,"%s",&str);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     if(mle==1)         else fprintf(ficgp," \%%*lf (\%%*lf)");
       printf("%s",str);       }
     fprintf(ficlog,"%s",str);       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);
     fprintf(ficparo,"%s",str);       for (i=1; i<= nlstate ; i ++) {
     for(j=1; j <=i; j++){         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       fscanf(ficpar," %le",&matcov[i][j]);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       if(mle==1){       } 
         printf(" %.5le",matcov[i][j]);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
         fprintf(ficlog," %.5le",matcov[i][j]);       for (i=1; i<= nlstate ; i ++) {
       }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       else         else fprintf(ficgp," \%%*lf (\%%*lf)");
         fprintf(ficlog," %.5le",matcov[i][j]);       }  
       fprintf(ficparo," %.5le",matcov[i][j]);       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
     }     }
     fscanf(ficpar,"\n");    }
     if(mle==1)    /*2 eme*/
       printf("\n");    
     fprintf(ficlog,"\n");    for (k1=1; k1<= m ; k1 ++) { 
     fprintf(ficparo,"\n");      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
   }      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
   for(i=1; i <=npar; i++)      
     for(j=i+1;j<=npar;j++)      for (i=1; i<= nlstate+1 ; i ++) {
       matcov[i][j]=matcov[j][i];        k=2*i;
            fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   if(mle==1)        for (j=1; j<= nlstate+1 ; j ++) {
     printf("\n");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   fprintf(ficlog,"\n");          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
     /*-------- Rewriting paramater file ----------*/        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
      strcpy(rfileres,"r");    /* "Rparameterfile */        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        for (j=1; j<= nlstate+1 ; j ++) {
      strcat(rfileres,".");    /* */          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
      strcat(rfileres,optionfilext);    /* Other files have txt extension */          else fprintf(ficgp," \%%*lf (\%%*lf)");
     if((ficres =fopen(rfileres,"w"))==NULL) {        }   
       printf("Problem writing new parameter file: %s\n", fileres);goto end;        fprintf(ficgp,"\" t\"\" w l 0,");
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;        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 ++) {
     fprintf(ficres,"#%s\n",version);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
              else fprintf(ficgp," \%%*lf (\%%*lf)");
     /*-------- data file ----------*/        }   
     if((fic=fopen(datafile,"r"))==NULL)    {        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
       printf("Problem with datafile: %s\n", datafile);goto end;        else fprintf(ficgp,"\" t\"\" w l 0,");
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;      }
     }    }
     
     n= lastobs;    /*3eme*/
     severity = vector(1,maxwav);    
     outcome=imatrix(1,maxwav+1,1,n);    for (k1=1; k1<= m ; k1 ++) { 
     num=ivector(1,n);      for (cpt=1; cpt<= nlstate ; cpt ++) {
     moisnais=vector(1,n);        k=2+nlstate*(2*cpt-2);
     annais=vector(1,n);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
     moisdc=vector(1,n);        fprintf(ficgp,"set ter png small\n\
     andc=vector(1,n);  set size 0.65,0.65\n\
     agedc=vector(1,n);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
     cod=ivector(1,n);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     weight=vector(1,n);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     mint=matrix(1,maxwav,1,n);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     anint=matrix(1,maxwav,1,n);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     s=imatrix(1,maxwav+1,1,n);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     adl=imatrix(1,maxwav+1,1,n);              
     tab=ivector(1,NCOVMAX);        */
     ncodemax=ivector(1,8);        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);
     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);    /* CV preval stable (period) */
           strcpy(line,stra);    for (k1=1; k1<= m ; k1 ++) { 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      for (cpt=1; cpt<=nlstate ; cpt ++) {
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        k=3;
         }        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
                fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  set ter png small\nset size 0.65,0.65\n\
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         for (j=ncovcol;j>=1;j--){        
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        l=3+(nlstate+ndeath)*cpt;
         }        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         num[i]=atol(stra);        for (i=1; i< nlstate ; i ++) {
                  l=3+(nlstate+ndeath)*cpt;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          fprintf(ficgp,"+$%d",l+i+1);
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/        }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
         i=i+1;      } 
       }    }  
     }    
     /* printf("ii=%d", ij);    /* proba elementaires */
        scanf("%d",i);*/    for(i=1,jk=1; i <=nlstate; i++){
   imx=i-1; /* Number of individuals */      for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
   /* for (i=1; i<=imx; i++){          for(j=1; j <=ncovmodel; j++){
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;            jk++; 
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;            fprintf(ficgp,"\n");
     }*/          }
    /*  for (i=1; i<=imx; i++){        }
      if (s[4][i]==9)  s[4][i]=-1;      }
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/     }
    
       for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   /* Calculation of the number of parameter from char model*/       for(jk=1; jk <=m; jk++) {
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
   Tprod=ivector(1,15);         if (ng==2)
   Tvaraff=ivector(1,15);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   Tvard=imatrix(1,15,1,2);         else
   Tage=ivector(1,15);                 fprintf(ficgp,"\nset title \"Probability\"\n");
             fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
   if (strlen(model) >1){         i=1;
     j=0, j1=0, k1=1, k2=1;         for(k2=1; k2<=nlstate; k2++) {
     j=nbocc(model,'+');           k3=i;
     j1=nbocc(model,'*');           for(k=1; k<=(nlstate+ndeath); k++) {
     cptcovn=j+1;             if (k != k2){
     cptcovprod=j1;               if(ng==2)
                     fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
     strcpy(modelsav,model);               else
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
       printf("Error. Non available option model=%s ",model);               ij=1;
       fprintf(ficlog,"Error. Non available option model=%s ",model);               for(j=3; j <=ncovmodel; j++) {
       goto end;                 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++;
     for(i=(j+1); i>=1;i--){                 }
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */                 else
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/               }
       /*scanf("%d",i);*/               fprintf(ficgp,")/(1");
       if (strchr(strb,'*')) {  /* Model includes a product */               
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/               for(k1=1; k1 <=nlstate; k1++){   
         if (strcmp(strc,"age")==0) { /* Vn*age */                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
           cptcovprod--;                 ij=1;
           cutv(strb,stre,strd,'V');                 for(j=3; j <=ncovmodel; j++){
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
           cptcovage++;                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
             Tage[cptcovage]=i;                     ij++;
             /*printf("stre=%s ", stre);*/                   }
         }                   else
         else if (strcmp(strd,"age")==0) { /* or age*Vn */                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
           cptcovprod--;                 }
           cutv(strb,stre,strc,'V');                 fprintf(ficgp,")");
           Tvar[i]=atoi(stre);               }
           cptcovage++;               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
           Tage[cptcovage]=i;               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
         }               i=i+ncovmodel;
         else {  /* Age is not in the model */             }
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/           } /* end k */
           Tvar[i]=ncovcol+k1;         } /* end k2 */
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */       } /* end jk */
           Tprod[k1]=i;     } /* end ng */
           Tvard[k1][1]=atoi(strc); /* m*/     fflush(ficgp); 
           Tvard[k1][2]=atoi(stre); /* n */  }  /* end gnuplot */
           Tvar[cptcovn+k2]=Tvard[k1][1];  
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  
           for (k=1; k<=lastobs;k++)  /*************** Moving average **************/
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
           k1++;  
           k2=k2+2;    int i, cpt, cptcod;
         }    int modcovmax =1;
       }    int mobilavrange, mob;
       else { /* no more sum */    double age;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  
        /*  scanf("%d",i);*/    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
       cutv(strd,strc,strb,'V');                             a covariate has 2 modalities */
       Tvar[i]=atoi(strc);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
       }  
       strcpy(modelsav,stra);      if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      if(mobilav==1) mobilavrange=5; /* default */
         scanf("%d",i);*/      else mobilavrange=mobilav;
     } /* end of loop + */      for (age=bage; age<=fage; age++)
   } /* end model */        for (i=1; i<=nlstate;i++)
            for (cptcod=1;cptcod<=modcovmax;cptcod++)
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   printf("cptcovprod=%d ", cptcovprod);      /* We keep the original values on the extreme ages bage, fage and for 
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
   scanf("%d ",i);*/         we use a 5 terms etc. until the borders are no more concerned. 
     fclose(fic);      */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
     /*  if(mle==1){*/        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
     if (weightopt != 1) { /* Maximisation without weights*/          for (i=1; i<=nlstate;i++){
       for(i=1;i<=n;i++) weight[i]=1.0;            for (cptcod=1;cptcod<=modcovmax;cptcod++){
     }              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
     /*-calculation of age at interview from date of interview and age at death -*/                for (cpt=1;cpt<=(mob-1)/2;cpt++){
     agev=matrix(1,maxwav,1,imx);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
     for (i=1; i<=imx; i++) {                }
       for(m=2; (m<= maxwav); m++) {              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){            }
          anint[m][i]=9999;          }
          s[m][i]=-1;        }/* end age */
        }      }/* end mob */
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    }else return -1;
       }    return 0;
     }  }/* End movingaverage */
   
     for (i=1; i<=imx; i++)  {  
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  /************** Forecasting ******************/
       for(m=1; (m<= maxwav); m++){  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){
         if(s[m][i] >0){    /* proj1, year, month, day of starting projection 
           if (s[m][i] >= nlstate+1) {       agemin, agemax range of age
             if(agedc[i]>0)       dateprev1 dateprev2 range of dates during which prevalence is computed
               if(moisdc[i]!=99 && andc[i]!=9999)       anproj2 year of en of projection (same day and month as proj1).
                 agev[m][i]=agedc[i];    */
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
            else {    int *popage;
               if (andc[i]!=9999){    double agec; /* generic age */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);    double *popeffectif,*popcount;
               agev[m][i]=-1;    double ***p3mat;
               }    double ***mobaverage;
             }    char fileresf[FILENAMELENGTH];
           }  
           else if(s[m][i] !=9){ /* Should no more exist */    agelim=AGESUP;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
             if(mint[m][i]==99 || anint[m][i]==9999)   
               agev[m][i]=1;    strcpy(fileresf,"f"); 
             else if(agev[m][i] <agemin){    strcat(fileresf,fileres);
               agemin=agev[m][i];    if((ficresf=fopen(fileresf,"w"))==NULL) {
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      printf("Problem with forecast resultfile: %s\n", fileresf);
             }      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
             else if(agev[m][i] >agemax){    }
               agemax=agev[m][i];    printf("Computing forecasting: result on file '%s' \n", fileresf);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
             }  
             /*agev[m][i]=anint[m][i]-annais[i];*/    if (cptcoveff==0) ncodemax[cptcoveff]=1;
             /*   agev[m][i] = age[i]+2*m;*/  
           }    if (mobilav!=0) {
           else { /* =9 */      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             agev[m][i]=1;      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
             s[m][i]=-1;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }      }
         else /*= 0 Unknown */    }
           agev[m][i]=1;  
       }    stepsize=(int) (stepm+YEARM-1)/YEARM;
        if (stepm<=12) stepsize=1;
     }    if(estepm < stepm){
     for (i=1; i<=imx; i++)  {      printf ("Problem %d lower than %d\n",estepm, stepm);
       for(m=1; (m<= maxwav); m++){    }
         if (s[m][i] > (nlstate+ndeath)) {    else  hstepm=estepm;   
           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);      hstepm=hstepm/stepm; 
           goto end;    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
         }                                 fractional in yp1 */
       }    anprojmean=yp;
     }    yp2=modf((yp1*12),&yp);
     mprojmean=yp;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    yp1=modf((yp2*30.5),&yp);
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     free_vector(severity,1,maxwav);    if(mprojmean==0) jprojmean=1;
     free_imatrix(outcome,1,maxwav+1,1,n);  
     free_vector(moisnais,1,n);    i1=cptcoveff;
     free_vector(annais,1,n);    if (cptcovn < 1){i1=1;}
     /* free_matrix(mint,1,maxwav,1,n);    
        free_matrix(anint,1,maxwav,1,n);*/    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     free_vector(moisdc,1,n);    
     free_vector(andc,1,n);    fprintf(ficresf,"#****** Routine prevforecast **\n");
   
      /*            if (h==(int)(YEARM*yearp)){ */
     wav=ivector(1,imx);    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        k=k+1;
            fprintf(ficresf,"\n#******");
     /* Concatenates waves */        for(j=1;j<=cptcoveff;j++) {
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          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");
       Tcode=ivector(1,100);        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        for(j=1; j<=nlstate+ndeath;j++){ 
       ncodemax[1]=1;          for(i=1; i<=nlstate;i++)              
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);            fprintf(ficresf," p%d%d",i,j);
                fprintf(ficresf," p.%d",j);
    codtab=imatrix(1,100,1,10);        }
    h=0;        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
    m=pow(2,cptcoveff);          fprintf(ficresf,"\n");
            fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){          for (agec=fage; agec>=(ageminpar-1); agec--){ 
        for(j=1; j <= ncodemax[k]; j++){            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){            nhstepm = nhstepm/hstepm; 
            h++;            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;            oldm=oldms;savm=savms;
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/            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");
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);                for(j=1;j<=cptcoveff;j++) 
       codtab[1][2]=1;codtab[2][2]=2; */                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
    /* for(i=1; i <=m ;i++){                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
       for(k=1; k <=cptcovn; k++){              } 
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);              for(j=1; j<=nlstate+ndeath;j++) {
       }                ppij=0.;
       printf("\n");                for(i=1; i<=nlstate;i++) {
       }                  if (mobilav==1) 
       scanf("%d",i);*/                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                      else {
    /* Calculates basic frequencies. Computes observed prevalence at single age                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
        and prints on file fileres'p'. */                  }
                   if (h*hstepm/YEARM*stepm== yearp) {
                        fprintf(ficresf," %.3f", p3mat[i][j][h]);
                      }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                } /* end i */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                if (h*hstepm/YEARM*stepm==yearp) {
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                  fprintf(ficresf," %.3f", ppij);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                }
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              }/* end j */
                  } /* end h */
     /* For Powell, parameters are in a vector p[] starting at p[1]            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          } /* end agec */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        } /* end yearp */
       } /* end cptcod */
     if(mle==1){    } /* end  cptcov */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);         
     }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      
     /*--------- results files --------------*/    fclose(ficresf);
     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);  }
    
   /************** Forecasting *****not tested NB*************/
    jk=1;  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){
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    int *popage;
    for(i=1,jk=1; i <=nlstate; i++){    double calagedatem, agelim, kk1, kk2;
      for(k=1; k <=(nlstate+ndeath); k++){    double *popeffectif,*popcount;
        if (k != i)    double ***p3mat,***tabpop,***tabpopprev;
          {    double ***mobaverage;
            printf("%d%d ",i,k);    char filerespop[FILENAMELENGTH];
            fprintf(ficlog,"%d%d ",i,k);  
            fprintf(ficres,"%1d%1d ",i,k);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
            for(j=1; j <=ncovmodel; j++){    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
              printf("%f ",p[jk]);    agelim=AGESUP;
              fprintf(ficlog,"%f ",p[jk]);    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
              fprintf(ficres,"%f ",p[jk]);    
              jk++;    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
            }    
            printf("\n");    
            fprintf(ficlog,"\n");    strcpy(filerespop,"pop"); 
            fprintf(ficres,"\n");    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);
    if(mle==1){    }
      /* Computing hessian and covariance matrix */    printf("Computing forecasting: result on file '%s' \n", filerespop);
      ftolhess=ftol; /* Usually correct */    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
      hesscov(matcov, p, npar, delti, ftolhess, func);  
    }    if (cptcoveff==0) ncodemax[cptcoveff]=1;
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");  
    printf("# Scales (for hessian or gradient estimation)\n");    if (mobilav!=0) {
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    for(i=1,jk=1; i <=nlstate; i++){      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
      for(j=1; j <=nlstate+ndeath; j++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
        if (j!=i) {        printf(" Error in movingaverage mobilav=%d\n",mobilav);
          fprintf(ficres,"%1d%1d",i,j);      }
          printf("%1d%1d",i,j);    }
          fprintf(ficlog,"%1d%1d",i,j);  
          for(k=1; k<=ncovmodel;k++){    stepsize=(int) (stepm+YEARM-1)/YEARM;
            printf(" %.5e",delti[jk]);    if (stepm<=12) stepsize=1;
            fprintf(ficlog," %.5e",delti[jk]);    
            fprintf(ficres," %.5e",delti[jk]);    agelim=AGESUP;
            jk++;    
          }    hstepm=1;
          printf("\n");    hstepm=hstepm/stepm; 
          fprintf(ficlog,"\n");    
          fprintf(ficres,"\n");    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);
          } 
    k=1;      popage=ivector(0,AGESUP);
    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");      popeffectif=vector(0,AGESUP);
    if(mle==1)      popcount=vector(0,AGESUP);
      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");      i=1;   
    for(i=1;i<=npar;i++){      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      /*  if (k>nlstate) k=1;     
          i1=(i-1)/(ncovmodel*nlstate)+1;      imx=i;
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
          printf("%s%d%d",alph[k],i1,tab[i]);*/    }
      fprintf(ficres,"%3d",i);  
      if(mle==1)    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
        printf("%3d",i);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
      fprintf(ficlog,"%3d",i);        k=k+1;
      for(j=1; j<=i;j++){        fprintf(ficrespop,"\n#******");
        fprintf(ficres," %.5e",matcov[i][j]);        for(j=1;j<=cptcoveff;j++) {
        if(mle==1)          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
          printf(" %.5e",matcov[i][j]);        }
        fprintf(ficlog," %.5e",matcov[i][j]);        fprintf(ficrespop,"******\n");
      }        fprintf(ficrespop,"# Age");
      fprintf(ficres,"\n");        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
      if(mle==1)        if (popforecast==1)  fprintf(ficrespop," [Population]");
        printf("\n");        
      fprintf(ficlog,"\n");        for (cpt=0; cpt<=0;cpt++) { 
      k++;          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--){ 
    while((c=getc(ficpar))=='#' && c!= EOF){            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
      ungetc(c,ficpar);            nhstepm = nhstepm/hstepm; 
      fgets(line, MAXLINE, ficpar);            
      puts(line);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      fputs(line,ficparo);            oldm=oldms;savm=savms;
    }            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
    ungetc(c,ficpar);          
    estepm=0;            for (h=0; h<=nhstepm; h++){
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);              if (h==(int) (calagedatem+YEARM*cpt)) {
    if (estepm==0 || estepm < stepm) estepm=stepm;                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
    if (fage <= 2) {              } 
      bage = ageminpar;              for(j=1; j<=nlstate+ndeath;j++) {
      fage = agemaxpar;                kk1=0.;kk2=0;
    }                for(i=1; i<=nlstate;i++) {              
                      if (mobilav==1) 
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                  else {
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                      }
    while((c=getc(ficpar))=='#' && c!= EOF){                }
      ungetc(c,ficpar);                if (h==(int)(calagedatem+12*cpt)){
      fgets(line, MAXLINE, ficpar);                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
      puts(line);                    /*fprintf(ficrespop," %.3f", kk1);
      fputs(line,ficparo);                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
    }                }
    ungetc(c,ficpar);              }
                for(i=1; i<=nlstate;i++){
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                kk1=0.;
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                  for(j=1; j<=nlstate;j++){
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                      }
    while((c=getc(ficpar))=='#' && c!= EOF){                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
      ungetc(c,ficpar);              }
      fgets(line, MAXLINE, ficpar);  
      puts(line);              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
      fputs(line,ficparo);                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
    }            }
    ungetc(c,ficpar);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            }
         }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;   
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    /******/
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
   fprintf(ficparo,"pop_based=%d\n",popbased);            fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   fprintf(ficres,"pop_based=%d\n",popbased);            for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
              nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   while((c=getc(ficpar))=='#' && c!= EOF){            nhstepm = nhstepm/hstepm; 
     ungetc(c,ficpar);            
     fgets(line, MAXLINE, ficpar);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     puts(line);            oldm=oldms;savm=savms;
     fputs(line,ficparo);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   }            for (h=0; h<=nhstepm; h++){
   ungetc(c,ficpar);              if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   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);              for(j=1; j<=nlstate+ndeath;j++) {
 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);                kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
 while((c=getc(ficpar))=='#' && c!= EOF){                }
     ungetc(c,ficpar);                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
     fgets(line, MAXLINE, ficpar);              }
     puts(line);            }
     fputs(line,ficparo);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }          }
   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);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
 /*------------ gnuplot -------------*/      free_vector(popeffectif,0,AGESUP);
   strcpy(optionfilegnuplot,optionfilefiname);      free_vector(popcount,0,AGESUP);
   strcat(optionfilegnuplot,".gp");    }
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     printf("Problem with file %s",optionfilegnuplot);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   }    fclose(ficrespop);
   fclose(ficgp);  } /* End of popforecast */
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);  
 /*--------- index.htm --------*/  int fileappend(FILE *fichier, char *optionfich)
   {
   strcpy(optionfilehtm,optionfile);    if((fichier=fopen(optionfich,"a"))==NULL) {
   strcat(optionfilehtm,".htm");      printf("Problem with file: %s\n", optionfich);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      fprintf(ficlog,"Problem with file: %s\n", optionfich);
     printf("Problem with %s \n",optionfilehtm), exit(0);      return (0);
   }    }
     fflush(fichier);
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    return (1);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n  }
 \n  void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
 Total number of observations=%d <br>\n  {
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n  
 <hr  size=\"2\" color=\"#EC5E5E\">    char ca[32], cb[32], cc[32];
  <ul><li><h4>Parameter files</h4>\n    int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    int numlinepar;
  - Log file of the run: <a href=\"%s\">%s</a><br>\n  
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   fclose(fichtm);    fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);      jj=0;
        for(j=1; j <=nlstate+ndeath; j++){
 /*------------ free_vector  -------------*/        if(j==i) continue;
  chdir(path);        jj++;
          /*ca[0]= k+'a'-1;ca[1]='\0';*/
  free_ivector(wav,1,imx);        printf("%1d%1d",i,j);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        fprintf(ficparo,"%1d%1d",i,j);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          for(k=1; k<=ncovmodel;k++){
  free_ivector(num,1,n);          /*        printf(" %lf",param[i][j][k]); */
  free_vector(agedc,1,n);          /*        fprintf(ficparo," %lf",param[i][j][k]); */
  /*free_matrix(covar,1,NCOVMAX,1,n);*/          printf(" 0.");
  fclose(ficparo);          fprintf(ficparo," 0.");
  fclose(ficres);        }
         printf("\n");
         fprintf(ficparo,"\n");
   /*--------------- Prevalence limit --------------*/      }
      }
   strcpy(filerespl,"pl");    printf("# Scales (for hessian or gradient estimation)\n");
   strcat(filerespl,fileres);    fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    for(i=1; i <=nlstate; i++){
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;      jj=0;
   }      for(j=1; j <=nlstate+ndeath; j++){
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);        if(j==i) continue;
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);        jj++;
   fprintf(ficrespl,"#Prevalence limit\n");        fprintf(ficparo,"%1d%1d",i,j);
   fprintf(ficrespl,"#Age ");        printf("%1d%1d",i,j);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        fflush(stdout);
   fprintf(ficrespl,"\n");        for(k=1; k<=ncovmodel;k++){
            /*      printf(" %le",delti3[i][j][k]); */
   prlim=matrix(1,nlstate,1,nlstate);          /*      fprintf(ficparo," %le",delti3[i][j][k]); */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          printf(" 0.");
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficparo," 0.");
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        numlinepar++;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        printf("\n");
   k=0;        fprintf(ficparo,"\n");
   agebase=ageminpar;      }
   agelim=agemaxpar;    }
   ftolpl=1.e-10;    printf("# Covariance matrix\n");
   i1=cptcoveff;  /* # 121 Var(a12)\n\ */
   if (cptcovn < 1){i1=1;}  /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   for(cptcov=1;cptcov<=i1;cptcov++){  /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
         k=k+1;  /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
         fprintf(ficrespl,"\n#******");  /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
         printf("\n#******");    fflush(stdout);
         fprintf(ficlog,"\n#******");    fprintf(ficparo,"# Covariance matrix\n");
         for(j=1;j<=cptcoveff;j++) {    /* # 121 Var(a12)\n\ */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* # 122 Cov(b12,a12) Var(b12)\n\ */
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* #   ...\n\ */
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
         }    
         fprintf(ficrespl,"******\n");    for(itimes=1;itimes<=2;itimes++){
         printf("******\n");      jj=0;
         fprintf(ficlog,"******\n");      for(i=1; i <=nlstate; i++){
                for(j=1; j <=nlstate+ndeath; j++){
         for (age=agebase; age<=agelim; age++){          if(j==i) continue;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          for(k=1; k<=ncovmodel;k++){
           fprintf(ficrespl,"%.0f",age );            jj++;
           for(i=1; i<=nlstate;i++)            ca[0]= k+'a'-1;ca[1]='\0';
           fprintf(ficrespl," %.5f", prlim[i][i]);            if(itimes==1){
           fprintf(ficrespl,"\n");              printf("#%1d%1d%d",i,j,k);
         }              fprintf(ficparo,"#%1d%1d%d",i,j,k);
       }            }else{
     }              printf("%1d%1d%d",i,j,k);
   fclose(ficrespl);              fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
   /*------------- h Pij x at various ages ------------*/            }
              ll=0;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);            for(li=1;li <=nlstate; li++){
   if((ficrespij=fopen(filerespij,"w"))==NULL) {              for(lj=1;lj <=nlstate+ndeath; lj++){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                if(lj==li) continue;
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;                for(lk=1;lk<=ncovmodel;lk++){
   }                  ll++;
   printf("Computing pij: result on file '%s' \n", filerespij);                  if(ll<=jj){
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);                    cb[0]= lk +'a'-1;cb[1]='\0';
                      if(ll<jj){
   stepsize=(int) (stepm+YEARM-1)/YEARM;                      if(itimes==1){
   /*if (stepm<=24) stepsize=2;*/                        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);
   agelim=AGESUP;                      }else{
   hstepm=stepsize*YEARM; /* Every year of age */                        printf(" 0.");
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */                        fprintf(ficparo," 0.");
                       }
   /* hstepm=1;   aff par mois*/                    }else{
                       if(itimes==1){
   k=0;                        printf(" Var(%s%1d%1d)",ca,i,j);
   for(cptcov=1;cptcov<=i1;cptcov++){                        fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                      }else{
       k=k+1;                        printf(" 0.");
         fprintf(ficrespij,"\n#****** ");                        fprintf(ficparo," 0.");
         for(j=1;j<=cptcoveff;j++)                      }
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    }
         fprintf(ficrespij,"******\n");                  }
                        } /* end lk */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */              } /* end lj */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            } /* end li */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            printf("\n");
             fprintf(ficparo,"\n");
           /*      nhstepm=nhstepm*YEARM; aff par mois*/            numlinepar++;
           } /* end k*/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        } /*end j */
           oldm=oldms;savm=savms;      } /* end i */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      }
           fprintf(ficrespij,"# Age");  
           for(i=1; i<=nlstate;i++)  } /* end of prwizard */
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %1d-%1d",i,j);  
           fprintf(ficrespij,"\n");  /***********************************************/
            for (h=0; h<=nhstepm; h++){  /**************** Main Program *****************/
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  /***********************************************/
             for(i=1; i<=nlstate;i++)  
               for(j=1; j<=nlstate+ndeath;j++)  int main(int argc, char *argv[])
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  {
             fprintf(ficrespij,"\n");    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
              }    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int jj, imk;
           fprintf(ficrespij,"\n");    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;
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);  
     double fret;
   fclose(ficrespij);    double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
   /*---------- Forecasting ------------------*/    double ***p3mat;
   if((stepm == 1) && (strcmp(model,".")==0)){    double ***mobaverage;
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    int *indx;
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    char line[MAXLINE], linepar[MAXLINE];
   }    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
   else{    char pathr[MAXLINE]; 
     erreur=108;    int firstobs=1, lastobs=10;
     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);    int sdeb, sfin; /* Status at beginning and end */
     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);    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; 
   /*---------- Health expectancies and variances ------------*/    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
   strcpy(filerest,"t");    int hstepm, nhstepm;
   strcat(filerest,fileres);    double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
   if((ficrest=fopen(filerest,"w"))==NULL) {    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;    double bage, fage, age, agelim, agebase;
   }    double ftolpl=FTOL;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    double **prlim;
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);    double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
   strcpy(filerese,"e");    double **matcov; /* Matrix of covariance */
   strcat(filerese,fileres);    double ***delti3; /* Scale */
   if((ficreseij=fopen(filerese,"w"))==NULL) {    double *delti; /* Scale */
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    double ***eij, ***vareij;
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    double **varpl; /* Variances of prevalence limits by age */
   }    double *epj, vepp;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    double kk1, kk2;
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
   strcpy(fileresv,"v");    char *alph[]={"a","a","b","c","d","e"}, str[4];
   strcat(fileresv,fileres);  
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    char z[1]="c", occ;
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    char strstart[80], *strt, strtend[80];
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    char *stratrunc;
   calagedate=-1;    int lstra;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  
     long total_usecs;
   k=0;   
   for(cptcov=1;cptcov<=i1;cptcov++){    /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    (void) gettimeofday(&start_time,&tzp);
       k=k+1;    curr_time=start_time;
       fprintf(ficrest,"\n#****** ");    tm = *localtime(&start_time.tv_sec);
       for(j=1;j<=cptcoveff;j++)    tmg = *gmtime(&start_time.tv_sec);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    strcpy(strstart,asctime(&tm));
       fprintf(ficrest,"******\n");  
   /*  printf("Localtime (at start)=%s",strstart); */
       fprintf(ficreseij,"\n#****** ");  /*  tp.tv_sec = tp.tv_sec +86400; */
       for(j=1;j<=cptcoveff;j++)  /*  tm = *localtime(&start_time.tv_sec); */
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
       fprintf(ficreseij,"******\n");  /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
       fprintf(ficresvij,"\n#****** ");  /*   tp.tv_sec = mktime(&tmg); */
       for(j=1;j<=cptcoveff;j++)  /*   strt=asctime(&tmg); */
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*   printf("Time(after) =%s",strstart);  */
       fprintf(ficresvij,"******\n");  /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  *  tm = *localtime(&time_value);
       oldm=oldms;savm=savms;  *  strstart=asctime(&tm);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);    *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
    */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;    nberr=0; /* Number of errors and warnings */
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);    nbwarn=0;
       if(popbased==1){    getcwd(pathcd, size);
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);  
        }    printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
        printf("\nEnter the parameter file name: ");
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      scanf("%s",pathtot);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    }
       fprintf(ficrest,"\n");    else{
       strcpy(pathtot,argv[1]);
       epj=vector(1,nlstate+1);    }
       for(age=bage; age <=fage ;age++){    /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    /*cygwin_split_path(pathtot,path,optionfile);
         if (popbased==1) {      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
           for(i=1; i<=nlstate;i++)    /* cutv(path,optionfile,pathtot,'\\');*/
             prlim[i][i]=probs[(int)age][i][k];  
         }    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
            printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
         fprintf(ficrest," %4.0f",age);    chdir(path);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    strcpy(command,"mkdir ");
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    strcat(command,optionfilefiname);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    if((outcmd=system(command)) != 0){
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/      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); */
           epj[nlstate+1] +=epj[j];      /* fclose(ficlog); */
         }  /*     exit(1); */
     }
         for(i=1, vepp=0.;i <=nlstate;i++)  /*   if((imk=mkdir(optionfilefiname))<0){ */
           for(j=1;j <=nlstate;j++)  /*     perror("mkdir"); */
             vepp += vareij[i][j][(int)age];  /*   } */
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));  
         for(j=1;j <=nlstate;j++){    /*-------- arguments in the command line --------*/
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));  
         }    /* Log file */
         fprintf(ficrest,"\n");    strcat(filelog, optionfilefiname);
       }    strcat(filelog,".log");    /* */
     }    if((ficlog=fopen(filelog,"w"))==NULL)    {
   }      printf("Problem with logfile %s\n",filelog);
 free_matrix(mint,1,maxwav,1,n);      goto end;
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    }
     free_vector(weight,1,n);    fprintf(ficlog,"Log filename:%s\n",filelog);
   fclose(ficreseij);    fprintf(ficlog,"\n%s\n%s",version,fullversion);
   fclose(ficresvij);    fprintf(ficlog,"\nEnter the parameter file name: ");
   fclose(ficrest);    fprintf(ficlog,"pathtot=%s\n\
   fclose(ficpar);   path=%s \n\
   free_vector(epj,1,nlstate+1);   optionfile=%s\n\
     optionfilext=%s\n\
   /*------- Variance limit prevalence------*/     optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   
   strcpy(fileresvpl,"vpl");    printf("Localtime (at start):%s",strstart);
   strcat(fileresvpl,fileres);    fprintf(ficlog,"Localtime (at start): %s",strstart);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    fflush(ficlog);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  /*   (void) gettimeofday(&curr_time,&tzp); */
     exit(0);  /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   }  
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    /* */
     strcpy(fileres,"r");
   k=0;    strcat(fileres, optionfilefiname);
   for(cptcov=1;cptcov<=i1;cptcov++){    strcat(fileres,".txt");    /* Other files have txt extension */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;    /*---------arguments file --------*/
       fprintf(ficresvpl,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)    if((ficpar=fopen(optionfile,"r"))==NULL)    {
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficresvpl,"******\n");      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
            fflush(ficlog);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);      goto end;
       oldm=oldms;savm=savms;    }
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
     }  
  }  
     strcpy(filereso,"o");
   fclose(ficresvpl);    strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
   /*---------- End : free ----------------*/      printf("Problem with Output resultfile: %s\n", filereso);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
        fflush(ficlog);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      goto end;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    }
    
      /* Reads comments: lines beginning with '#' */
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    numlinepar=0;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    while((c=getc(ficpar))=='#' && c!= EOF){
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      ungetc(c,ficpar);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      fgets(line, MAXLINE, ficpar);
        numlinepar++;
   free_matrix(matcov,1,npar,1,npar);      puts(line);
   free_vector(delti,1,npar);      fputs(line,ficparo);
   free_matrix(agev,1,maxwav,1,imx);      fputs(line,ficlog);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    }
     ungetc(c,ficpar);
   fprintf(fichtm,"\n</body>");  
   fclose(fichtm);    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);
   fclose(ficgp);    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);
   if(erreur >0){    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);
     printf("End of Imach with error or warning %d\n",erreur);    fflush(ficlog);
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);    while((c=getc(ficpar))=='#' && c!= EOF){
   }else{      ungetc(c,ficpar);
    printf("End of Imach\n");      fgets(line, MAXLINE, ficpar);
    fprintf(ficlog,"End of Imach\n");      numlinepar++;
   }      puts(line);
   printf("See log file on %s\n",filelog);      fputs(line,ficparo);
   fclose(ficlog);      fputs(line,ficlog);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    }
      ungetc(c,ficpar);
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/  
   /*printf("Total time was %d uSec.\n", total_usecs);*/     
   /*------ End -----------*/    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;
  end:  
 #ifdef windows    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
   /* chdir(pathcd);*/    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
 #endif   
  /*system("wgnuplot graph.plt");*/    if(mle==-1){ /* Print a wizard for help writing covariance matrix */
  /*system("../gp37mgw/wgnuplot graph.plt");*/      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
  /*system("cd ../gp37mgw");*/      printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
  strcpy(plotcmd,GNUPLOTPROGRAM);      fclose (ficparo);
  strcat(plotcmd," ");      fclose (ficlog);
  strcat(plotcmd,optionfilegnuplot);      exit(0);
  system(plotcmd);    }
     /* Read guess parameters */
 #ifdef windows    /* Reads comments: lines beginning with '#' */
   while (z[0] != 'q') {    while((c=getc(ficpar))=='#' && c!= EOF){
     /* chdir(path); */      ungetc(c,ficpar);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");      fgets(line, MAXLINE, ficpar);
     scanf("%s",z);      numlinepar++;
     if (z[0] == 'c') system("./imach");      puts(line);
     else if (z[0] == 'e') system(optionfilehtm);      fputs(line,ficparo);
     else if (z[0] == 'g') system(plotcmd);      fputs(line,ficlog);
     else if (z[0] == 'q') exit(0);    }
   }    ungetc(c,ficpar);
 #endif  
 }    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 */
     strcpy(lfileres,fileres);
     strcat(lfileres,"/");
     strcat(lfileres,optionfilefiname);
     
     /* 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("Localtime at start %s\nLocaltime at end   %s",strstart, strtend); 
     fprintf(ficlog,"Localtime 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.1.52  
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  Added in v.1.93


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