Diff for /imach/src/imach.c between versions 1.25 and 1.93

version 1.25, 2002/02/26 17:11:54 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
   probabibility 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 "..\\gp37mgw\\wgnuplot"  
 #define FILENAMELENGTH 80    Revision 1.83  2003/06/10 13:39:11  lievre
 /*#define DEBUG*/    *** empty log message ***
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.82  2003/06/05 15:57:20  brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Add log in  imach.c and  fullversion number is now printed.
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  */
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  /*
      Interpolated Markov Chain
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Short summary of the programme:
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    
 #define NCOVMAX 8 /* Maximum number of covariates */    This program computes Healthy Life Expectancies from
 #define MAXN 20000    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #define YEARM 12. /* Number of months per year */    first survey ("cross") where individuals from different ages are
 #define AGESUP 130    interviewed on their health status or degree of disability (in the
 #define AGEBASE 40    case of a health survey which is our main interest) -2- at least a
     second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
 int erreur; /* Error number */    computed from the time spent in each health state according to a
 int nvar;    model. More health states you consider, more time is necessary to reach the
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Maximum Likelihood of the parameters involved in the model.  The
 int npar=NPARMAX;    simplest model is the multinomial logistic model where pij is the
 int nlstate=2; /* Number of live states */    probability to be observed in state j at the second wave
 int ndeath=1; /* Number of dead states */    conditional to be observed in state i at the first wave. Therefore
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 int popbased=0;    'age' is age and 'sex' is a covariate. If you want to have a more
     complex model than "constant and age", you should modify the program
 int *wav; /* Number of waves for this individuual 0 is possible */    where the markup *Covariates have to be included here again* invites
 int maxwav; /* Maxim number of waves */    you to do it.  More covariates you add, slower the
 int jmin, jmax; /* min, max spacing between 2 waves */    convergence.
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    The advantage of this computer programme, compared to a simple
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    multinomial logistic model, is clear when the delay between waves is not
 double jmean; /* Mean space between 2 waves */    identical for each individual. Also, if a individual missed an
 double **oldm, **newm, **savm; /* Working pointers to matrices */    intermediate interview, the information is lost, but taken into
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    account using an interpolation or extrapolation.  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;  
 FILE *ficgp,*ficresprob,*ficpop;    hPijx is the probability to be observed in state i at age x+h
 FILE *ficreseij;    conditional to the observed state i at age x. The delay 'h' can be
   char filerese[FILENAMELENGTH];    split into an exact number (nh*stepm) of unobserved intermediate
  FILE  *ficresvij;    states. This elementary transition (by month, quarter,
   char fileresv[FILENAMELENGTH];    semester or year) is modelled as a multinomial logistic.  The hPx
  FILE  *ficresvpl;    matrix is simply the matrix product of nh*stepm elementary matrices
   char fileresvpl[FILENAMELENGTH];    and the contribution of each individual to the likelihood is simply
     hPijx.
 #define NR_END 1  
 #define FREE_ARG char*    Also this programme outputs the covariance matrix of the parameters but also
 #define FTOL 1.0e-10    of the life expectancies. It also computes the stable prevalence. 
     
 #define NRANSI    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #define ITMAX 200             Institut national d'études démographiques, Paris.
     This software have been partly granted by Euro-REVES, a concerted action
 #define TOL 2.0e-4    from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
 #define CGOLD 0.3819660    software can be distributed freely for non commercial use. Latest version
 #define ZEPS 1.0e-10    can be accessed at http://euroreves.ined.fr/imach .
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #define GOLD 1.618034    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #define GLIMIT 100.0    
 #define TINY 1.0e-20    **********************************************************************/
   /*
 static double maxarg1,maxarg2;    main
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    read parameterfile
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    read datafile
      concatwav
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    freqsummary
 #define rint(a) floor(a+0.5)    if (mle >= 1)
       mlikeli
 static double sqrarg;    print results files
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    if mle==1 
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 int imx;        begin-prev-date,...
 int stepm;    open gnuplot file
 /* Stepm, step in month: minimum step interpolation*/    open html file
     stable prevalence
 int m,nb;     for age prevalim()
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    h Pij x
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    variance of p varprob
 double **pmmij, ***probs, ***mobaverage;    forecasting if prevfcast==1 prevforecast call prevalence()
 double dateintmean=0;    health expectancies
     Variance-covariance of DFLE
 double *weight;    prevalence()
 int **s; /* Status */     movingaverage()
 double *agedc, **covar, idx;    varevsij() 
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    if popbased==1 varevsij(,popbased)
     total life expectancies
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Variance of stable prevalence
 double ftolhess; /* Tolerance for computing hessian */   end
   */
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {  
    char *s;                             /* pointer */   
    int  l1, l2;                         /* length counters */  #include <math.h>
   #include <stdio.h>
    l1 = strlen( path );                 /* length of path */  #include <stdlib.h>
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #include <unistd.h>
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */  #include <sys/time.h>
 #else  #include <time.h>
    s = strrchr( path, '/' );            /* find last / */  #include "timeval.h"
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */  #define MAXLINE 256
 #if     defined(__bsd__)                /* get current working directory */  #define GNUPLOTPROGRAM "gnuplot"
       extern char       *getwd( );  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
       if ( getwd( dirc ) == NULL ) {  /*#define DEBUG*/
 #else  /*#define windows*/
       extern char       *getcwd( );  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
          return( GLOCK_ERROR_GETCWD );  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
       }  
       strcpy( name, path );             /* we've got it */  #define NINTERVMAX 8
    } else {                             /* strip direcotry from path */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
       s++;                              /* after this, the filename */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
       l2 = strlen( s );                 /* length of filename */  #define NCOVMAX 8 /* Maximum number of covariates */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define MAXN 20000
       strcpy( name, s );                /* save file name */  #define YEARM 12. /* Number of months per year */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define AGESUP 130
       dirc[l1-l2] = 0;                  /* add zero */  #define AGEBASE 40
    }  #ifdef unix
    l1 = strlen( dirc );                 /* length of directory */  #define DIRSEPARATOR '/'
 #ifdef windows  #define ODIRSEPARATOR '\\'
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #else
 #else  #define DIRSEPARATOR '\\'
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  #define ODIRSEPARATOR '/'
 #endif  #endif
    s = strrchr( name, '.' );            /* find last / */  
    s++;  /* $Id$ */
    strcpy(ext,s);                       /* save extension */  /* $State$ */
    l1= strlen( name);  
    l2= strlen( s)+1;  char version[]="Imach version 0.96b, June 2003, INED-EUROREVES ";
    strncpy( finame, name, l1-l2);  char fullversion[]="$Revision$ $Date$"; 
    finame[l1-l2]= 0;  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
    return( 0 );                         /* we're done */  int nvar;
 }  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
 /******************************************/  int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 void replace(char *s, char*t)  int popbased=0;
 {  
   int i;  int *wav; /* Number of waves for this individuual 0 is possible */
   int lg=20;  int maxwav; /* Maxim number of waves */
   i=0;  int jmin, jmax; /* min, max spacing between 2 waves */
   lg=strlen(t);  int gipmx, gsw; /* Global variables on the number of contributions 
   for(i=0; i<= lg; i++) {                     to the likelihood and the sum of weights (done by funcone)*/
     (s[i] = t[i]);  int mle, weightopt;
     if (t[i]== '\\') s[i]='/';  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   }  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 }  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
              * wave mi and wave mi+1 is not an exact multiple of stepm. */
 int nbocc(char *s, char occ)  double jmean; /* Mean space between 2 waves */
 {  double **oldm, **newm, **savm; /* Working pointers to matrices */
   int i,j=0;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   int lg=20;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   i=0;  FILE *ficlog, *ficrespow;
   lg=strlen(s);  int globpr; /* Global variable for printing or not */
   for(i=0; i<= lg; i++) {  double fretone; /* Only one call to likelihood */
   if  (s[i] == occ ) j++;  long ipmx; /* Number of contributions */
   }  double sw; /* Sum of weights */
   return j;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 }  FILE *ficresilk;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 void cutv(char *u,char *v, char*t, char occ)  FILE *ficresprobmorprev;
 {  FILE *fichtm, *fichtmcov; /* Html File */
   int i,lg,j,p=0;  FILE *ficreseij;
   i=0;  char filerese[FILENAMELENGTH];
   for(j=0; j<=strlen(t)-1; j++) {  FILE  *ficresvij;
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  char fileresv[FILENAMELENGTH];
   }  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
   lg=strlen(t);  char title[MAXLINE];
   for(j=0; j<p; j++) {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     (u[j] = t[j]);  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   }  char tmpout[FILENAMELENGTH]; 
      u[p]='\0';  char command[FILENAMELENGTH];
   int  outcmd=0;
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   }  char lfileres[FILENAMELENGTH];
 }  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
 /********************** nrerror ********************/  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
 void nrerror(char error_text[])  
 {  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   exit(1);  struct timezone tzp;
 }  extern int gettimeofday();
 /*********************** vector *******************/  struct tm tmg, tm, tmf, *gmtime(), *localtime();
 double *vector(int nl, int nh)  long time_value;
 {  extern long time();
   double *v;  char strcurr[80], strfor[80];
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  #define NR_END 1
   return v-nl+NR_END;  #define FREE_ARG char*
 }  #define FTOL 1.0e-10
   
 /************************ free vector ******************/  #define NRANSI 
 void free_vector(double*v, int nl, int nh)  #define ITMAX 200 
 {  
   free((FREE_ARG)(v+nl-NR_END));  #define TOL 2.0e-4 
 }  
   #define CGOLD 0.3819660 
 /************************ivector *******************************/  #define ZEPS 1.0e-10 
 int *ivector(long nl,long nh)  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 {  
   int *v;  #define GOLD 1.618034 
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #define GLIMIT 100.0 
   if (!v) nrerror("allocation failure in ivector");  #define TINY 1.0e-20 
   return v-nl+NR_END;  
 }  static double maxarg1,maxarg2;
   #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 /******************free ivector **************************/  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 void free_ivector(int *v, long nl, long nh)    
 {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   free((FREE_ARG)(v+nl-NR_END));  #define rint(a) floor(a+0.5)
 }  
   static double sqrarg;
 /******************* imatrix *******************************/  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {  int imx; 
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  int stepm;
   int **m;  /* Stepm, step in month: minimum step interpolation*/
    
   /* allocate pointers to rows */  int estepm;
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  int m,nb;
   m -= nrl;  long *num;
    int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
    double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   /* allocate rows and set pointers to them */  double **pmmij, ***probs;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  double dateintmean=0;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  double *weight;
   m[nrl] -= ncl;  int **s; /* Status */
    double *agedc, **covar, idx;
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
    
   /* return pointer to array of pointers to rows */  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   return m;  double ftolhess; /* Tolerance for computing hessian */
 }  
   /**************** split *************************/
 /****************** free_imatrix *************************/  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 void free_imatrix(m,nrl,nrh,ncl,nch)  {
       int **m;    char  *ss;                            /* pointer */
       long nch,ncl,nrh,nrl;    int   l1, l2;                         /* length counters */
      /* free an int matrix allocated by imatrix() */  
 {    l1 = strlen(path );                   /* length of path */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   free((FREE_ARG) (m+nrl-NR_END));    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 }    if ( ss == NULL ) {                   /* no directory, so use current */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 /******************* matrix *******************************/        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 double **matrix(long nrl, long nrh, long ncl, long nch)      /* get current working directory */
 {      /*    extern  char* getcwd ( char *buf , int len);*/
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   double **m;        return( GLOCK_ERROR_GETCWD );
       }
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));      strcpy( name, path );               /* we've got it */
   if (!m) nrerror("allocation failure 1 in matrix()");    } else {                              /* strip direcotry from path */
   m += NR_END;      ss++;                               /* after this, the filename */
   m -= nrl;      l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));      strcpy( name, ss );         /* save file name */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   m[nrl] += NR_END;      dirc[l1-l2] = 0;                    /* add zero */
   m[nrl] -= ncl;    }
     l1 = strlen( dirc );                  /* length of directory */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    /*#ifdef windows
   return m;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 }  #else
     if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 /*************************free matrix ************************/  #endif
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    */
 {    ss = strrchr( name, '.' );            /* find last / */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    ss++;
   free((FREE_ARG)(m+nrl-NR_END));    strcpy(ext,ss);                       /* save extension */
 }    l1= strlen( name);
     l2= strlen(ss)+1;
 /******************* ma3x *******************************/    strncpy( finame, name, l1-l2);
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    finame[l1-l2]= 0;
 {    return( 0 );                          /* we're done */
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  }
   double ***m;  
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  /******************************************/
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  void replace_back_to_slash(char *s, char*t)
   m -= nrl;  {
     int i;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    int lg=0;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    i=0;
   m[nrl] += NR_END;    lg=strlen(t);
   m[nrl] -= ncl;    for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;      if (t[i]== '\\') s[i]='/';
     }
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  }
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  int nbocc(char *s, char occ)
   m[nrl][ncl] -= nll;  {
   for (j=ncl+1; j<=nch; j++)    int i,j=0;
     m[nrl][j]=m[nrl][j-1]+nlay;    int lg=20;
      i=0;
   for (i=nrl+1; i<=nrh; i++) {    lg=strlen(s);
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    for(i=0; i<= lg; i++) {
     for (j=ncl+1; j<=nch; j++)    if  (s[i] == occ ) j++;
       m[i][j]=m[i][j-1]+nlay;    }
   }    return j;
   return m;  }
 }  
   void cutv(char *u,char *v, char*t, char occ)
 /*************************free ma3x ************************/  {
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    /* cuts string t into u and v where u is ended by char occ excluding it
 {       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));       gives u="abcedf" and v="ghi2j" */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    int i,lg,j,p=0;
   free((FREE_ARG)(m+nrl-NR_END));    i=0;
 }    for(j=0; j<=strlen(t)-1; j++) {
       if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 /***************** f1dim *************************/    }
 extern int ncom;  
 extern double *pcom,*xicom;    lg=strlen(t);
 extern double (*nrfunc)(double []);    for(j=0; j<p; j++) {
        (u[j] = t[j]);
 double f1dim(double x)    }
 {       u[p]='\0';
   int j;  
   double f;     for(j=0; j<= lg; j++) {
   double *xt;      if (j>=(p+1))(v[j-p-1] = t[j]);
      }
   xt=vector(1,ncom);  }
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);  /********************** nrerror ********************/
   free_vector(xt,1,ncom);  
   return f;  void nrerror(char error_text[])
 }  {
     fprintf(stderr,"ERREUR ...\n");
 /*****************brent *************************/    fprintf(stderr,"%s\n",error_text);
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    exit(EXIT_FAILURE);
 {  }
   int iter;  /*********************** vector *******************/
   double a,b,d,etemp;  double *vector(int nl, int nh)
   double fu,fv,fw,fx;  {
   double ftemp;    double *v;
   double p,q,r,tol1,tol2,u,v,w,x,xm;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   double e=0.0;    if (!v) nrerror("allocation failure in vector");
      return v-nl+NR_END;
   a=(ax < cx ? ax : cx);  }
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;  /************************ free vector ******************/
   fw=fv=fx=(*f)(x);  void free_vector(double*v, int nl, int nh)
   for (iter=1;iter<=ITMAX;iter++) {  {
     xm=0.5*(a+b);    free((FREE_ARG)(v+nl-NR_END));
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  }
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  /************************ivector *******************************/
 #ifdef DEBUG  int *ivector(long nl,long nh)
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  {
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    int *v;
 #endif    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    if (!v) nrerror("allocation failure in ivector");
       *xmin=x;    return v-nl+NR_END;
       return fx;  }
     }  
     ftemp=fu;  /******************free ivector **************************/
     if (fabs(e) > tol1) {  void free_ivector(int *v, long nl, long nh)
       r=(x-w)*(fx-fv);  {
       q=(x-v)*(fx-fw);    free((FREE_ARG)(v+nl-NR_END));
       p=(x-v)*q-(x-w)*r;  }
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;  /************************lvector *******************************/
       q=fabs(q);  long *lvector(long nl,long nh)
       etemp=e;  {
       e=d;    long *v;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    if (!v) nrerror("allocation failure in ivector");
       else {    return v-nl+NR_END;
         d=p/q;  }
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)  /******************free lvector **************************/
           d=SIGN(tol1,xm-x);  void free_lvector(long *v, long nl, long nh)
       }  {
     } else {    free((FREE_ARG)(v+nl-NR_END));
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  }
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  /******************* imatrix *******************************/
     fu=(*f)(u);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     if (fu <= fx) {       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       if (u >= x) a=x; else b=x;  { 
       SHFT(v,w,x,u)    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
         SHFT(fv,fw,fx,fu)    int **m; 
         } else {    
           if (u < x) a=u; else b=u;    /* allocate pointers to rows */ 
           if (fu <= fw || w == x) {    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
             v=w;    if (!m) nrerror("allocation failure 1 in matrix()"); 
             w=u;    m += NR_END; 
             fv=fw;    m -= nrl; 
             fw=fu;    
           } else if (fu <= fv || v == x || v == w) {    
             v=u;    /* allocate rows and set pointers to them */ 
             fv=fu;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
           }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
         }    m[nrl] += NR_END; 
   }    m[nrl] -= ncl; 
   nrerror("Too many iterations in brent");    
   *xmin=x;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   return fx;    
 }    /* return pointer to array of pointers to rows */ 
     return m; 
 /****************** mnbrak ***********************/  } 
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  /****************** free_imatrix *************************/
             double (*func)(double))  void free_imatrix(m,nrl,nrh,ncl,nch)
 {        int **m;
   double ulim,u,r,q, dum;        long nch,ncl,nrh,nrl; 
   double fu;       /* free an int matrix allocated by imatrix() */ 
    { 
   *fa=(*func)(*ax);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   *fb=(*func)(*bx);    free((FREE_ARG) (m+nrl-NR_END)); 
   if (*fb > *fa) {  } 
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  /******************* matrix *******************************/
       }  double **matrix(long nrl, long nrh, long ncl, long nch)
   *cx=(*bx)+GOLD*(*bx-*ax);  {
   *fc=(*func)(*cx);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   while (*fb > *fc) {    double **m;
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    if (!m) nrerror("allocation failure 1 in matrix()");
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    m += NR_END;
     ulim=(*bx)+GLIMIT*(*cx-*bx);    m -= nrl;
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     } else if ((*cx-u)*(u-ulim) > 0.0) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       fu=(*func)(u);    m[nrl] += NR_END;
       if (fu < *fc) {    m[nrl] -= ncl;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
           }    return m;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       u=ulim;     */
       fu=(*func)(u);  }
     } else {  
       u=(*cx)+GOLD*(*cx-*bx);  /*************************free matrix ************************/
       fu=(*func)(u);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     }  {
     SHFT(*ax,*bx,*cx,u)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       SHFT(*fa,*fb,*fc,fu)    free((FREE_ARG)(m+nrl-NR_END));
       }  }
 }  
   /******************* ma3x *******************************/
 /*************** linmin ************************/  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   {
 int ncom;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
 double *pcom,*xicom;    double ***m;
 double (*nrfunc)(double []);  
      m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    if (!m) nrerror("allocation failure 1 in matrix()");
 {    m += NR_END;
   double brent(double ax, double bx, double cx,    m -= nrl;
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
               double *fc, double (*func)(double));    m[nrl] += NR_END;
   int j;    m[nrl] -= ncl;
   double xx,xmin,bx,ax;  
   double fx,fb,fa;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
    
   ncom=n;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   pcom=vector(1,n);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   xicom=vector(1,n);    m[nrl][ncl] += NR_END;
   nrfunc=func;    m[nrl][ncl] -= nll;
   for (j=1;j<=n;j++) {    for (j=ncl+1; j<=nch; j++) 
     pcom[j]=p[j];      m[nrl][j]=m[nrl][j-1]+nlay;
     xicom[j]=xi[j];    
   }    for (i=nrl+1; i<=nrh; i++) {
   ax=0.0;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   xx=1.0;      for (j=ncl+1; j<=nch; j++) 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);        m[i][j]=m[i][j-1]+nlay;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    }
 #ifdef DEBUG    return m; 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 #endif             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   for (j=1;j<=n;j++) {    */
     xi[j] *= xmin;  }
     p[j] += xi[j];  
   }  /*************************free ma3x ************************/
   free_vector(xicom,1,n);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   free_vector(pcom,1,n);  {
 }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
 /*************** powell ************************/    free((FREE_ARG)(m+nrl-NR_END));
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  }
             double (*func)(double []))  
 {  /***************** f1dim *************************/
   void linmin(double p[], double xi[], int n, double *fret,  extern int ncom; 
               double (*func)(double []));  extern double *pcom,*xicom;
   int i,ibig,j;  extern double (*nrfunc)(double []); 
   double del,t,*pt,*ptt,*xit;   
   double fp,fptt;  double f1dim(double x) 
   double *xits;  { 
   pt=vector(1,n);    int j; 
   ptt=vector(1,n);    double f;
   xit=vector(1,n);    double *xt; 
   xits=vector(1,n);   
   *fret=(*func)(p);    xt=vector(1,ncom); 
   for (j=1;j<=n;j++) pt[j]=p[j];    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   for (*iter=1;;++(*iter)) {    f=(*nrfunc)(xt); 
     fp=(*fret);    free_vector(xt,1,ncom); 
     ibig=0;    return f; 
     del=0.0;  } 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     for (i=1;i<=n;i++)  /*****************brent *************************/
       printf(" %d %.12f",i, p[i]);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     printf("\n");  { 
     for (i=1;i<=n;i++) {    int iter; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    double a,b,d,etemp;
       fptt=(*fret);    double fu,fv,fw,fx;
 #ifdef DEBUG    double ftemp;
       printf("fret=%lf \n",*fret);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
 #endif    double e=0.0; 
       printf("%d",i);fflush(stdout);   
       linmin(p,xit,n,fret,func);    a=(ax < cx ? ax : cx); 
       if (fabs(fptt-(*fret)) > del) {    b=(ax > cx ? ax : cx); 
         del=fabs(fptt-(*fret));    x=w=v=bx; 
         ibig=i;    fw=fv=fx=(*f)(x); 
       }    for (iter=1;iter<=ITMAX;iter++) { 
 #ifdef DEBUG      xm=0.5*(a+b); 
       printf("%d %.12e",i,(*fret));      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       for (j=1;j<=n;j++) {      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      printf(".");fflush(stdout);
         printf(" x(%d)=%.12e",j,xit[j]);      fprintf(ficlog,".");fflush(ficlog);
       }  #ifdef DEBUG
       for(j=1;j<=n;j++)      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);
         printf(" p=%.12e",p[j]);      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);
       printf("\n");      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 #endif  #endif
     }      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {        *xmin=x; 
 #ifdef DEBUG        return fx; 
       int k[2],l;      } 
       k[0]=1;      ftemp=fu;
       k[1]=-1;      if (fabs(e) > tol1) { 
       printf("Max: %.12e",(*func)(p));        r=(x-w)*(fx-fv); 
       for (j=1;j<=n;j++)        q=(x-v)*(fx-fw); 
         printf(" %.12e",p[j]);        p=(x-v)*q-(x-w)*r; 
       printf("\n");        q=2.0*(q-r); 
       for(l=0;l<=1;l++) {        if (q > 0.0) p = -p; 
         for (j=1;j<=n;j++) {        q=fabs(q); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        etemp=e; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);        e=d; 
         }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       }        else { 
 #endif          d=p/q; 
           u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
       free_vector(xit,1,n);            d=SIGN(tol1,xm-x); 
       free_vector(xits,1,n);        } 
       free_vector(ptt,1,n);      } else { 
       free_vector(pt,1,n);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       return;      } 
     }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");      fu=(*f)(u); 
     for (j=1;j<=n;j++) {      if (fu <= fx) { 
       ptt[j]=2.0*p[j]-pt[j];        if (u >= x) a=x; else b=x; 
       xit[j]=p[j]-pt[j];        SHFT(v,w,x,u) 
       pt[j]=p[j];          SHFT(fv,fw,fx,fu) 
     }          } else { 
     fptt=(*func)(ptt);            if (u < x) a=u; else b=u; 
     if (fptt < fp) {            if (fu <= fw || w == x) { 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);              v=w; 
       if (t < 0.0) {              w=u; 
         linmin(p,xit,n,fret,func);              fv=fw; 
         for (j=1;j<=n;j++) {              fw=fu; 
           xi[j][ibig]=xi[j][n];            } else if (fu <= fv || v == x || v == w) { 
           xi[j][n]=xit[j];              v=u; 
         }              fv=fu; 
 #ifdef DEBUG            } 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);          } 
         for(j=1;j<=n;j++)    } 
           printf(" %.12e",xit[j]);    nrerror("Too many iterations in brent"); 
         printf("\n");    *xmin=x; 
 #endif    return fx; 
       }  } 
     }  
   }  /****************** mnbrak ***********************/
 }  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
 /**** Prevalence limit ****************/              double (*func)(double)) 
   { 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    double ulim,u,r,q, dum;
 {    double fu; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit   
      matrix by transitions matrix until convergence is reached */    *fa=(*func)(*ax); 
     *fb=(*func)(*bx); 
   int i, ii,j,k;    if (*fb > *fa) { 
   double min, max, maxmin, maxmax,sumnew=0.;      SHFT(dum,*ax,*bx,dum) 
   double **matprod2();        SHFT(dum,*fb,*fa,dum) 
   double **out, cov[NCOVMAX], **pmij();        } 
   double **newm;    *cx=(*bx)+GOLD*(*bx-*ax); 
   double agefin, delaymax=50 ; /* Max number of years to converge */    *fc=(*func)(*cx); 
     while (*fb > *fc) { 
   for (ii=1;ii<=nlstate+ndeath;ii++)      r=(*bx-*ax)*(*fb-*fc); 
     for (j=1;j<=nlstate+ndeath;j++){      q=(*bx-*cx)*(*fb-*fa); 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
    cov[1]=1.;      if ((*bx-u)*(u-*cx) > 0.0) { 
          fu=(*func)(u); 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        fu=(*func)(u); 
     newm=savm;        if (fu < *fc) { 
     /* Covariates have to be included here again */          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
      cov[2]=agefin;            SHFT(*fb,*fc,fu,(*func)(u)) 
              } 
       for (k=1; k<=cptcovn;k++) {      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        u=ulim; 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/        fu=(*func)(u); 
       }      } else { 
       for (k=1; k<=cptcovage;k++)        u=(*cx)+GOLD*(*cx-*bx); 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        fu=(*func)(u); 
       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]]];      SHFT(*ax,*bx,*cx,u) 
         SHFT(*fa,*fb,*fc,fu) 
       /*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]);*/  } 
   
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  /*************** linmin ************************/
   
     savm=oldm;  int ncom; 
     oldm=newm;  double *pcom,*xicom;
     maxmax=0.;  double (*nrfunc)(double []); 
     for(j=1;j<=nlstate;j++){   
       min=1.;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       max=0.;  { 
       for(i=1; i<=nlstate; i++) {    double brent(double ax, double bx, double cx, 
         sumnew=0;                 double (*f)(double), double tol, double *xmin); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    double f1dim(double x); 
         prlim[i][j]= newm[i][j]/(1-sumnew);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         max=FMAX(max,prlim[i][j]);                double *fc, double (*func)(double)); 
         min=FMIN(min,prlim[i][j]);    int j; 
       }    double xx,xmin,bx,ax; 
       maxmin=max-min;    double fx,fb,fa;
       maxmax=FMAX(maxmax,maxmin);   
     }    ncom=n; 
     if(maxmax < ftolpl){    pcom=vector(1,n); 
       return prlim;    xicom=vector(1,n); 
     }    nrfunc=func; 
   }    for (j=1;j<=n;j++) { 
 }      pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
 /*************** transition probabilities ***************/    } 
     ax=0.0; 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    xx=1.0; 
 {    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   double s1, s2;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   /*double t34;*/  #ifdef DEBUG
   int i,j,j1, nc, ii, jj;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     for(i=1; i<= nlstate; i++){  #endif
     for(j=1; j<i;j++){    for (j=1;j<=n;j++) { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      xi[j] *= xmin; 
         /*s2 += param[i][j][nc]*cov[nc];*/      p[j] += xi[j]; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    } 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    free_vector(xicom,1,n); 
       }    free_vector(pcom,1,n); 
       ps[i][j]=s2;  } 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }  char *asc_diff_time(long time_sec, char ascdiff[])
     for(j=i+1; j<=nlstate+ndeath;j++){  {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    long sec_left, days, hours, minutes;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    days = (time_sec) / (60*60*24);
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    sec_left = (time_sec) % (60*60*24);
       }    hours = (sec_left) / (60*60) ;
       ps[i][j]=s2;    sec_left = (sec_left) %(60*60);
     }    minutes = (sec_left) /60;
   }    sec_left = (sec_left) % (60);
     /*ps[3][2]=1;*/    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     return ascdiff;
   for(i=1; i<= nlstate; i++){  }
      s1=0;  
     for(j=1; j<i; j++)  /*************** powell ************************/
       s1+=exp(ps[i][j]);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     for(j=i+1; j<=nlstate+ndeath; j++)              double (*func)(double [])) 
       s1+=exp(ps[i][j]);  { 
     ps[i][i]=1./(s1+1.);    void linmin(double p[], double xi[], int n, double *fret, 
     for(j=1; j<i; j++)                double (*func)(double [])); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    int i,ibig,j; 
     for(j=i+1; j<=nlstate+ndeath; j++)    double del,t,*pt,*ptt,*xit;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    double fp,fptt;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    double *xits;
   } /* end i */    int niterf, itmp;
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    pt=vector(1,n); 
     for(jj=1; jj<= nlstate+ndeath; jj++){    ptt=vector(1,n); 
       ps[ii][jj]=0;    xit=vector(1,n); 
       ps[ii][ii]=1;    xits=vector(1,n); 
     }    *fret=(*func)(p); 
   }    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      ibig=0; 
     for(jj=1; jj<= nlstate+ndeath; jj++){      del=0.0; 
      printf("%lf ",ps[ii][jj]);      last_time=curr_time;
    }      (void) gettimeofday(&curr_time,&tzp);
     printf("\n ");      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);
     printf("\n ");printf("%lf ",cov[2]);*/      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
 /*      for (i=1;i<=n;i++) {
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        printf(" %d %.12f",i, p[i]);
   goto end;*/        fprintf(ficlog," %d %.12lf",i, p[i]);
     return ps;        fprintf(ficrespow," %.12lf", p[i]);
 }      }
       printf("\n");
 /**************** Product of 2 matrices ******************/      fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");fflush(ficrespow);
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      if(*iter <=3){
 {        tm = *localtime(&curr_time.tv_sec);
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        strcpy(strcurr,asctime(&tmf));
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  /*       asctime_r(&tm,strcurr); */
   /* in, b, out are matrice of pointers which should have been initialized        forecast_time=curr_time;
      before: only the contents of out is modified. The function returns        itmp = strlen(strcurr);
      a pointer to pointers identical to out */        if(strcurr[itmp-1]=='\n')
   long i, j, k;          strcurr[itmp-1]='\0';
   for(i=nrl; i<= nrh; i++)        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     for(k=ncolol; k<=ncoloh; k++)        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        for(niterf=10;niterf<=30;niterf+=10){
         out[i][k] +=in[i][j]*b[j][k];          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
           tmf = *localtime(&forecast_time.tv_sec);
   return out;  /*      asctime_r(&tmf,strfor); */
 }          strcpy(strfor,asctime(&tmf));
           itmp = strlen(strfor);
           if(strfor[itmp-1]=='\n')
 /************* Higher Matrix Product ***************/          strfor[itmp-1]='\0';
           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);
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )          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);
 {        }
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      }
      duration (i.e. until      for (i=1;i<=n;i++) { 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        fptt=(*fret); 
      (typically every 2 years instead of every month which is too big).  #ifdef DEBUG
      Model is determined by parameters x and covariates have to be        printf("fret=%lf \n",*fret);
      included manually here.        fprintf(ficlog,"fret=%lf \n",*fret);
   #endif
      */        printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
   int i, j, d, h, k;        linmin(p,xit,n,fret,func); 
   double **out, cov[NCOVMAX];        if (fabs(fptt-(*fret)) > del) { 
   double **newm;          del=fabs(fptt-(*fret)); 
           ibig=i; 
   /* Hstepm could be zero and should return the unit matrix */        } 
   for (i=1;i<=nlstate+ndeath;i++)  #ifdef DEBUG
     for (j=1;j<=nlstate+ndeath;j++){        printf("%d %.12e",i,(*fret));
       oldm[i][j]=(i==j ? 1.0 : 0.0);        fprintf(ficlog,"%d %.12e",i,(*fret));
       po[i][j][0]=(i==j ? 1.0 : 0.0);        for (j=1;j<=n;j++) {
     }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */          printf(" x(%d)=%.12e",j,xit[j]);
   for(h=1; h <=nhstepm; h++){          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     for(d=1; d <=hstepm; d++){        }
       newm=savm;        for(j=1;j<=n;j++) {
       /* Covariates have to be included here again */          printf(" p=%.12e",p[j]);
       cov[1]=1.;          fprintf(ficlog," p=%.12e",p[j]);
       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]]];        printf("\n");
       for (k=1; k<=cptcovage;k++)        fprintf(ficlog,"\n");
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  #endif
       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]]];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   #ifdef DEBUG
         int k[2],l;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        k[0]=1;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        k[1]=-1;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        printf("Max: %.12e",(*func)(p));
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        fprintf(ficlog,"Max: %.12e",(*func)(p));
       savm=oldm;        for (j=1;j<=n;j++) {
       oldm=newm;          printf(" %.12e",p[j]);
     }          fprintf(ficlog," %.12e",p[j]);
     for(i=1; i<=nlstate+ndeath; i++)        }
       for(j=1;j<=nlstate+ndeath;j++) {        printf("\n");
         po[i][j][h]=newm[i][j];        fprintf(ficlog,"\n");
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        for(l=0;l<=1;l++) {
          */          for (j=1;j<=n;j++) {
       }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   } /* end h */            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   return po;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 }          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 /*************** log-likelihood *************/        }
 double func( double *x)  #endif
 {  
   int i, ii, j, k, mi, d, kk;  
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        free_vector(xit,1,n); 
   double **out;        free_vector(xits,1,n); 
   double sw; /* Sum of weights */        free_vector(ptt,1,n); 
   double lli; /* Individual log likelihood */        free_vector(pt,1,n); 
   long ipmx;        return; 
   /*extern weight */      } 
   /* We are differentiating ll according to initial status */      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      for (j=1;j<=n;j++) { 
   /*for(i=1;i<imx;i++)        ptt[j]=2.0*p[j]-pt[j]; 
     printf(" %d\n",s[4][i]);        xit[j]=p[j]-pt[j]; 
   */        pt[j]=p[j]; 
   cov[1]=1.;      } 
       fptt=(*func)(ptt); 
   for(k=1; k<=nlstate; k++) ll[k]=0.;      if (fptt < fp) { 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        if (t < 0.0) { 
     for(mi=1; mi<= wav[i]-1; mi++){          linmin(p,xit,n,fret,func); 
       for (ii=1;ii<=nlstate+ndeath;ii++)          for (j=1;j<=n;j++) { 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);            xi[j][ibig]=xi[j][n]; 
       for(d=0; d<dh[mi][i]; d++){            xi[j][n]=xit[j]; 
         newm=savm;          }
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  #ifdef DEBUG
         for (kk=1; kk<=cptcovage;kk++) {          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[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]);
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            fprintf(ficlog," %.12e",xit[j]);
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));          }
         savm=oldm;          printf("\n");
         oldm=newm;          fprintf(ficlog,"\n");
          #endif
                }
       } /* end mult */      } 
          } 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  } 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  
       ipmx +=1;  /**** Prevalence limit (stable prevalence)  ****************/
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     } /* end of wave */  {
   } /* end of individual */    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
        matrix by transitions matrix until convergence is reached */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    int i, ii,j,k;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    double min, max, maxmin, maxmax,sumnew=0.;
   return -l;    double **matprod2();
 }    double **out, cov[NCOVMAX], **pmij();
     double **newm;
     double agefin, delaymax=50 ; /* Max number of years to converge */
 /*********** Maximum Likelihood Estimation ***************/  
     for (ii=1;ii<=nlstate+ndeath;ii++)
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      for (j=1;j<=nlstate+ndeath;j++){
 {        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i,j, iter;      }
   double **xi,*delti;  
   double fret;     cov[1]=1.;
   xi=matrix(1,npar,1,npar);   
   for (i=1;i<=npar;i++)   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for (j=1;j<=npar;j++)    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       xi[i][j]=(i==j ? 1.0 : 0.0);      newm=savm;
   printf("Powell\n");      /* Covariates have to be included here again */
   powell(p,xi,npar,ftol,&iter,&fret,func);       cov[2]=agefin;
     
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        for (k=1; k<=cptcovn;k++) {
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
 }        }
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 /**** Computes Hessian and covariance matrix ***/        for (k=1; k<=cptcovprod;k++)
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 {  
   double  **a,**y,*x,pd;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   double **hess;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   int i, j,jk;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   int *indx;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
   double hessii(double p[], double delta, int theta, double delti[]);      savm=oldm;
   double hessij(double p[], double delti[], int i, int j);      oldm=newm;
   void lubksb(double **a, int npar, int *indx, double b[]) ;      maxmax=0.;
   void ludcmp(double **a, int npar, int *indx, double *d) ;      for(j=1;j<=nlstate;j++){
         min=1.;
   hess=matrix(1,npar,1,npar);        max=0.;
         for(i=1; i<=nlstate; i++) {
   printf("\nCalculation of the hessian matrix. Wait...\n");          sumnew=0;
   for (i=1;i<=npar;i++){          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     printf("%d",i);fflush(stdout);          prlim[i][j]= newm[i][j]/(1-sumnew);
     hess[i][i]=hessii(p,ftolhess,i,delti);          max=FMAX(max,prlim[i][j]);
     /*printf(" %f ",p[i]);*/          min=FMIN(min,prlim[i][j]);
     /*printf(" %lf ",hess[i][i]);*/        }
   }        maxmin=max-min;
          maxmax=FMAX(maxmax,maxmin);
   for (i=1;i<=npar;i++) {      }
     for (j=1;j<=npar;j++)  {      if(maxmax < ftolpl){
       if (j>i) {        return prlim;
         printf(".%d%d",i,j);fflush(stdout);      }
         hess[i][j]=hessij(p,delti,i,j);    }
         hess[j][i]=hess[i][j];      }
         /*printf(" %lf ",hess[i][j]);*/  
       }  /*************** transition probabilities ***************/ 
     }  
   }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   printf("\n");  {
     double s1, s2;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    /*double t34;*/
      int i,j,j1, nc, ii, jj;
   a=matrix(1,npar,1,npar);  
   y=matrix(1,npar,1,npar);      for(i=1; i<= nlstate; i++){
   x=vector(1,npar);      for(j=1; j<i;j++){
   indx=ivector(1,npar);        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   for (i=1;i<=npar;i++)          /*s2 += param[i][j][nc]*cov[nc];*/
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   ludcmp(a,npar,indx,&pd);          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         }
   for (j=1;j<=npar;j++) {        ps[i][j]=s2;
     for (i=1;i<=npar;i++) x[i]=0;        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
     x[j]=1;      }
     lubksb(a,npar,indx,x);      for(j=i+1; j<=nlstate+ndeath;j++){
     for (i=1;i<=npar;i++){        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       matcov[i][j]=x[i];          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     }          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   }        }
         ps[i][j]=s2;
   printf("\n#Hessian matrix#\n");      }
   for (i=1;i<=npar;i++) {    }
     for (j=1;j<=npar;j++) {      /*ps[3][2]=1;*/
       printf("%.3e ",hess[i][j]);  
     }    for(i=1; i<= nlstate; i++){
     printf("\n");       s1=0;
   }      for(j=1; j<i; j++)
         s1+=exp(ps[i][j]);
   /* Recompute Inverse */      for(j=i+1; j<=nlstate+ndeath; j++)
   for (i=1;i<=npar;i++)        s1+=exp(ps[i][j]);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      ps[i][i]=1./(s1+1.);
   ludcmp(a,npar,indx,&pd);      for(j=1; j<i; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
   /*  printf("\n#Hessian matrix recomputed#\n");      for(j=i+1; j<=nlstate+ndeath; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
   for (j=1;j<=npar;j++) {      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     for (i=1;i<=npar;i++) x[i]=0;    } /* end i */
     x[j]=1;  
     lubksb(a,npar,indx,x);    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     for (i=1;i<=npar;i++){      for(jj=1; jj<= nlstate+ndeath; jj++){
       y[i][j]=x[i];        ps[ii][jj]=0;
       printf("%.3e ",y[i][j]);        ps[ii][ii]=1;
     }      }
     printf("\n");    }
   }  
   */  
     /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   free_matrix(a,1,npar,1,npar);      for(jj=1; jj<= nlstate+ndeath; jj++){
   free_matrix(y,1,npar,1,npar);       printf("%lf ",ps[ii][jj]);
   free_vector(x,1,npar);     }
   free_ivector(indx,1,npar);      printf("\n ");
   free_matrix(hess,1,npar,1,npar);      }
       printf("\n ");printf("%lf ",cov[2]);*/
   /*
 }    for(i=1; i<= npar; i++) printf("%f ",x[i]);
     goto end;*/
 /*************** hessian matrix ****************/      return ps;
 double hessii( double x[], double delta, int theta, double delti[])  }
 {  
   int i;  /**************** Product of 2 matrices ******************/
   int l=1, lmax=20;  
   double k1,k2;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   double p2[NPARMAX+1];  {
   double res;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   double fx;    /* in, b, out are matrice of pointers which should have been initialized 
   int k=0,kmax=10;       before: only the contents of out is modified. The function returns
   double l1;       a pointer to pointers identical to out */
     long i, j, k;
   fx=func(x);    for(i=nrl; i<= nrh; i++)
   for (i=1;i<=npar;i++) p2[i]=x[i];      for(k=ncolol; k<=ncoloh; k++)
   for(l=0 ; l <=lmax; l++){        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     l1=pow(10,l);          out[i][k] +=in[i][j]*b[j][k];
     delts=delt;  
     for(k=1 ; k <kmax; k=k+1){    return out;
       delt = delta*(l1*k);  }
       p2[theta]=x[theta] +delt;  
       k1=func(p2)-fx;  
       p2[theta]=x[theta]-delt;  /************* Higher Matrix Product ***************/
       k2=func(p2)-fx;  
       /*res= (k1-2.0*fx+k2)/delt/delt; */  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  {
          /* Computes the transition matrix starting at age 'age' over 
 #ifdef DEBUG       'nhstepm*hstepm*stepm' months (i.e. until
       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);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
 #endif       nhstepm*hstepm matrices. 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){       (typically every 2 years instead of every month which is too big 
         k=kmax;       for the memory).
       }       Model is determined by parameters x and covariates have to be 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */       included manually here. 
         k=kmax; l=lmax*10.;  
       }       */
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  
         delts=delt;    int i, j, d, h, k;
       }    double **out, cov[NCOVMAX];
     }    double **newm;
   }  
   delti[theta]=delts;    /* Hstepm could be zero and should return the unit matrix */
   return res;    for (i=1;i<=nlstate+ndeath;i++)
        for (j=1;j<=nlstate+ndeath;j++){
 }        oldm[i][j]=(i==j ? 1.0 : 0.0);
         po[i][j][0]=(i==j ? 1.0 : 0.0);
 double hessij( double x[], double delti[], int thetai,int thetaj)      }
 {    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   int i;    for(h=1; h <=nhstepm; h++){
   int l=1, l1, lmax=20;      for(d=1; d <=hstepm; d++){
   double k1,k2,k3,k4,res,fx;        newm=savm;
   double p2[NPARMAX+1];        /* Covariates have to be included here again */
   int k;        cov[1]=1.;
         cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   fx=func(x);        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   for (k=1; k<=2; k++) {        for (k=1; k<=cptcovage;k++)
     for (i=1;i<=npar;i++) p2[i]=x[i];          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     p2[thetai]=x[thetai]+delti[thetai]/k;        for (k=1; k<=cptcovprod;k++)
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     k1=func(p2)-fx;  
    
     p2[thetai]=x[thetai]+delti[thetai]/k;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     k2=func(p2)-fx;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,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;
     k3=func(p2)-fx;      }
        for(i=1; i<=nlstate+ndeath; i++)
     p2[thetai]=x[thetai]-delti[thetai]/k;        for(j=1;j<=nlstate+ndeath;j++) {
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          po[i][j][h]=newm[i][j];
     k4=func(p2)-fx;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     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);    } /* end h */
 #endif    return po;
   }  }
   return res;  
 }  
   /*************** log-likelihood *************/
 /************** Inverse of matrix **************/  double func( double *x)
 void ludcmp(double **a, int n, int *indx, double *d)  {
 {    int i, ii, j, k, mi, d, kk;
   int i,imax,j,k;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   double big,dum,sum,temp;    double **out;
   double *vv;    double sw; /* Sum of weights */
      double lli; /* Individual log likelihood */
   vv=vector(1,n);    int s1, s2;
   *d=1.0;    double bbh, survp;
   for (i=1;i<=n;i++) {    long ipmx;
     big=0.0;    /*extern weight */
     for (j=1;j<=n;j++)    /* We are differentiating ll according to initial status */
       if ((temp=fabs(a[i][j])) > big) big=temp;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    /*for(i=1;i<imx;i++) 
     vv[i]=1.0/big;      printf(" %d\n",s[4][i]);
   }    */
   for (j=1;j<=n;j++) {    cov[1]=1.;
     for (i=1;i<j;i++) {  
       sum=a[i][j];    for(k=1; k<=nlstate; k++) ll[k]=0.;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;    if(mle==1){
     }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     big=0.0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for (i=j;i<=n;i++) {        for(mi=1; mi<= wav[i]-1; mi++){
       sum=a[i][j];          for (ii=1;ii<=nlstate+ndeath;ii++)
       for (k=1;k<j;k++)            for (j=1;j<=nlstate+ndeath;j++){
         sum -= a[i][k]*a[k][j];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       a[i][j]=sum;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       if ( (dum=vv[i]*fabs(sum)) >= big) {            }
         big=dum;          for(d=0; d<dh[mi][i]; d++){
         imax=i;            newm=savm;
       }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     }            for (kk=1; kk<=cptcovage;kk++) {
     if (j != imax) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for (k=1;k<=n;k++) {            }
         dum=a[imax][k];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         a[imax][k]=a[j][k];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         a[j][k]=dum;            savm=oldm;
       }            oldm=newm;
       *d = -(*d);          } /* end mult */
       vv[imax]=vv[j];        
     }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     indx[j]=imax;          /* But now since version 0.9 we anticipate for bias and large stepm.
     if (a[j][j] == 0.0) a[j][j]=TINY;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     if (j != n) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
       dum=1.0/(a[j][j]);           * the nearest (and in case of equal distance, to the lowest) interval but now
       for (i=j+1;i<=n;i++) a[i][j] *= dum;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     }           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   }           * probability in order to take into account the bias as a fraction of the way
   free_vector(vv,1,n);  /* Doesn't work */           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
 ;           * -stepm/2 to stepm/2 .
 }           * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
 void lubksb(double **a, int n, int *indx, double b[])           */
 {          s1=s[mw[mi][i]][i];
   int i,ii=0,ip,j;          s2=s[mw[mi+1][i]][i];
   double sum;          bbh=(double)bh[mi][i]/(double)stepm; 
            /* bias is positive if real duration
   for (i=1;i<=n;i++) {           * is higher than the multiple of stepm and negative otherwise.
     ip=indx[i];           */
     sum=b[ip];          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     b[ip]=b[i];          if( s2 > nlstate){ 
     if (ii)            /* i.e. if s2 is a death state and if the date of death is known then the contribution
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];               to the likelihood is the probability to die between last step unit time and current 
     else if (sum) ii=i;               step unit time, which is also the differences between probability to die before dh 
     b[i]=sum;               and probability to die before dh-stepm . 
   }               In version up to 0.92 likelihood was computed
   for (i=n;i>=1;i--) {          as if date of death was unknown. Death was treated as any other
     sum=b[i];          health state: the date of the interview describes the actual state
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          and not the date of a change in health state. The former idea was
     b[i]=sum/a[i][i];          to consider that at each interview the state was recorded
   }          (healthy, disable or death) and IMaCh was corrected; but when we
 }          introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
 /************ Frequencies ********************/          contribution is smaller and very dependent of the step unit
 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)          stepm. It is no more the probability to die between last interview
 {  /* Some frequencies */          and month of death but the probability to survive from last
            interview up to one month before death multiplied by the
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          probability to die within a month. Thanks to Chris
   double ***freq; /* Frequencies */          Jackson for correcting this bug.  Former versions increased
   double *pp;          mortality artificially. The bad side is that we add another loop
   double pos, k2, dateintsum=0,k2cpt=0;          which slows down the processing. The difference can be up to 10%
   FILE *ficresp;          lower mortality.
   char fileresp[FILENAMELENGTH];            */
             lli=log(out[s1][s2] - savm[s1][s2]);
   pp=vector(1,nlstate);          }else{
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   strcpy(fileresp,"p");            /*  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 */
   strcat(fileresp,fileres);          } 
   if((ficresp=fopen(fileresp,"w"))==NULL) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     printf("Problem with prevalence resultfile: %s\n", fileresp);          /*if(lli ==000.0)*/
     exit(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;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          sw += weight[i];
   j1=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
   j=cptcoveff;      } /* end of individual */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for(k1=1; k1<=j;k1++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
    for(i1=1; i1<=ncodemax[k1];i1++){        for(mi=1; mi<= wav[i]-1; mi++){
        j1++;          for (ii=1;ii<=nlstate+ndeath;ii++)
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);            for (j=1;j<=nlstate+ndeath;j++){
          scanf("%d", i);*/              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for (i=-1; i<=nlstate+ndeath; i++)                savm[ii][j]=(ii==j ? 1.0 : 0.0);
          for (jk=-1; jk<=nlstate+ndeath; jk++)              }
            for(m=agemin; m <= agemax+3; m++)          for(d=0; d<=dh[mi][i]; d++){
              freq[i][jk][m]=0;            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         dateintsum=0;            for (kk=1; kk<=cptcovage;kk++) {
         k2cpt=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        for (i=1; i<=imx; i++) {            }
          bool=1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
          if  (cptcovn>0) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
            for (z1=1; z1<=cptcoveff; z1++)            savm=oldm;
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            oldm=newm;
                bool=0;          } /* end mult */
          }        
          if (bool==1) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
            for(m=firstpass; m<=lastpass; m++){          /* But now since version 0.9 we anticipate for bias and large stepm.
              k2=anint[m][i]+(mint[m][i]/12.);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
              if ((k2>=dateprev1) && (k2<=dateprev2)) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
                if(agev[m][i]==0) agev[m][i]=agemax+1;           * the nearest (and in case of equal distance, to the lowest) interval but now
                if(agev[m][i]==1) agev[m][i]=agemax+2;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];           * probability in order to take into account the bias as a fraction of the way
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
                  dateintsum=dateintsum+k2;           * -stepm/2 to stepm/2 .
                  k2cpt++;           * For stepm=1 the results are the same as for previous versions of Imach.
                }           * For stepm > 1 the results are less biased than in previous versions. 
            */
              }          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
         if  (cptcovn>0) {           * is higher than the multiple of stepm and negative otherwise.
          fprintf(ficresp, "\n#********** Variable ");           */
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
        fprintf(ficresp, "**********\n#");          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         }          /*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 */
        for(i=1; i<=nlstate;i++)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          /*if(lli ==000.0)*/
        fprintf(ficresp, "\n");          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
                  ipmx +=1;
   for(i=(int)agemin; i <= (int)agemax+3; i++){          sw += weight[i];
     if(i==(int)agemax+3)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       printf("Total");        } /* end of wave */
     else      } /* end of individual */
       printf("Age %d", i);    }  else if(mle==3){  /* exponential inter-extrapolation */
     for(jk=1; jk <=nlstate ; jk++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         pp[jk] += freq[jk][m][i];        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
     for(jk=1; jk <=nlstate ; jk++){            for (j=1;j<=nlstate+ndeath;j++){
       for(m=-1, pos=0; m <=0 ; m++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         pos += freq[jk][m][i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       if(pp[jk]>=1.e-10)            }
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          for(d=0; d<dh[mi][i]; d++){
       else            newm=savm;
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      for(jk=1; jk <=nlstate ; jk++){            }
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         pp[jk] += freq[jk][m][i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      }            savm=oldm;
             oldm=newm;
     for(jk=1,pos=0; jk <=nlstate ; jk++)          } /* end mult */
       pos += pp[jk];        
     for(jk=1; jk <=nlstate ; jk++){          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       if(pos>=1.e-5)          /* But now since version 0.9 we anticipate for bias and large stepm.
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       else           * (in months) between two waves is not a multiple of stepm, we rounded to 
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);           * the nearest (and in case of equal distance, to the lowest) interval but now
       if( i <= (int) agemax){           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         if(pos>=1.e-5){           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);           * probability in order to take into account the bias as a fraction of the way
           probs[i][jk][j1]= pp[jk]/pos;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/           * -stepm/2 to stepm/2 .
         }           * For stepm=1 the results are the same as for previous versions of Imach.
       else           * For stepm > 1 the results are less biased than in previous versions. 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);           */
       }          s1=s[mw[mi][i]][i];
     }          s2=s[mw[mi+1][i]][i];
     for(jk=-1; jk <=nlstate+ndeath; jk++)          bbh=(double)bh[mi][i]/(double)stepm; 
       for(m=-1; m <=nlstate+ndeath; m++)          /* bias is positive if real duration
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);           * is higher than the multiple of stepm and negative otherwise.
     if(i <= (int) agemax)           */
       fprintf(ficresp,"\n");          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
     printf("\n");          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 */
     }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     }          /*if(lli ==000.0)*/
  }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   dateintmean=dateintsum/k2cpt;          ipmx +=1;
            sw += weight[i];
   fclose(ficresp);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        } /* end of wave */
   free_vector(pp,1,nlstate);      } /* end of individual */
     }else if (mle==4){  /* ml=4 no inter-extrapolation */
   /* 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, 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 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);            }
            
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   j1=0;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
   j=cptcoveff;            oldm=newm;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          } /* end mult */
          
  for(k1=1; k1<=j;k1++){          s1=s[mw[mi][i]][i];
     for(i1=1; i1<=ncodemax[k1];i1++){          s2=s[mw[mi+1][i]][i];
       j1++;          if( s2 > nlstate){ 
              lli=log(out[s1][s2] - savm[s1][s2]);
       for (i=-1; i<=nlstate+ndeath; i++)            }else{
         for (jk=-1; jk<=nlstate+ndeath; jk++)              lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           for(m=agemin; m <= agemax+3; m++)          }
             freq[i][jk][m]=0;          ipmx +=1;
                sw += weight[i];
       for (i=1; i<=imx; i++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         bool=1;  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         if  (cptcovn>0) {        } /* end of wave */
           for (z1=1; z1<=cptcoveff; z1++)      } /* end of individual */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
               bool=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         if (bool==1) {        for(mi=1; mi<= wav[i]-1; mi++){
           for(m=firstpass; m<=lastpass; m++){          for (ii=1;ii<=nlstate+ndeath;ii++)
             k2=anint[m][i]+(mint[m][i]/12.);            for (j=1;j<=nlstate+ndeath;j++){
             if ((k2>=dateprev1) && (k2<=dateprev2)) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               if(agev[m][i]==0) agev[m][i]=agemax+1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
               if(agev[m][i]==1) agev[m][i]=agemax+2;            }
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          for(d=0; d<dh[mi][i]; d++){
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];              newm=savm;
             }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           }            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
                
         for(i=(int)agemin; i <= (int)agemax+3; i++){            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));
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            savm=oldm;
               pp[jk] += freq[jk][m][i];            oldm=newm;
           }          } /* end mult */
           for(jk=1; jk <=nlstate ; jk++){        
             for(m=-1, pos=0; m <=0 ; m++)          s1=s[mw[mi][i]][i];
             pos += freq[jk][m][i];          s2=s[mw[mi+1][i]][i];
         }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                  ipmx +=1;
          for(jk=1; jk <=nlstate ; jk++){          sw += weight[i];
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
              pp[jk] += freq[jk][m][i];          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
          }        } /* end of wave */
                } /* end of individual */
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
          for(jk=1; jk <=nlstate ; jk++){              /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
            if( i <= (int) agemax){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
              if(pos>=1.e-5){    return -l;
                probs[i][jk][j1]= pp[jk]/pos;  }
              }  
            }  /*************** log-likelihood *************/
          }  double funcone( double *x)
            {
         }    /* Same as likeli but slower because of a lot of printf and if */
     }    int i, ii, j, k, mi, d, kk;
   }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
      double **out;
      double lli; /* Individual log likelihood */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    double llt;
   free_vector(pp,1,nlstate);    int s1, s2;
      double bbh, survp;
 }  /* End of Freq */    /*extern weight */
     /* We are differentiating ll according to initial status */
 /************* Waves Concatenation ***************/    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      printf(" %d\n",s[4][i]);
 {    */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    cov[1]=1.;
      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    for(k=1; k<=nlstate; k++) ll[k]=0.;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  
      and mw[mi+1][i]. dh depends on stepm.    for (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++){
   int i, mi, m;        for (ii=1;ii<=nlstate+ndeath;ii++)
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          for (j=1;j<=nlstate+ndeath;j++){
      double sum=0., jmean=0.;*/            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int j, k=0,jk, ju, jl;          }
   double sum=0.;        for(d=0; d<dh[mi][i]; d++){
   jmin=1e+5;          newm=savm;
   jmax=-1;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   jmean=0.;          for (kk=1; kk<=cptcovage;kk++) {
   for(i=1; i<=imx; i++){            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     mi=0;          }
     m=firstpass;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     while(s[m][i] <= nlstate){                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       if(s[m][i]>=1)          savm=oldm;
         mw[++mi][i]=m;          oldm=newm;
       if(m >=lastpass)        } /* end mult */
         break;        
       else        s1=s[mw[mi][i]][i];
         m++;        s2=s[mw[mi+1][i]][i];
     }/* end while */        bbh=(double)bh[mi][i]/(double)stepm; 
     if (s[m][i] > nlstate){        /* bias is positive if real duration
       mi++;     /* Death is another wave */         * is higher than the multiple of stepm and negative otherwise.
       /* if(mi==0)  never been interviewed correctly before death */         */
          /* Only death is a correct wave */        if( s2 > nlstate && (mle <5) ){  /* Jackson */
       mw[mi][i]=m;          lli=log(out[s1][s2] - savm[s1][s2]);
     }        } else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     wav[i]=mi;        } else if(mle==2){
     if(mi==0)          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        } else if(mle==3){  /* exponential inter-extrapolation */
   }          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         } else if (mle==4){  /* mle=4 no inter-extrapolation */
   for(i=1; i<=imx; i++){          lli=log(out[s1][s2]); /* Original formula */
     for(mi=1; mi<wav[i];mi++){        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
       if (stepm <=0)          lli=log(out[s1][s2]); /* Original formula */
         dh[mi][i]=1;        } /* End of if */
       else{        ipmx +=1;
         if (s[mw[mi+1][i]][i] > nlstate) {        sw += weight[i];
           if (agedc[i] < 2*AGESUP) {        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
           if(j==0) j=1;  /* Survives at least one month after exam */        if(globpr){
           k=k+1;          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
           if (j >= jmax) jmax=j;   %10.6f %10.6f %10.6f ", \
           if (j <= jmin) jmin=j;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
           sum=sum+j;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           /* if (j<10) printf("j=%d num=%d ",j,i); */          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
           }            llt +=ll[k]*gipmx/gsw;
         }            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
         else{          }
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          fprintf(ficresilk," %10.6f\n", -llt);
           k=k+1;        }
           if (j >= jmax) jmax=j;      } /* end of wave */
           else if (j <= jmin)jmin=j;    } /* end of individual */
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           sum=sum+j;    /* 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 */
         jk= j/stepm;    if(globpr==0){ /* First time we count the contributions and weights */
         jl= j -jk*stepm;      gipmx=ipmx;
         ju= j -(jk+1)*stepm;      gsw=sw;
         if(jl <= -ju)    }
           dh[mi][i]=jk;    return -l;
         else  }
           dh[mi][i]=jk+1;  
         if(dh[mi][i]==0)  char *subdirf(char fileres[])
           dh[mi][i]=1; /* At least one step */  {
       }    /* Caution optionfilefiname is hidden */
     }    strcpy(tmpout,optionfilefiname);
   }    strcat(tmpout,"/"); /* Add to the right */
   jmean=sum/k;    strcat(tmpout,fileres);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    return tmpout;
  }  }
 /*********** Tricode ****************************/  
 void tricode(int *Tvar, int **nbcode, int imx)  char *subdirf2(char fileres[], char *preop)
 {  {
   int Ndum[20],ij=1, k, j, i;    
   int cptcode=0;    strcpy(tmpout,optionfilefiname);
   cptcoveff=0;    strcat(tmpout,"/");
      strcat(tmpout,preop);
   for (k=0; k<19; k++) Ndum[k]=0;    strcat(tmpout,fileres);
   for (k=1; k<=7; k++) ncodemax[k]=0;    return tmpout;
   }
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  char *subdirf3(char fileres[], char *preop, char *preop2)
     for (i=1; i<=imx; i++) {  {
       ij=(int)(covar[Tvar[j]][i]);    
       Ndum[ij]++;    strcpy(tmpout,optionfilefiname);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    strcat(tmpout,"/");
       if (ij > cptcode) cptcode=ij;    strcat(tmpout,preop);
     }    strcat(tmpout,preop2);
     strcat(tmpout,fileres);
     for (i=0; i<=cptcode; i++) {    return tmpout;
       if(Ndum[i]!=0) ncodemax[j]++;  }
     }  
     ij=1;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   {
     /* This routine should help understanding what is done with 
     for (i=1; i<=ncodemax[j]; i++) {       the selection of individuals/waves and
       for (k=0; k<=19; k++) {       to check the exact contribution to the likelihood.
         if (Ndum[k] != 0) {       Plotting could be done.
           nbcode[Tvar[j]][ij]=k;     */
           ij++;    int k;
         }  
         if (ij > ncodemax[j]) break;    if(*globpri !=0){ /* Just counts and sums, no printings */
       }        strcpy(fileresilk,"ilk"); 
     }      strcat(fileresilk,fileres);
   }        if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", fileresilk);
  for (k=0; k<19; k++) Ndum[k]=0;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
  for (i=1; i<=ncovmodel-2; i++) {      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");
       ij=Tvar[i];      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       Ndum[ij]++;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     }      for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
  ij=1;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
  for (i=1; i<=10; i++) {    }
    if((Ndum[i]!=0) && (i<=ncov)){  
      Tvaraff[ij]=i;    *fretone=(*funcone)(p);
      ij++;    if(*globpri !=0){
    }      fclose(ficresilk);
  }      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
        fflush(fichtm); 
     cptcoveff=ij-1;    } 
 }    return;
   }
 /*********** Health Expectancies ****************/  
   
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)  /*********** Maximum Likelihood Estimation ***************/
 {  
   /* Health expectancies */  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   int i, j, nhstepm, hstepm, h;  {
   double age, agelim,hf;    int i,j, iter;
   double ***p3mat;    double **xi;
      double fret;
   fprintf(ficreseij,"# Health expectancies\n");    double fretone; /* Only one call to likelihood */
   fprintf(ficreseij,"# Age");    char filerespow[FILENAMELENGTH];
   for(i=1; i<=nlstate;i++)    xi=matrix(1,npar,1,npar);
     for(j=1; j<=nlstate;j++)    for (i=1;i<=npar;i++)
       fprintf(ficreseij," %1d-%1d",i,j);      for (j=1;j<=npar;j++)
   fprintf(ficreseij,"\n");        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
   hstepm=1*YEARM; /*  Every j years of age (in month) */    strcpy(filerespow,"pow"); 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
   agelim=AGESUP;      printf("Problem with resultfile: %s\n", filerespow);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     /* nhstepm age range expressed in number of stepm */    }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     /* Typically if 20 years = 20*12/6=40 stepm */    for (i=1;i<=nlstate;i++)
     if (stepm >= YEARM) hstepm=1;      for(j=1;j<=nlstate+ndeath;j++)
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficrespow,"\n");
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    powell(p,xi,npar,ftol,&iter,&fret,func);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    
     fclose(ficrespow);
     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     for(i=1; i<=nlstate;i++)    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       for(j=1; j<=nlstate;j++)    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){  
           eij[i][j][(int)age] +=p3mat[i][j][h];  }
         }  
      /**** Computes Hessian and covariance matrix ***/
     hf=1;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     if (stepm >= YEARM) hf=stepm/YEARM;  {
     fprintf(ficreseij,"%.0f",age );    double  **a,**y,*x,pd;
     for(i=1; i<=nlstate;i++)    double **hess;
       for(j=1; j<=nlstate;j++){    int i, j,jk;
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);    int *indx;
       }  
     fprintf(ficreseij,"\n");    double hessii(double p[], double delta, int theta, double delti[]);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double hessij(double p[], double delti[], int i, int j);
   }    void lubksb(double **a, int npar, int *indx, double b[]) ;
 }    void ludcmp(double **a, int npar, int *indx, double *d) ;
   
 /************ Variance ******************/    hess=matrix(1,npar,1,npar);
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)  
 {    printf("\nCalculation of the hessian matrix. Wait...\n");
   /* Variance of health expectancies */    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    for (i=1;i<=npar;i++){
   double **newm;      printf("%d",i);fflush(stdout);
   double **dnewm,**doldm;      fprintf(ficlog,"%d",i);fflush(ficlog);
   int i, j, nhstepm, hstepm, h;      hess[i][i]=hessii(p,ftolhess,i,delti);
   int k, cptcode;      /*printf(" %f ",p[i]);*/
   double *xp;      /*printf(" %lf ",hess[i][i]);*/
   double **gp, **gm;    }
   double ***gradg, ***trgradg;    
   double ***p3mat;    for (i=1;i<=npar;i++) {
   double age,agelim;      for (j=1;j<=npar;j++)  {
   int theta;        if (j>i) { 
           printf(".%d%d",i,j);fflush(stdout);
    fprintf(ficresvij,"# Covariances of life expectancies\n");          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   fprintf(ficresvij,"# Age");          hess[i][j]=hessij(p,delti,i,j);
   for(i=1; i<=nlstate;i++)          hess[j][i]=hess[i][j];    
     for(j=1; j<=nlstate;j++)          /*printf(" %lf ",hess[i][j]);*/
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        }
   fprintf(ficresvij,"\n");      }
     }
   xp=vector(1,npar);    printf("\n");
   dnewm=matrix(1,nlstate,1,npar);    fprintf(ficlog,"\n");
   doldm=matrix(1,nlstate,1,nlstate);  
      printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   hstepm=1*YEARM; /* Every year of age */    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    
   agelim = AGESUP;    a=matrix(1,npar,1,npar);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    y=matrix(1,npar,1,npar);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    x=vector(1,npar);
     if (stepm >= YEARM) hstepm=1;    indx=ivector(1,npar);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    for (i=1;i<=npar;i++)
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    ludcmp(a,npar,indx,&pd);
     gp=matrix(0,nhstepm,1,nlstate);  
     gm=matrix(0,nhstepm,1,nlstate);    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
     for(theta=1; theta <=npar; theta++){      x[j]=1;
       for(i=1; i<=npar; i++){ /* Computes gradient */      lubksb(a,npar,indx,x);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      for (i=1;i<=npar;i++){ 
       }        matcov[i][j]=x[i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    }
   
       if (popbased==1) {    printf("\n#Hessian matrix#\n");
         for(i=1; i<=nlstate;i++)    fprintf(ficlog,"\n#Hessian matrix#\n");
           prlim[i][i]=probs[(int)age][i][ij];    for (i=1;i<=npar;i++) { 
       }      for (j=1;j<=npar;j++) { 
              printf("%.3e ",hess[i][j]);
       for(j=1; j<= nlstate; j++){        fprintf(ficlog,"%.3e ",hess[i][j]);
         for(h=0; h<=nhstepm; h++){      }
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      printf("\n");
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      fprintf(ficlog,"\n");
         }    }
       }  
        /* Recompute Inverse */
       for(i=1; i<=npar; i++) /* Computes gradient */    for (i=1;i<=npar;i++)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      ludcmp(a,npar,indx,&pd);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
     /*  printf("\n#Hessian matrix recomputed#\n");
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)    for (j=1;j<=npar;j++) {
           prlim[i][i]=probs[(int)age][i][ij];      for (i=1;i<=npar;i++) x[i]=0;
       }      x[j]=1;
       lubksb(a,npar,indx,x);
       for(j=1; j<= nlstate; j++){      for (i=1;i<=npar;i++){ 
         for(h=0; h<=nhstepm; h++){        y[i][j]=x[i];
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        printf("%.3e ",y[i][j]);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        fprintf(ficlog,"%.3e ",y[i][j]);
         }      }
       }      printf("\n");
       fprintf(ficlog,"\n");
       for(j=1; j<= nlstate; j++)    }
         for(h=0; h<=nhstepm; h++){    */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  
         }    free_matrix(a,1,npar,1,npar);
     } /* End theta */    free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
     for(h=0; h<=nhstepm; h++)  
       for(j=1; j<=nlstate;j++)  
         for(theta=1; theta <=npar; theta++)  }
           trgradg[h][j][theta]=gradg[h][theta][j];  
   /*************** hessian matrix ****************/
     for(i=1;i<=nlstate;i++)  double hessii( double x[], double delta, int theta, double delti[])
       for(j=1;j<=nlstate;j++)  {
         vareij[i][j][(int)age] =0.;    int i;
     for(h=0;h<=nhstepm;h++){    int l=1, lmax=20;
       for(k=0;k<=nhstepm;k++){    double k1,k2;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    double p2[NPARMAX+1];
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    double res;
         for(i=1;i<=nlstate;i++)    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           for(j=1;j<=nlstate;j++)    double fx;
             vareij[i][j][(int)age] += doldm[i][j];    int k=0,kmax=10;
       }    double l1;
     }  
     h=1;    fx=func(x);
     if (stepm >= YEARM) h=stepm/YEARM;    for (i=1;i<=npar;i++) p2[i]=x[i];
     fprintf(ficresvij,"%.0f ",age );    for(l=0 ; l <=lmax; l++){
     for(i=1; i<=nlstate;i++)      l1=pow(10,l);
       for(j=1; j<=nlstate;j++){      delts=delt;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);      for(k=1 ; k <kmax; k=k+1){
       }        delt = delta*(l1*k);
     fprintf(ficresvij,"\n");        p2[theta]=x[theta] +delt;
     free_matrix(gp,0,nhstepm,1,nlstate);        k1=func(p2)-fx;
     free_matrix(gm,0,nhstepm,1,nlstate);        p2[theta]=x[theta]-delt;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        k2=func(p2)-fx;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        /*res= (k1-2.0*fx+k2)/delt/delt; */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   } /* End age */        
    #ifdef DEBUG
   free_vector(xp,1,npar);        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);
   free_matrix(doldm,1,nlstate,1,npar);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   free_matrix(dnewm,1,nlstate,1,nlstate);  #endif
         /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
 }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k=kmax;
 /************ Variance of prevlim ******************/        }
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
 {          k=kmax; l=lmax*10.;
   /* Variance of prevalence limit */        }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   double **newm;          delts=delt;
   double **dnewm,**doldm;        }
   int i, j, nhstepm, hstepm;      }
   int k, cptcode;    }
   double *xp;    delti[theta]=delts;
   double *gp, *gm;    return res; 
   double **gradg, **trgradg;    
   double age,agelim;  }
   int theta;  
      double hessij( double x[], double delti[], int thetai,int thetaj)
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");  {
   fprintf(ficresvpl,"# Age");    int i;
   for(i=1; i<=nlstate;i++)    int l=1, l1, lmax=20;
       fprintf(ficresvpl," %1d-%1d",i,i);    double k1,k2,k3,k4,res,fx;
   fprintf(ficresvpl,"\n");    double p2[NPARMAX+1];
     int k;
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);    fx=func(x);
   doldm=matrix(1,nlstate,1,nlstate);    for (k=1; k<=2; k++) {
        for (i=1;i<=npar;i++) p2[i]=x[i];
   hstepm=1*YEARM; /* Every year of age */      p2[thetai]=x[thetai]+delti[thetai]/k;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   agelim = AGESUP;      k1=func(p2)-fx;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      p2[thetai]=x[thetai]+delti[thetai]/k;
     if (stepm >= YEARM) hstepm=1;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      k2=func(p2)-fx;
     gradg=matrix(1,npar,1,nlstate);    
     gp=vector(1,nlstate);      p2[thetai]=x[thetai]-delti[thetai]/k;
     gm=vector(1,nlstate);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
     for(theta=1; theta <=npar; theta++){    
       for(i=1; i<=npar; i++){ /* Computes gradient */      p2[thetai]=x[thetai]-delti[thetai]/k;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       }      k4=func(p2)-fx;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       for(i=1;i<=nlstate;i++)  #ifdef DEBUG
         gp[i] = prlim[i][i];      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
          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(i=1; i<=npar; i++) /* Computes gradient */  #endif
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    return res;
       for(i=1;i<=nlstate;i++)  }
         gm[i] = prlim[i][i];  
   /************** Inverse of matrix **************/
       for(i=1;i<=nlstate;i++)  void ludcmp(double **a, int n, int *indx, double *d) 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  { 
     } /* End theta */    int i,imax,j,k; 
     double big,dum,sum,temp; 
     trgradg =matrix(1,nlstate,1,npar);    double *vv; 
    
     for(j=1; j<=nlstate;j++)    vv=vector(1,n); 
       for(theta=1; theta <=npar; theta++)    *d=1.0; 
         trgradg[j][theta]=gradg[theta][j];    for (i=1;i<=n;i++) { 
       big=0.0; 
     for(i=1;i<=nlstate;i++)      for (j=1;j<=n;j++) 
       varpl[i][(int)age] =0.;        if ((temp=fabs(a[i][j])) > big) big=temp; 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      vv[i]=1.0/big; 
     for(i=1;i<=nlstate;i++)    } 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
     fprintf(ficresvpl,"%.0f ",age );        sum=a[i][j]; 
     for(i=1; i<=nlstate;i++)        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        a[i][j]=sum; 
     fprintf(ficresvpl,"\n");      } 
     free_vector(gp,1,nlstate);      big=0.0; 
     free_vector(gm,1,nlstate);      for (i=j;i<=n;i++) { 
     free_matrix(gradg,1,npar,1,nlstate);        sum=a[i][j]; 
     free_matrix(trgradg,1,nlstate,1,npar);        for (k=1;k<j;k++) 
   } /* End age */          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
   free_vector(xp,1,npar);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   free_matrix(doldm,1,nlstate,1,npar);          big=dum; 
   free_matrix(dnewm,1,nlstate,1,nlstate);          imax=i; 
         } 
 }      } 
       if (j != imax) { 
 /************ Variance of one-step probabilities  ******************/        for (k=1;k<=n;k++) { 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)          dum=a[imax][k]; 
 {          a[imax][k]=a[j][k]; 
   int i, j;          a[j][k]=dum; 
   int k=0, cptcode;        } 
   double **dnewm,**doldm;        *d = -(*d); 
   double *xp;        vv[imax]=vv[j]; 
   double *gp, *gm;      } 
   double **gradg, **trgradg;      indx[j]=imax; 
   double age,agelim, cov[NCOVMAX];      if (a[j][j] == 0.0) a[j][j]=TINY; 
   int theta;      if (j != n) { 
   char fileresprob[FILENAMELENGTH];        dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   strcpy(fileresprob,"prob");      } 
   strcat(fileresprob,fileres);    } 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    free_vector(vv,1,n);  /* Doesn't work */
     printf("Problem with resultfile: %s\n", fileresprob);  ;
   }  } 
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);  
    void lubksb(double **a, int n, int *indx, double b[]) 
   { 
   xp=vector(1,npar);    int i,ii=0,ip,j; 
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    double sum; 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));   
      for (i=1;i<=n;i++) { 
   cov[1]=1;      ip=indx[i]; 
   for (age=bage; age<=fage; age ++){      sum=b[ip]; 
     cov[2]=age;      b[ip]=b[i]; 
     gradg=matrix(1,npar,1,9);      if (ii) 
     trgradg=matrix(1,9,1,npar);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      else if (sum) ii=i; 
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      b[i]=sum; 
        } 
     for(theta=1; theta <=npar; theta++){    for (i=n;i>=1;i--) { 
       for(i=1; i<=npar; i++)      sum=b[i]; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
            b[i]=sum/a[i][i]; 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    } 
      } 
       k=0;  
       for(i=1; i<= (nlstate+ndeath); i++){  /************ Frequencies ********************/
         for(j=1; j<=(nlstate+ndeath);j++){  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)
            k=k+1;  {  /* Some frequencies */
           gp[k]=pmmij[i][j];    
         }    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       }    int first;
     double ***freq; /* Frequencies */
       for(i=1; i<=npar; i++)    double *pp, **prop;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
        FILE *ficresp;
     char fileresp[FILENAMELENGTH];
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    
       k=0;    pp=vector(1,nlstate);
       for(i=1; i<=(nlstate+ndeath); i++){    prop=matrix(1,nlstate,iagemin,iagemax+3);
         for(j=1; j<=(nlstate+ndeath);j++){    strcpy(fileresp,"p");
           k=k+1;    strcat(fileresp,fileres);
           gm[k]=pmmij[i][j];    if((ficresp=fopen(fileresp,"w"))==NULL) {
         }      printf("Problem with prevalence resultfile: %s\n", fileresp);
       }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
            exit(0);
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    }
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     }    j1=0;
     
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    j=cptcoveff;
       for(theta=1; theta <=npar; theta++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       trgradg[j][theta]=gradg[theta][j];  
      first=1;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);  
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
      pmij(pmmij,cov,ncovmodel,x,nlstate);        j1++;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
      k=0;          scanf("%d", i);*/
      for(i=1; i<=(nlstate+ndeath); i++){        for (i=-1; i<=nlstate+ndeath; i++)  
        for(j=1; j<=(nlstate+ndeath);j++){          for (jk=-1; jk<=nlstate+ndeath; jk++)  
          k=k+1;            for(m=iagemin; m <= iagemax+3; m++)
          gm[k]=pmmij[i][j];              freq[i][jk][m]=0;
         }  
      }      for (i=1; i<=nlstate; i++)  
              for(m=iagemin; m <= iagemax+3; m++)
      /*printf("\n%d ",(int)age);          prop[i][m]=0;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        
                dateintsum=0;
         k2cpt=0;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        for (i=1; i<=imx; i++) {
      }*/          bool=1;
           if  (cptcovn>0) {
   fprintf(ficresprob,"\n%d ",(int)age);            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){                bool=0;
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          }
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          if (bool==1){
   }            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
 }                if (m<lastpass) {
  free_vector(xp,1,npar);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
 fclose(ficresprob);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
  exit(0);                }
 }                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
 /******************* Printing html file ***********/                  dateintsum=dateintsum+k2;
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[] ){                  k2cpt++;
   int jj1, k1, i1, cpt;                }
   FILE *fichtm;                /*}*/
   /*char optionfilehtm[FILENAMELENGTH];*/            }
           }
   strcpy(optionfilehtm,optionfile);        }
   strcat(optionfilehtm,".htm");         
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     printf("Problem with %s \n",optionfilehtm), exit(0);  
   }        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>          fprintf(ficresp, "**********\n#");
         }
 Total number of observations=%d <br>        for(i=1; i<=nlstate;i++) 
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 <hr  size=\"2\" color=\"#EC5E5E\">        fprintf(ficresp, "\n");
 <li>Outputs files<br><br>\n        
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n        for(i=iagemin; i <= iagemax+3; i++){
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>          if(i==iagemax+3){
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>            fprintf(ficlog,"Total");
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>          }else{
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>            if(first==1){
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>              first=0;
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>              printf("See log file for details...\n");
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>            }
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>            fprintf(ficlog,"Age %d", i);
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>          }
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);          for(jk=1; jk <=nlstate ; jk++){
              for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 fprintf(fichtm," <li>Graphs</li><p>");              pp[jk] += freq[jk][m][i]; 
           }
  m=cptcoveff;          for(jk=1; jk <=nlstate ; jk++){
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}            for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
  jj1=0;            if(pp[jk]>=1.e-10){
  for(k1=1; k1<=m;k1++){              if(first==1){
    for(i1=1; i1<=ncodemax[k1];i1++){              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
        jj1++;              }
        if (cptcovn > 0) {              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");            }else{
          for (cpt=1; cpt<=cptcoveff;cpt++)              if(first==1)
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
        }            }
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          }
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      
        for(cpt=1; cpt<nlstate;cpt++){          for(jk=1; jk <=nlstate ; jk++){
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              pp[jk] += freq[jk][m][i];
        }          }       
     for(cpt=1; cpt<=nlstate;cpt++) {          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident            pos += pp[jk];
 interval) in state (%d): v%s%d%d.gif <br>            posprop += prop[jk][i];
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            }
      }          for(jk=1; jk <=nlstate ; jk++){
      for(cpt=1; cpt<=nlstate;cpt++) {            if(pos>=1.e-5){
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>              if(first==1)
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
      }              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            }else{
 health expectancies in states (1) and (2): e%s%d.gif<br>              if(first==1)
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 fprintf(fichtm,"\n</body>");              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
    }            }
    }            if( i <= iagemax){
 fclose(fichtm);              if(pos>=1.e-5){
 }                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
 /******************* Gnuplot file **************/                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemax, double fage , char pathc[], double p[]){              }
               else
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
   strcpy(optionfilegnuplot,optionfilefiname);          }
   strcat(optionfilegnuplot,".plt");          
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {          for(jk=-1; jk <=nlstate+ndeath; jk++)
     printf("Problem with file %s",optionfilegnuplot);            for(m=-1; m <=nlstate+ndeath; m++)
   }              if(freq[jk][m][i] !=0 ) {
               if(first==1)
 #ifdef windows                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     fprintf(ficgp,"cd \"%s\" \n",pathc);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
 #endif              }
 m=pow(2,cptcoveff);          if(i <= iagemax)
              fprintf(ficresp,"\n");
  /* 1eme*/          if(first==1)
   for (cpt=1; cpt<= nlstate ; cpt ++) {            printf("Others in log...\n");
    for (k1=1; k1<= m ; k1 ++) {          fprintf(ficlog,"\n");
         }
 #ifdef windows      }
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);    }
 #endif    dateintmean=dateintsum/k2cpt; 
 #ifdef unix   
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    fclose(ficresp);
 #endif    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
 for (i=1; i<= nlstate ; i ++) {    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /* End of Freq */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  }
 }  
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  /************ 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)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  {  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
 }       in each health status at the date of interview (if between dateprev1 and dateprev2).
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);       We still use firstpass and lastpass as another selection.
      for (i=1; i<= nlstate ; i ++) {    */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");   
   else fprintf(ficgp," \%%*lf (\%%*lf)");    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
 }      double ***freq; /* Frequencies */
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    double *pp, **prop;
 #ifdef unix    double pos,posprop; 
 fprintf(ficgp,"\nset ter gif small size 400,300");    double  y2; /* in fractional years */
 #endif    int iagemin, iagemax;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
    }    iagemin= (int) agemin;
   }    iagemax= (int) agemax;
   /*2 eme*/    /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin,iagemax+3); 
   for (k1=1; k1<= m ; k1 ++) {    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    j1=0;
        
     for (i=1; i<= nlstate+1 ; i ++) {    j=cptcoveff;
       k=2*i;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    
       for (j=1; j<= nlstate+1 ; j ++) {    for(k1=1; k1<=j;k1++){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      for(i1=1; i1<=ncodemax[k1];i1++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");        j1++;
 }          
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        for (i=1; i<=nlstate; i++)  
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          for(m=iagemin; m <= iagemax+3; m++)
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);            prop[i][m]=0.0;
       for (j=1; j<= nlstate+1 ; j ++) {       
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for (i=1; i<=imx; i++) { /* Each individual */
         else fprintf(ficgp," \%%*lf (\%%*lf)");          bool=1;
 }            if  (cptcovn>0) {
       fprintf(ficgp,"\" t\"\" w l 0,");            for (z1=1; z1<=cptcoveff; z1++) 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       for (j=1; j<= nlstate+1 ; j ++) {                bool=0;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          if (bool==1) { 
 }              for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       else fprintf(ficgp,"\" t\"\" w l 0,");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                  if (s[m][i]>0 && s[m][i]<=nlstate) { 
   /*3eme*/                  /*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]]);*/
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];
   for (k1=1; k1<= m ; k1 ++) {                  prop[s[m][i]][iagemax+3] += weight[i]; 
     for (cpt=1; cpt<= nlstate ; cpt ++) {                } 
       k=2+nlstate*(cpt-1);              }
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);            } /* end selection of waves */
       for (i=1; i< nlstate ; i ++) {          }
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);        }
       }        for(i=iagemin; i <= iagemax+3; i++){  
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          
     }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     }            posprop += prop[jk][i]; 
            } 
   /* CV preval stat */  
     for (k1=1; k1<= m ; k1 ++) {          for(jk=1; jk <=nlstate ; jk++){     
     for (cpt=1; cpt<nlstate ; cpt ++) {            if( i <=  iagemax){ 
       k=3;              if(posprop>=1.e-5){ 
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);                probs[i][jk][j1]= prop[jk][i]/posprop;
               } 
       for (i=1; i< nlstate ; i ++)            } 
         fprintf(ficgp,"+$%d",k+i+1);          }/* end jk */ 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        }/* end i */ 
            } /* end i1 */
       l=3+(nlstate+ndeath)*cpt;    } /* end k1 */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    
       for (i=1; i< nlstate ; i ++) {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
         l=3+(nlstate+ndeath)*cpt;    /*free_vector(pp,1,nlstate);*/
         fprintf(ficgp,"+$%d",l+i+1);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       }  }  /* End of prevalence */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  /************* Waves Concatenation ***************/
     }  
   }    void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
    {
   /* proba elementaires */    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
    for(i=1,jk=1; i <=nlstate; i++){       Death is a valid wave (if date is known).
     for(k=1; k <=(nlstate+ndeath); k++){       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       if (k != i) {       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         for(j=1; j <=ncovmodel; j++){       and mw[mi+1][i]. dh depends on stepm.
               */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  
           jk++;    int i, mi, m;
           fprintf(ficgp,"\n");    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         }       double sum=0., jmean=0.;*/
       }    int first;
     }    int j, k=0,jk, ju, jl;
     }    double sum=0.;
     first=0;
     for(jk=1; jk <=m; jk++) {    jmin=1e+5;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    jmax=-1;
    i=1;    jmean=0.;
    for(k2=1; k2<=nlstate; k2++) {    for(i=1; i<=imx; i++){
      k3=i;      mi=0;
      for(k=1; k<=(nlstate+ndeath); k++) {      m=firstpass;
        if (k != k2){      while(s[m][i] <= nlstate){
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        if(s[m][i]>=1)
 ij=1;          mw[++mi][i]=m;
         for(j=3; j <=ncovmodel; j++) {        if(m >=lastpass)
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          break;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        else
             ij++;          m++;
           }      }/* end while */
           else      if (s[m][i] > nlstate){
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        mi++;     /* Death is another wave */
         }        /* if(mi==0)  never been interviewed correctly before death */
           fprintf(ficgp,")/(1");           /* Only death is a correct wave */
                mw[mi][i]=m;
         for(k1=1; k1 <=nlstate; k1++){        }
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);  
 ij=1;      wav[i]=mi;
           for(j=3; j <=ncovmodel; j++){      if(mi==0){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        nbwarn++;
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        if(first==0){
             ij++;          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           }          first=1;
           else        }
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        if(first==1){
           }          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
           fprintf(ficgp,")");        }
         }      } /* end mi==0 */
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    } /* End individuals */
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");  
         i=i+ncovmodel;    for(i=1; i<=imx; i++){
        }      for(mi=1; mi<wav[i];mi++){
      }        if (stepm <=0)
    }          dh[mi][i]=1;
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        else{
    }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                if (agedc[i] < 2*AGESUP) {
   fclose(ficgp);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
 }  /* end gnuplot */              if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
                 nberr++;
 /*************** Moving average **************/                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]);
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){                j=1; /* Temporary Dangerous patch */
                 printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
   int i, cpt, cptcod;                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]);
     for (agedeb=agemin; agedeb<=fage; agedeb++)                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++)              }
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)              k=k+1;
           mobaverage[(int)agedeb][i][cptcod]=0.;              if (j >= jmax) jmax=j;
                  if (j <= jmin) jmin=j;
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){              sum=sum+j;
       for (i=1; i<=nlstate;i++){              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           for (cpt=0;cpt<=4;cpt++){            }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          }
           }          else{
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         }            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       }            k=k+1;
     }            if (j >= jmax) jmax=j;
                else if (j <= jmin)jmin=j;
 }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
 /***********************************************/            if(j<0){
 /**************** Main Program *****************/              nberr++;
 /***********************************************/              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               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]);
 int main(int argc, char *argv[])            }
 {            sum=sum+j;
           }
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;          jk= j/stepm;
   double agedeb, agefin,hf;          jl= j -jk*stepm;
   double agemin=1.e20, agemax=-1.e20;          ju= j -(jk+1)*stepm;
           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   double fret;            if(jl==0){
   double **xi,tmp,delta;              dh[mi][i]=jk;
               bh[mi][i]=0;
   double dum; /* Dummy variable */            }else{ /* We want a negative bias in order to only have interpolation ie
   double ***p3mat;                    * at the price of an extra matrix product in likelihood */
   int *indx;              dh[mi][i]=jk+1;
   char line[MAXLINE], linepar[MAXLINE];              bh[mi][i]=ju;
   char title[MAXLINE];            }
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          }else{
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];            if(jl <= -ju){
                dh[mi][i]=jk;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];              bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
   char filerest[FILENAMELENGTH];                                   */
   char fileregp[FILENAMELENGTH];            }
   char popfile[FILENAMELENGTH];            else{
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];              dh[mi][i]=jk+1;
   int firstobs=1, lastobs=10;              bh[mi][i]=ju;
   int sdeb, sfin; /* Status at beginning and end */            }
   int c,  h , cpt,l;            if(dh[mi][i]==0){
   int ju,jl, mi;              dh[mi][i]=1; /* At least one step */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;              bh[mi][i]=ju; /* At least one step */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;              /*  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);*/
   int mobilav=0,popforecast=0;            }
   int hstepm, nhstepm;          } /* end if mle */
   int *popage;/*boolprev=0 if date and zero if wave*/        }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;      } /* end wave */
     }
   double bage, fage, age, agelim, agebase;    jmean=sum/k;
   double ftolpl=FTOL;    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   double **prlim;    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   double *severity;   }
   double ***param; /* Matrix of parameters */  
   double  *p;  /*********** Tricode ****************************/
   double **matcov; /* Matrix of covariance */  void tricode(int *Tvar, int **nbcode, int imx)
   double ***delti3; /* Scale */  {
   double *delti; /* Scale */    
   double ***eij, ***vareij;    int Ndum[20],ij=1, k, j, i, maxncov=19;
   double **varpl; /* Variances of prevalence limits by age */    int cptcode=0;
   double *epj, vepp;    cptcoveff=0; 
   double kk1, kk2;   
   double *popeffectif,*popcount;    for (k=0; k<maxncov; k++) Ndum[k]=0;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;    for (k=1; k<=7; k++) ncodemax[k]=0;
   double yp,yp1,yp2;  
     for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   char *alph[]={"a","a","b","c","d","e"}, str[4];                                 modality*/ 
         ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         Ndum[ij]++; /*store the modality */
   char z[1]="c", occ;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
 #include <sys/time.h>        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
 #include <time.h>                                         Tvar[j]. If V=sex and male is 0 and 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];                                         female is 1, then  cptcode=1.*/
        }
   /* long total_usecs;  
   struct timeval start_time, end_time;      for (i=0; i<=cptcode; i++) {
          if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      }
   
       ij=1; 
   printf("\n%s",version);      for (i=1; i<=ncodemax[j]; i++) {
   if(argc <=1){        for (k=0; k<= maxncov; k++) {
     printf("\nEnter the parameter file name: ");          if (Ndum[k] != 0) {
     scanf("%s",pathtot);            nbcode[Tvar[j]][ij]=k; 
   }            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   else{            
     strcpy(pathtot,argv[1]);            ij++;
   }          }
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/          if (ij > ncodemax[j]) break; 
   /*cygwin_split_path(pathtot,path,optionfile);        }  
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      } 
   /* cutv(path,optionfile,pathtot,'\\');*/    }  
   
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);   for (k=0; k< maxncov; k++) Ndum[k]=0;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  
   chdir(path);   for (i=1; i<=ncovmodel-2; i++) { 
   replace(pathc,path);     /* 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];
 /*-------- arguments in the command line --------*/     Ndum[ij]++;
    }
   strcpy(fileres,"r");  
   strcat(fileres, optionfilefiname);   ij=1;
   strcat(fileres,".txt");    /* Other files have txt extension */   for (i=1; i<= maxncov; i++) {
      if((Ndum[i]!=0) && (i<=ncovcol)){
   /*---------arguments file --------*/       Tvaraff[ij]=i; /*For printing */
        ij++;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {     }
     printf("Problem with optionfile %s\n",optionfile);   }
     goto end;   
   }   cptcoveff=ij-1; /*Number of simple covariates*/
   }
   strcpy(filereso,"o");  
   strcat(filereso,fileres);  /*********** Health Expectancies ****************/
   if((ficparo=fopen(filereso,"w"))==NULL) {  
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  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 )
   }  
   {
   /* Reads comments: lines beginning with '#' */    /* Health expectancies */
   while((c=getc(ficpar))=='#' && c!= EOF){    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     ungetc(c,ficpar);    double age, agelim, hf;
     fgets(line, MAXLINE, ficpar);    double ***p3mat,***varhe;
     puts(line);    double **dnewm,**doldm;
     fputs(line,ficparo);    double *xp;
   }    double **gp, **gm;
   ungetc(c,ficpar);    double ***gradg, ***trgradg;
     int theta;
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);  
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    xp=vector(1,npar);
 while((c=getc(ficpar))=='#' && c!= EOF){    dnewm=matrix(1,nlstate*nlstate,1,npar);
     ungetc(c,ficpar);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     fgets(line, MAXLINE, ficpar);    
     puts(line);    fprintf(ficreseij,"# Health expectancies\n");
     fputs(line,ficparo);    fprintf(ficreseij,"# Age");
   }    for(i=1; i<=nlstate;i++)
   ungetc(c,ficpar);      for(j=1; j<=nlstate;j++)
          fprintf(ficreseij," %1d-%1d (SE)",i,j);
        fprintf(ficreseij,"\n");
   covar=matrix(0,NCOVMAX,1,n);  
   cptcovn=0;    if(estepm < stepm){
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
   ncovmodel=2+cptcovn;    else  hstepm=estepm;   
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    /* We compute the life expectancy from trapezoids spaced every estepm months
       * This is mainly to measure the difference between two models: for example
   /* Read guess parameters */     * if stepm=24 months pijx are given only every 2 years and by summing them
   /* Reads comments: lines beginning with '#' */     * we are calculating an estimate of the Life Expectancy assuming a linear 
   while((c=getc(ficpar))=='#' && c!= EOF){     * progression in between and thus overestimating or underestimating according
     ungetc(c,ficpar);     * to the curvature of the survival function. If, for the same date, we 
     fgets(line, MAXLINE, ficpar);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     puts(line);     * to compare the new estimate of Life expectancy with the same linear 
     fputs(line,ficparo);     * hypothesis. A more precise result, taking into account a more precise
   }     * curvature will be obtained if estepm is as small as stepm. */
   ungetc(c,ficpar);  
      /* For example we decided to compute the life expectancy with the smallest unit */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     for(i=1; i <=nlstate; i++)       nhstepm is the number of hstepm from age to agelim 
     for(j=1; j <=nlstate+ndeath-1; j++){       nstepm is the number of stepm from age to agelin. 
       fscanf(ficpar,"%1d%1d",&i1,&j1);       Look at hpijx to understand the reason of that which relies in memory size
       fprintf(ficparo,"%1d%1d",i1,j1);       and note for a fixed period like estepm months */
       printf("%1d%1d",i,j);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       for(k=1; k<=ncovmodel;k++){       survival function given by stepm (the optimization length). Unfortunately it
         fscanf(ficpar," %lf",&param[i][j][k]);       means that if the survival funtion is printed only each two years of age and if
         printf(" %lf",param[i][j][k]);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         fprintf(ficparo," %lf",param[i][j][k]);       results. So we changed our mind and took the option of the best precision.
       }    */
       fscanf(ficpar,"\n");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       printf("\n");  
       fprintf(ficparo,"\n");    agelim=AGESUP;
     }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        /* nhstepm age range expressed in number of stepm */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   p=param[1][1];      /* if (stepm >= YEARM) hstepm=1;*/
        nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   /* Reads comments: lines beginning with '#' */      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   while((c=getc(ficpar))=='#' && c!= EOF){      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     ungetc(c,ficpar);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
     fgets(line, MAXLINE, ficpar);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
     puts(line);  
     fputs(line,ficparo);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   ungetc(c,ficpar);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
    
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   for(i=1; i <=nlstate; i++){  
     for(j=1; j <=nlstate+ndeath-1; j++){      /* Computing Variances of health expectancies */
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);       for(theta=1; theta <=npar; theta++){
       fprintf(ficparo,"%1d%1d",i1,j1);        for(i=1; i<=npar; i++){ 
       for(k=1; k<=ncovmodel;k++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         fscanf(ficpar,"%le",&delti3[i][j][k]);        }
         printf(" %le",delti3[i][j][k]);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         fprintf(ficparo," %le",delti3[i][j][k]);    
       }        cptj=0;
       fscanf(ficpar,"\n");        for(j=1; j<= nlstate; j++){
       printf("\n");          for(i=1; i<=nlstate; i++){
       fprintf(ficparo,"\n");            cptj=cptj+1;
     }            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   }              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   delti=delti3[1][1];            }
            }
   /* Reads comments: lines beginning with '#' */        }
   while((c=getc(ficpar))=='#' && c!= EOF){       
     ungetc(c,ficpar);       
     fgets(line, MAXLINE, ficpar);        for(i=1; i<=npar; i++) 
     puts(line);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     fputs(line,ficparo);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   }        
   ungetc(c,ficpar);        cptj=0;
          for(j=1; j<= nlstate; j++){
   matcov=matrix(1,npar,1,npar);          for(i=1;i<=nlstate;i++){
   for(i=1; i <=npar; i++){            cptj=cptj+1;
     fscanf(ficpar,"%s",&str);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     printf("%s",str);  
     fprintf(ficparo,"%s",str);              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     for(j=1; j <=i; j++){            }
       fscanf(ficpar," %le",&matcov[i][j]);          }
       printf(" %.5le",matcov[i][j]);        }
       fprintf(ficparo," %.5le",matcov[i][j]);        for(j=1; j<= nlstate*nlstate; j++)
     }          for(h=0; h<=nhstepm-1; h++){
     fscanf(ficpar,"\n");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     printf("\n");          }
     fprintf(ficparo,"\n");       } 
   }     
   for(i=1; i <=npar; i++)  /* End theta */
     for(j=i+1;j<=npar;j++)  
       matcov[i][j]=matcov[j][i];       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
      
   printf("\n");       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
     /*-------- data file ----------*/            trgradg[h][j][theta]=gradg[h][theta][j];
     if((ficres =fopen(fileres,"w"))==NULL) {       
       printf("Problem with resultfile: %s\n", fileres);goto end;  
     }       for(i=1;i<=nlstate*nlstate;i++)
     fprintf(ficres,"#%s\n",version);        for(j=1;j<=nlstate*nlstate;j++)
              varhe[i][j][(int)age] =0.;
     if((fic=fopen(datafile,"r"))==NULL)    {  
       printf("Problem with datafile: %s\n", datafile);goto end;       printf("%d|",(int)age);fflush(stdout);
     }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
     n= lastobs;        for(k=0;k<=nhstepm-1;k++){
     severity = vector(1,maxwav);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     outcome=imatrix(1,maxwav+1,1,n);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     num=ivector(1,n);          for(i=1;i<=nlstate*nlstate;i++)
     moisnais=vector(1,n);            for(j=1;j<=nlstate*nlstate;j++)
     annais=vector(1,n);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
     moisdc=vector(1,n);        }
     andc=vector(1,n);      }
     agedc=vector(1,n);      /* Computing expectancies */
     cod=ivector(1,n);      for(i=1; i<=nlstate;i++)
     weight=vector(1,n);        for(j=1; j<=nlstate;j++)
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     mint=matrix(1,maxwav,1,n);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     anint=matrix(1,maxwav,1,n);            
     s=imatrix(1,maxwav+1,1,n);  /* 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]);*/
     adl=imatrix(1,maxwav+1,1,n);      
     tab=ivector(1,NCOVMAX);          }
     ncodemax=ivector(1,8);  
       fprintf(ficreseij,"%3.0f",age );
     i=1;      cptj=0;
     while (fgets(line, MAXLINE, fic) != NULL)    {      for(i=1; i<=nlstate;i++)
       if ((i >= firstobs) && (i <=lastobs)) {        for(j=1; j<=nlstate;j++){
                  cptj++;
         for (j=maxwav;j>=1;j--){          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        }
           strcpy(line,stra);      fprintf(ficreseij,"\n");
           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);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
         }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
              free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    printf("\n");
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficlog,"\n");
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    free_vector(xp,1,npar);
         for (j=ncov;j>=1;j--){    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
         }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
         num[i]=atol(stra);  }
          
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){  /************ Variance ******************/
           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;}*/  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)
   {
         i=i+1;    /* Variance of health expectancies */
       }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     }    /* double **newm;*/
     /* printf("ii=%d", ij);    double **dnewm,**doldm;
        scanf("%d",i);*/    double **dnewmp,**doldmp;
   imx=i-1; /* Number of individuals */    int i, j, nhstepm, hstepm, h, nstepm ;
     int k, cptcode;
   /* for (i=1; i<=imx; i++){    double *xp;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    double **gp, **gm;  /* for var eij */
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    double ***gradg, ***trgradg; /*for var eij */
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    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 */
     for (i=1; i<=imx; i++)    double ***p3mat;
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/    double age,agelim, hf;
     double ***mobaverage;
   /* Calculation of the number of parameter from char model*/    int theta;
   Tvar=ivector(1,15);    char digit[4];
   Tprod=ivector(1,15);    char digitp[25];
   Tvaraff=ivector(1,15);  
   Tvard=imatrix(1,15,1,2);    char fileresprobmorprev[FILENAMELENGTH];
   Tage=ivector(1,15);        
        if(popbased==1){
   if (strlen(model) >1){      if(mobilav!=0)
     j=0, j1=0, k1=1, k2=1;        strcpy(digitp,"-populbased-mobilav-");
     j=nbocc(model,'+');      else strcpy(digitp,"-populbased-nomobil-");
     j1=nbocc(model,'*');    }
     cptcovn=j+1;    else 
     cptcovprod=j1;      strcpy(digitp,"-stablbased-");
      
        if (mobilav!=0) {
     strcpy(modelsav,model);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       printf("Error. Non available option model=%s ",model);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       goto end;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     }      }
        }
     for(i=(j+1); i>=1;i--){  
       cutv(stra,strb,modelsav,'+');    strcpy(fileresprobmorprev,"prmorprev"); 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    sprintf(digit,"%-d",ij);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       /*scanf("%d",i);*/    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       if (strchr(strb,'*')) {    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         cutv(strd,strc,strb,'*');    strcat(fileresprobmorprev,fileres);
         if (strcmp(strc,"age")==0) {    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
           cptcovprod--;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
           cutv(strb,stre,strd,'V');      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
           Tvar[i]=atoi(stre);    }
           cptcovage++;    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
             Tage[cptcovage]=i;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
             /*printf("stre=%s ", stre);*/    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
         }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
         else if (strcmp(strd,"age")==0) {    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           cptcovprod--;      fprintf(ficresprobmorprev," p.%-d SE",j);
           cutv(strb,stre,strc,'V');      for(i=1; i<=nlstate;i++)
           Tvar[i]=atoi(stre);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
           cptcovage++;    }  
           Tage[cptcovage]=i;    fprintf(ficresprobmorprev,"\n");
         }    fprintf(ficgp,"\n# Routine varevsij");
         else {    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");
           cutv(strb,stre,strc,'V');    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
           Tvar[i]=ncov+k1;  /*   } */
           cutv(strb,strc,strd,'V');    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc);    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");
           Tvard[k1][2]=atoi(stre);    fprintf(ficresvij,"# Age");
           Tvar[cptcovn+k2]=Tvard[k1][1];    for(i=1; i<=nlstate;i++)
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      for(j=1; j<=nlstate;j++)
           for (k=1; k<=lastobs;k++)        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    fprintf(ficresvij,"\n");
           k1++;  
           k2=k2+2;    xp=vector(1,npar);
         }    dnewm=matrix(1,nlstate,1,npar);
       }    doldm=matrix(1,nlstate,1,nlstate);
       else {    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       Tvar[i]=atoi(strc);    gpp=vector(nlstate+1,nlstate+ndeath);
       }    gmp=vector(nlstate+1,nlstate+ndeath);
       strcpy(modelsav,stra);      trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    
         scanf("%d",i);*/    if(estepm < stepm){
     }      printf ("Problem %d lower than %d\n",estepm, stepm);
 }    }
      else  hstepm=estepm;   
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    /* For example we decided to compute the life expectancy with the smallest unit */
   printf("cptcovprod=%d ", cptcovprod);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   scanf("%d ",i);*/       nhstepm is the number of hstepm from age to agelim 
     fclose(fic);       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
     /*  if(mle==1){*/       and note for a fixed period like k years */
     if (weightopt != 1) { /* Maximisation without weights*/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       for(i=1;i<=n;i++) weight[i]=1.0;       survival function given by stepm (the optimization length). Unfortunately it
     }       means that if the survival funtion is printed every two years of age and if
     /*-calculation of age at interview from date of interview and age at death -*/       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     agev=matrix(1,maxwav,1,imx);       results. So we changed our mind and took the option of the best precision.
     */
    for (i=1; i<=imx; i++)    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      for(m=2; (m<= maxwav); m++)    agelim = AGESUP;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
          anint[m][i]=9999;      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
          s[m][i]=-1;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
        }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     for (i=1; i<=imx; i++)  {      gp=matrix(0,nhstepm,1,nlstate);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      gm=matrix(0,nhstepm,1,nlstate);
       for(m=1; (m<= maxwav); m++){  
         if(s[m][i] >0){  
           if (s[m][i] == nlstate+1) {      for(theta=1; theta <=npar; theta++){
             if(agedc[i]>0)        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
               if(moisdc[i]!=99 && andc[i]!=9999)          xp[i] = x[i] + (i==theta ?delti[theta]:0);
               agev[m][i]=agedc[i];        }
             else {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
               if (andc[i]!=9999){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;        if (popbased==1) {
               }          if(mobilav ==0){
             }            for(i=1; i<=nlstate;i++)
           }              prlim[i][i]=probs[(int)age][i][ij];
           else if(s[m][i] !=9){ /* Should no more exist */          }else{ /* mobilav */ 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);            for(i=1; i<=nlstate;i++)
             if(mint[m][i]==99 || anint[m][i]==9999)              prlim[i][i]=mobaverage[(int)age][i][ij];
               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);*/        for(j=1; j<= nlstate; j++){
             }          for(h=0; h<=nhstepm; h++){
             else if(agev[m][i] >agemax){            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               agemax=agev[m][i];              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
              /* 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];*/        /* This for computing probability of death (h=1 means
             /*   agev[m][i] = age[i]+2*m;*/           computed over hstepm matrices product = hstepm*stepm months) 
           }           as a weighted average of prlim.
           else { /* =9 */        */
             agev[m][i]=1;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
             s[m][i]=-1;          for(i=1,gpp[j]=0.; i<= nlstate; i++)
           }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }        }    
         else /*= 0 Unknown */        /* end probability of death */
           agev[m][i]=1;  
       }        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
              xp[i] = x[i] - (i==theta ?delti[theta]:0);
     }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     for (i=1; i<=imx; i++)  {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       for(m=1; (m<= maxwav); m++){   
         if (s[m][i] > (nlstate+ndeath)) {        if (popbased==1) {
           printf("Error: Wrong value in nlstate or ndeath\n");            if(mobilav ==0){
           goto end;            for(i=1; i<=nlstate;i++)
         }              prlim[i][i]=probs[(int)age][i][ij];
       }          }else{ /* mobilav */ 
     }            for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
 printf("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);        for(j=1; j<= nlstate; j++){
     free_vector(moisnais,1,n);          for(h=0; h<=nhstepm; h++){
     free_vector(annais,1,n);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     /* free_matrix(mint,1,maxwav,1,n);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
        free_matrix(anint,1,maxwav,1,n);*/          }
     free_vector(moisdc,1,n);        }
     free_vector(andc,1,n);        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
               as a weighted average of prlim.
     wav=ivector(1,imx);        */
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
               gmp[j] += prlim[i][i]*p3mat[i][j][1];
     /* Concatenates waves */        }    
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
       Tcode=ivector(1,100);          for(h=0; h<=nhstepm; h++){
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       ncodemax[1]=1;          }
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  
              for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
    codtab=imatrix(1,100,1,10);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
    h=0;        }
    m=pow(2,cptcoveff);  
        } /* End theta */
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
        for(j=1; j <= ncodemax[k]; j++){  
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      for(h=0; h<=nhstepm; h++) /* veij */
            h++;        for(j=1; j<=nlstate;j++)
            if (h>m) h=1;codtab[h][k]=j;          for(theta=1; theta <=npar; theta++)
          }            trgradg[h][j][theta]=gradg[h][theta][j];
        }  
      }      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
    }        for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
    /*for(i=1; i <=m ;i++){  
      for(k=1; k <=cptcovn; k++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);      for(i=1;i<=nlstate;i++)
      }        for(j=1;j<=nlstate;j++)
      printf("\n");          vareij[i][j][(int)age] =0.;
    }  
    scanf("%d",i);*/      for(h=0;h<=nhstepm;h++){
            for(k=0;k<=nhstepm;k++){
    /* Calculates basic frequencies. Computes observed prevalence at single age          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
        and prints on file fileres'p'. */          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
                for(j=1;j<=nlstate;j++)
                  vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     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 */      /* pptj */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
            matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
     /* For Powell, parameters are in a vector p[] starting at p[1]      for(j=nlstate+1;j<=nlstate+ndeath;j++)
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          varppt[j][i]=doldmp[j][i];
       /* end ppptj */
     if(mle==1){      /*  x centered again */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     }      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
       
     /*--------- results files --------------*/      if (popbased==1) {
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);        if(mobilav ==0){
            for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
    jk=1;        }else{ /* mobilav */ 
    fprintf(ficres,"# Parameters\n");          for(i=1; i<=nlstate;i++)
    printf("# Parameters\n");            prlim[i][i]=mobaverage[(int)age][i][ij];
    for(i=1,jk=1; i <=nlstate; i++){        }
      for(k=1; k <=(nlstate+ndeath); k++){      }
        if (k != i)               
          {      /* This for computing probability of death (h=1 means
            printf("%d%d ",i,k);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
            fprintf(ficres,"%1d%1d ",i,k);         as a weighted average of prlim.
            for(j=1; j <=ncovmodel; j++){      */
              printf("%f ",p[jk]);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
              fprintf(ficres,"%f ",p[jk]);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
              jk++;          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
            }      }    
            printf("\n");      /* end probability of death */
            fprintf(ficres,"\n");  
          }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
      }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
    }        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
  if(mle==1){        for(i=1; i<=nlstate;i++){
     /* Computing hessian and covariance matrix */          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     ftolhess=ftol; /* Usually correct */        }
     hesscov(matcov, p, npar, delti, ftolhess, func);      } 
  }      fprintf(ficresprobmorprev,"\n");
     fprintf(ficres,"# Scales\n");  
     printf("# Scales\n");      fprintf(ficresvij,"%.0f ",age );
      for(i=1,jk=1; i <=nlstate; i++){      for(i=1; i<=nlstate;i++)
       for(j=1; j <=nlstate+ndeath; j++){        for(j=1; j<=nlstate;j++){
         if (j!=i) {          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
           fprintf(ficres,"%1d%1d",i,j);        }
           printf("%1d%1d",i,j);      fprintf(ficresvij,"\n");
           for(k=1; k<=ncovmodel;k++){      free_matrix(gp,0,nhstepm,1,nlstate);
             printf(" %.5e",delti[jk]);      free_matrix(gm,0,nhstepm,1,nlstate);
             fprintf(ficres," %.5e",delti[jk]);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
             jk++;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
           }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           printf("\n");    } /* End age */
           fprintf(ficres,"\n");    free_vector(gpp,nlstate+1,nlstate+ndeath);
         }    free_vector(gmp,nlstate+1,nlstate+ndeath);
       }    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");
     k=1;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficres,"# Covariance\n");    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     printf("# Covariance\n");  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     for(i=1;i<=npar;i++){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
       /*  if (k>nlstate) k=1;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
       i1=(i-1)/(ncovmodel*nlstate)+1;    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
       printf("%s%d%d",alph[k],i1,tab[i]);*/    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
       fprintf(ficres,"%3d",i);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
       printf("%3d",i);    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(j=1; j<=i;j++){    /*  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(ficres," %.5e",matcov[i][j]);  */
         printf(" %.5e",matcov[i][j]);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
       }    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
       fprintf(ficres,"\n");  
       printf("\n");    free_vector(xp,1,npar);
       k++;    free_matrix(doldm,1,nlstate,1,nlstate);
     }    free_matrix(dnewm,1,nlstate,1,npar);
        free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     while((c=getc(ficpar))=='#' && c!= EOF){    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
       ungetc(c,ficpar);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       fgets(line, MAXLINE, ficpar);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       puts(line);    fclose(ficresprobmorprev);
       fputs(line,ficparo);    fflush(ficgp);
     }    fflush(fichtm); 
     ungetc(c,ficpar);  }  /* end varevsij */
    
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);  /************ Variance of prevlim ******************/
      void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
     if (fage <= 2) {  {
       bage = agemin;    /* Variance of prevalence limit */
       fage = agemax;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     }    double **newm;
        double **dnewm,**doldm;
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    int i, j, nhstepm, hstepm;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    int k, cptcode;
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    double *xp;
      double *gp, *gm;
     while((c=getc(ficpar))=='#' && c!= EOF){    double **gradg, **trgradg;
     ungetc(c,ficpar);    double age,agelim;
     fgets(line, MAXLINE, ficpar);    int theta;
     puts(line);     
     fputs(line,ficparo);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   }    fprintf(ficresvpl,"# Age");
   ungetc(c,ficpar);    for(i=1; i<=nlstate;i++)
          fprintf(ficresvpl," %1d-%1d",i,i);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    fprintf(ficresvpl,"\n");
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    xp=vector(1,npar);
          dnewm=matrix(1,nlstate,1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){    doldm=matrix(1,nlstate,1,nlstate);
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    hstepm=1*YEARM; /* Every year of age */
     puts(line);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     fputs(line,ficparo);    agelim = AGESUP;
   }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   ungetc(c,ficpar);      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 */
    dateprev1=anprev1+mprev1/12.+jprev1/365.;      gradg=matrix(1,npar,1,nlstate);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   fscanf(ficpar,"pop_based=%d\n",&popbased);  
    fprintf(ficparo,"pop_based=%d\n",popbased);        for(theta=1; theta <=npar; theta++){
    fprintf(ficres,"pop_based=%d\n",popbased);          for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   while((c=getc(ficpar))=='#' && c!= EOF){        }
     ungetc(c,ficpar);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     fgets(line, MAXLINE, ficpar);        for(i=1;i<=nlstate;i++)
     puts(line);          gp[i] = prlim[i][i];
     fputs(line,ficparo);      
   }        for(i=1; i<=npar; i++) /* Computes gradient */
   ungetc(c,ficpar);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mob_average=%d\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mob_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);        for(i=1;i<=nlstate;i++)
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mob_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          gm[i] = prlim[i][i];
   
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);        for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
 /*------------ gnuplot -------------*/      } /* End theta */
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemax,fage, pathc,p);  
        trgradg =matrix(1,nlstate,1,npar);
 /*------------ free_vector  -------------*/  
  chdir(path);      for(j=1; j<=nlstate;j++)
          for(theta=1; theta <=npar; theta++)
  free_ivector(wav,1,imx);          trgradg[j][theta]=gradg[theta][j];
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        for(i=1;i<=nlstate;i++)
  free_ivector(num,1,n);        varpl[i][(int)age] =0.;
  free_vector(agedc,1,n);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
  fclose(ficparo);      for(i=1;i<=nlstate;i++)
  fclose(ficres);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
    
   /* Reads comments: lines beginning with '#' */      fprintf(ficresvpl,"%.0f ",age );
   while((c=getc(ficpar))=='#' && c!= EOF){      for(i=1; i<=nlstate;i++)
     ungetc(c,ficpar);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
     fgets(line, MAXLINE, ficpar);      fprintf(ficresvpl,"\n");
     puts(line);      free_vector(gp,1,nlstate);
     fputs(line,ficparo);      free_vector(gm,1,nlstate);
   }      free_matrix(gradg,1,npar,1,nlstate);
   ungetc(c,ficpar);      free_matrix(trgradg,1,nlstate,1,npar);
      } /* End age */
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);  
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);    free_vector(xp,1,npar);
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    free_matrix(doldm,1,nlstate,1,npar);
 /*--------- index.htm --------*/    free_matrix(dnewm,1,nlstate,1,nlstate);
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm);  }
   
    /************ Variance of one-step probabilities  ******************/
   /*--------------- Prevalence limit --------------*/  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
    {
   strcpy(filerespl,"pl");    int i, j=0,  i1, k1, l1, t, tj;
   strcat(filerespl,fileres);    int k2, l2, j1,  z1;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    int k=0,l, cptcode;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    int first=1, first1;
   }    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    double **dnewm,**doldm;
   fprintf(ficrespl,"#Prevalence limit\n");    double *xp;
   fprintf(ficrespl,"#Age ");    double *gp, *gm;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    double **gradg, **trgradg;
   fprintf(ficrespl,"\n");    double **mu;
      double age,agelim, cov[NCOVMAX];
   prlim=matrix(1,nlstate,1,nlstate);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int theta;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    char fileresprob[FILENAMELENGTH];
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    char fileresprobcov[FILENAMELENGTH];
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    char fileresprobcor[FILENAMELENGTH];
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
   k=0;    double ***varpij;
   agebase=agemin;  
   agelim=agemax;    strcpy(fileresprob,"prob"); 
   ftolpl=1.e-10;    strcat(fileresprob,fileres);
   i1=cptcoveff;    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   if (cptcovn < 1){i1=1;}      printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   for(cptcov=1;cptcov<=i1;cptcov++){    }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    strcpy(fileresprobcov,"probcov"); 
         k=k+1;    strcat(fileresprobcov,fileres);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
         fprintf(ficrespl,"\n#******");      printf("Problem with resultfile: %s\n", fileresprobcov);
         for(j=1;j<=cptcoveff;j++)      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    }
         fprintf(ficrespl,"******\n");    strcpy(fileresprobcor,"probcor"); 
            strcat(fileresprobcor,fileres);
         for (age=agebase; age<=agelim; age++){    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      printf("Problem with resultfile: %s\n", fileresprobcor);
           fprintf(ficrespl,"%.0f",age );      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
           for(i=1; i<=nlstate;i++)    }
           fprintf(ficrespl," %.5f", prlim[i][i]);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           fprintf(ficrespl,"\n");    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);
       }    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);
   fclose(ficrespl);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     
   /*------------- h Pij x at various ages ------------*/    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
      fprintf(ficresprob,"# Age");
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    fprintf(ficresprobcov,"# Age");
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   }    fprintf(ficresprobcov,"# Age");
   printf("Computing pij: result on file '%s' \n", filerespij);  
    
   stepsize=(int) (stepm+YEARM-1)/YEARM;    for(i=1; i<=nlstate;i++)
   /*if (stepm<=24) stepsize=2;*/      for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   agelim=AGESUP;        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   hstepm=stepsize*YEARM; /* Every year of age */        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      }  
     /* fprintf(ficresprob,"\n");
   k=0;    fprintf(ficresprobcov,"\n");
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficresprobcor,"\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   */
       k=k+1;   xp=vector(1,npar);
         fprintf(ficrespij,"\n#****** ");    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         for(j=1;j<=cptcoveff;j++)    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
         fprintf(ficrespij,"******\n");    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
            first=1;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    fprintf(ficgp,"\n# Routine varprob");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    fprintf(fichtm,"\n");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\
           fprintf(ficrespij,"# Age");    file %s<br>\n",optionfilehtmcov);
           for(i=1; i<=nlstate;i++)    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
             for(j=1; j<=nlstate+ndeath;j++)  and drawn. It helps understanding how is the covariance between two incidences.\
               fprintf(ficrespij," %1d-%1d",i,j);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
           fprintf(ficrespij,"\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. \
           for (h=0; h<=nhstepm; h++){  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
             for(i=1; i<=nlstate;i++)  standard deviations wide on each axis. <br>\
               for(j=1; j<=nlstate+ndeath;j++)   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
             fprintf(ficrespij,"\n");  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    cov[1]=1;
           fprintf(ficrespij,"\n");    tj=cptcoveff;
         }    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     }    j1=0;
   }    for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/        j1++;
         if  (cptcovn>0) {
   fclose(ficrespij);          fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if(stepm == 1) {          fprintf(ficresprob, "**********\n#\n");
   /*---------- Forecasting ------------------*/          fprintf(ficresprobcov, "\n#********** Variable "); 
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
   /*printf("calage= %f", calagedate);*/          
            fprintf(ficgp, "\n#********** Variable "); 
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
   strcpy(fileresf,"f");          
   strcat(fileresf,fileres);          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   if((ficresf=fopen(fileresf,"w"))==NULL) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   }          
   printf("Computing forecasting: result on file '%s' \n", fileresf);          fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   free_matrix(mint,1,maxwav,1,n);          fprintf(ficresprobcor, "**********\n#");    
   free_matrix(anint,1,maxwav,1,n);        }
   free_matrix(agev,1,maxwav,1,imx);        
         for (age=bage; age<=fage; age ++){ 
   /* Mobile average */          cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
   if (mobilav==1) {          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for (k=1; k<=cptcovprod;k++)
     movingaverage(agedeb, fage, agemin, mobaverage);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   }          
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   stepsize=(int) (stepm+YEARM-1)/YEARM;          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   if (stepm<=12) stepsize=1;          gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
   agelim=AGESUP;      
   /*hstepm=stepsize*YEARM; *//* Every year of age */          for(theta=1; theta <=npar; theta++){
   hstepm=1;            for(i=1; i<=npar; i++)
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   yp1=modf(dateintmean,&yp);            
   anprojmean=yp;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   yp2=modf((yp1*12),&yp);            
   mprojmean=yp;            k=0;
   yp1=modf((yp2*30.5),&yp);            for(i=1; i<= (nlstate); i++){
   jprojmean=yp;              for(j=1; j<=(nlstate+ndeath);j++){
   if(jprojmean==0) jprojmean=1;                k=k+1;
   if(mprojmean==0) jprojmean=1;                gp[k]=pmmij[i][j];
               }
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);            }
             
   if (popforecast==1) {            for(i=1; i<=npar; i++)
     if((ficpop=fopen(popfile,"r"))==NULL)    {              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       printf("Problem with population file : %s\n",popfile);goto end;      
     }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     popage=ivector(0,AGESUP);            k=0;
     popeffectif=vector(0,AGESUP);            for(i=1; i<=(nlstate); i++){
     popcount=vector(0,AGESUP);              for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
     i=1;                  gm[k]=pmmij[i][j];
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)              }
       {            }
         i=i+1;       
       }            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     imx=i;              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
              }
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];  
   }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
   for(cptcov=1;cptcov<=i1;cptcov++){              trgradg[j][theta]=gradg[theta][j];
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          
       k=k+1;          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
       fprintf(ficresf,"\n#******");          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
       for(j=1;j<=cptcoveff;j++) {          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
       }          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       fprintf(ficresf,"******\n");          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       fprintf(ficresf,"# StartingAge FinalAge");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);          pmij(pmmij,cov,ncovmodel,x,nlstate);
       if (popforecast==1)  fprintf(ficresf," [Population]");          
                k=0;
      for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {          for(i=1; i<=(nlstate); i++){
         fprintf(ficresf,"\n");            for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);                k=k+1;
               mu[k][(int) age]=pmmij[i][j];
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){            }
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          }
         nhstepm = nhstepm/hstepm;          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
                    for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              varpij[i][j][(int)age] = doldm[i][j];
         oldm=oldms;savm=savms;  
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            /*printf("\n%d ",(int)age);
                    for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         for (h=0; h<=nhstepm; h++){            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
           if (h==(int) (calagedate+YEARM*cpt)) {            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);            }*/
           }  
           for(j=1; j<=nlstate+ndeath;j++) {          fprintf(ficresprob,"\n%d ",(int)age);
             kk1=0.;kk2=0;          fprintf(ficresprobcov,"\n%d ",(int)age);
             for(i=1; i<=nlstate;i++) {                  fprintf(ficresprobcor,"\n%d ",(int)age);
               if (mobilav==1)  
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
               else {            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
               }            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];          i=0;
             }          for (k=1; k<=(nlstate);k++){
                      for (l=1; l<=(nlstate+ndeath);l++){ 
             if (h==(int)(calagedate+12*cpt)){              i=i++;
               fprintf(ficresf," %.3f", kk1);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
                            fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);              for (j=1; j<=i;j++){
             }                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
           }                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
         }              }
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
         }          }/* end of loop for state */
      }        } /* end of loop for age */
     }  
   }        /* Confidence intervalle of pij  */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        /*
           fprintf(ficgp,"\nset noparametric;unset label");
   if (popforecast==1) {          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     free_ivector(popage,0,AGESUP);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     free_vector(popeffectif,0,AGESUP);          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);
     free_vector(popcount,0,AGESUP);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   }          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   free_imatrix(s,1,maxwav+1,1,n);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   free_vector(weight,1,n);        */
   fclose(ficresf);  
   }/* End forecasting */        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   else{        first1=1;
     erreur=108;        for (k2=1; k2<=(nlstate);k2++){
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
   }            j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
                for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   /*---------- Health expectancies and variances ------------*/                if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
   strcpy(filerest,"t");                if(i<=j) continue;
   strcat(filerest,fileres);                for (age=bage; age<=fage; age ++){ 
   if((ficrest=fopen(filerest,"w"))==NULL) {                  if ((int)age %5==0){
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   }                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
   strcpy(filerese,"e");                    c12=cv12/sqrt(v1*v2);
   strcat(filerese,fileres);                    /* Computing eigen value of matrix of covariance */
   if((ficreseij=fopen(filerese,"w"))==NULL) {                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   }                    /* Eigen vectors */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
  strcpy(fileresv,"v");                    v21=(lc1-v1)/cv12*v11;
   strcat(fileresv,fileres);                    v12=-v21;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {                    v22=v11;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);                    tnalp=v21/v11;
   }                    if(first1==1){
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);                      first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
   k=0;                    }
   for(cptcov=1;cptcov<=i1;cptcov++){                    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);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    /*printf(fignu*/
       k=k+1;                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
       fprintf(ficrest,"\n#****** ");                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
       for(j=1;j<=cptcoveff;j++)                    if(first==1){
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                      first=0;
       fprintf(ficrest,"******\n");                      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(ficreseij,"\n#****** ");                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       for(j=1;j<=cptcoveff;j++)                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
       fprintf(ficreseij,"******\n");  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
       fprintf(ficresvij,"\n#****** ");                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
       for(j=1;j<=cptcoveff;j++)                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
       fprintf(ficresvij,"******\n");                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       oldm=oldms;savm=savms;                      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",\
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);                                mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       oldm=oldms;savm=savms;                    }else{
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                      first=0;
                            fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       fprintf(ficrest,"\n");                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                                      mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       hf=1;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       if (stepm >= YEARM) hf=stepm/YEARM;                    }/* if first */
       epj=vector(1,nlstate+1);                  } /* age mod 5 */
       for(age=bage; age <=fage ;age++){                } /* end loop age */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
         if (popbased==1) {                first=1;
           for(i=1; i<=nlstate;i++)              } /*l12 */
             prlim[i][i]=probs[(int)age][i][k];            } /* k12 */
         }          } /*l1 */
                }/* k1 */
         fprintf(ficrest," %.0f",age);      } /* loop covariates */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    }
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
           }    free_vector(xp,1,npar);
           epj[nlstate+1] +=epj[j];    fclose(ficresprob);
         }    fclose(ficresprobcov);
         for(i=1, vepp=0.;i <=nlstate;i++)    fclose(ficresprobcor);
           for(j=1;j <=nlstate;j++)    fflush(ficgp);
             vepp += vareij[i][j][(int)age];    fflush(fichtmcov);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));  }
         for(j=1;j <=nlstate;j++){  
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));  
         }  /******************* Printing html file ***********/
         fprintf(ficrest,"\n");  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
       }                    int lastpass, int stepm, int weightopt, char model[],\
     }                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   }                    int popforecast, int estepm ,\
                            double jprev1, double mprev1,double anprev1, \
                            double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
     /*char optionfilehtm[FILENAMELENGTH];*/
  fclose(ficreseij);  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
  fclose(ficresvij);  /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
   fclose(ficrest);  /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
   fclose(ficpar);  /*   } */
   free_vector(epj,1,nlstate+1);  
   /*  scanf("%d ",i); */     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 \
   /*------- Variance limit prevalence------*/     - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
    - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
 strcpy(fileresvpl,"vpl");   - Life expectancies by age and initial health status (estepm=%2d months): \
   strcat(fileresvpl,fileres);     <a href=\"%s\">%s</a> <br>\n</li>", \
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
     exit(0);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
   }             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
  k=0;  
  for(cptcov=1;cptcov<=i1;cptcov++){   m=cptcoveff;
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
      k=k+1;  
      fprintf(ficresvpl,"\n#****** ");   jj1=0;
      for(j=1;j<=cptcoveff;j++)   for(k1=1; k1<=m;k1++){
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     for(i1=1; i1<=ncodemax[k1];i1++){
      fprintf(ficresvpl,"******\n");       jj1++;
             if (cptcovn > 0) {
      varpl=matrix(1,nlstate,(int) bage, (int) fage);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
      oldm=oldms;savm=savms;         for (cpt=1; cpt<=cptcoveff;cpt++) 
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
    }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
  }       }
        /* Pij */
   fclose(ficresvpl);       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);     
   /*---------- End : free ----------------*/       /* Quasi-incidences */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);       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: %s%d2.png<br> \
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);         /* Stable prevalence in each health state */
           for(cpt=1; cpt<nlstate;cpt++){
             fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);         }
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);       for(cpt=1; cpt<=nlstate;cpt++) {
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
    <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
   free_matrix(matcov,1,npar,1,npar);       }
   free_vector(delti,1,npar);       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
    health expectancies in states (1) and (2): %s%d.png<br>\
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
   if(erreur >0)   }/* End k1 */
     printf("End of Imach with error %d\n",erreur);   fprintf(fichtm,"</ul>");
   else   printf("End of Imach\n");  
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
     fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
   /* 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);*/   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
   /*printf("Total time was %d uSec.\n", total_usecs);*/   - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
   /*------ End -----------*/   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
  end:   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
 #ifdef windows   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
   /* chdir(pathcd);*/           rfileres,rfileres,\
 #endif           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
  /*system("wgnuplot graph.plt");*/           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
  /*system("../gp37mgw/wgnuplot graph.plt");*/           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
  /*system("cd ../gp37mgw");*/           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/           subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
  strcpy(plotcmd,GNUPLOTPROGRAM);           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
  strcat(plotcmd," ");  
  strcat(plotcmd,optionfilegnuplot);  /*  if(popforecast==1) fprintf(fichtm,"\n */
  system(plotcmd);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
 #ifdef windows  /*      <br>",fileres,fileres,fileres,fileres); */
   while (z[0] != 'q') {  /*  else  */
     chdir(path);  /*    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); */
     printf("\nType e to edit output files, c to start again, and q for exiting: ");  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
     scanf("%s",z);  
     if (z[0] == 'c') system("./imach");   m=cptcoveff;
     else if (z[0] == 'e') {   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       chdir(path);  
       system(optionfilehtm);   jj1=0;
     }   for(k1=1; k1<=m;k1++){
     else if (z[0] == 'q') exit(0);     for(i1=1; i1<=ncodemax[k1];i1++){
   }       jj1++;
 #endif       if (cptcovn > 0) {
 }         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]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
   interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     }
   
   } /* end of prwizard */
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Localtime (at start):%s",strstart);
     fprintf(ficlog,"Localtime (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
    
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){
       j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;
         j++;
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) && (j1 != j)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     }  
     fflush(ficlog);
   
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1-i)*(j1-j)!=0){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         fprintf(ficlog,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
           fprintf(ficlog," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
         fprintf(ficlog,"\n");
       }
     }
     fflush(ficlog);
   
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
         }
         fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       numlinepar++;
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
     fflush(ficlog);
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     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.1.25  
changed lines
  Added in v.1.93


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