[BACK]Return to imach.c CVS log [TXT] [DIR] Up to [Local Repository] / imach / src

Diff for /imach/src/imach.c between versions 1.22 and 1.97

version 1.22, 2002/02/22 17:54:20 version 1.97, 2004/02/20 13:25:42
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolate Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.97  2004/02/20 13:25:42  lievre
      Version 0.96d. Population forecasting command line is (temporarily)
   This program computes Healthy Life Expectancies from    suppressed.
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  
   first survey ("cross") where individuals from different ages are    Revision 1.96  2003/07/15 15:38:55  brouard
   interviewed on their health status or degree of disability (in the    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   case of a health survey which is our main interest) -2- at least a    rewritten within the same printf. Workaround: many printfs.
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.95  2003/07/08 07:54:34  brouard
   computed from the time spent in each health state according to a    * imach.c (Repository):
   model. More health states you consider, more time is necessary to reach the    (Repository): Using imachwizard code to output a more meaningful covariance
   Maximum Likelihood of the parameters involved in the model.  The    matrix (cov(a12,c31) instead of numbers.
   simplest model is the multinomial logistic model where pij is the  
   probabibility to be observed in state j at the second wave    Revision 1.94  2003/06/27 13:00:02  brouard
   conditional to be observed in state i at the first wave. Therefore    Just cleaning
   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 1.93  2003/06/25 16:33:55  brouard
   complex model than "constant and age", you should modify the program    (Module): On windows (cygwin) function asctime_r doesn't
   where the markup *Covariates have to be included here again* invites    exist so I changed back to asctime which exists.
   you to do it.  More covariates you add, slower the    (Module): Version 0.96b
   convergence.  
     Revision 1.92  2003/06/25 16:30:45  brouard
   The advantage of this computer programme, compared to a simple    (Module): On windows (cygwin) function asctime_r doesn't
   multinomial logistic model, is clear when the delay between waves is not    exist so I changed back to asctime which exists.
   identical for each individual. Also, if a individual missed an  
   intermediate interview, the information is lost, but taken into    Revision 1.91  2003/06/25 15:30:29  brouard
   account using an interpolation or extrapolation.      * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
   hPijx is the probability to be observed in state i at age x+h    helps to forecast when convergence will be reached. Elapsed time
   conditional to the observed state i at age x. The delay 'h' can be    is stamped in powell.  We created a new html file for the graphs
   split into an exact number (nh*stepm) of unobserved intermediate    concerning matrix of covariance. It has extension -cov.htm.
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.90  2003/06/24 12:34:15  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    (Module): Some bugs corrected for windows. Also, when
   and the contribution of each individual to the likelihood is simply    mle=-1 a template is output in file "or"mypar.txt with the design
   hPijx.    of the covariance matrix to be input.
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.89  2003/06/24 12:30:52  brouard
   of the life expectancies. It also computes the prevalence limits.    (Module): Some bugs corrected for windows. Also, when
      mle=-1 a template is output in file "or"mypar.txt with the design
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    of the covariance matrix to be input.
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.88  2003/06/23 17:54:56  brouard
   from the European Union.    * 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.
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.87  2003/06/18 12:26:01  brouard
   can be accessed at http://euroreves.ined.fr/imach .    Version 0.96
   **********************************************************************/  
      Revision 1.86  2003/06/17 20:04:08  brouard
 #include <math.h>    (Module): Change position of html and gnuplot routines and added
 #include <stdio.h>    routine fileappend.
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
 #define MAXLINE 256    current date of interview. It may happen when the death was just
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    prior to the death. In this case, dh was negative and likelihood
 #define FILENAMELENGTH 80    was wrong (infinity). We still send an "Error" but patch by
 /*#define DEBUG*/    assuming that the date of death was just one stepm after the
 #define windows    interview.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    (Repository): Because some people have very long ID (first column)
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    truncation)
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (Repository): No more line truncation errors.
   
 #define NINTERVMAX 8    Revision 1.84  2003/06/13 21:44:43  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    * imach.c (Repository): Replace "freqsummary" at a correct
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    place. It differs from routine "prevalence" which may be called
 #define NCOVMAX 8 /* Maximum number of covariates */    many times. Probs is memory consuming and must be used with
 #define MAXN 20000    parcimony.
 #define YEARM 12. /* Number of months per year */    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
   
 int erreur; /* Error number */    Revision 1.82  2003/06/05 15:57:20  brouard
 int nvar;    Add log in  imach.c and  fullversion number is now printed.
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;  */
 int nlstate=2; /* Number of live states */  /*
 int ndeath=1; /* Number of dead states */     Interpolated Markov Chain
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Short summary of the programme:
     
 int *wav; /* Number of waves for this individuual 0 is possible */    This program computes Healthy Life Expectancies from
 int maxwav; /* Maxim number of waves */    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 int jmin, jmax; /* min, max spacing between 2 waves */    first survey ("cross") where individuals from different ages are
 int mle, weightopt;    interviewed on their health status or degree of disability (in the
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    case of a health survey which is our main interest) -2- at least a
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    second wave of interviews ("longitudinal") which measure each change
 double jmean; /* Mean space between 2 waves */    (if any) in individual health status.  Health expectancies are
 double **oldm, **newm, **savm; /* Working pointers to matrices */    computed from the time spent in each health state according to a
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    model. More health states you consider, more time is necessary to reach the
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    Maximum Likelihood of the parameters involved in the model.  The
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    simplest model is the multinomial logistic model where pij is the
 FILE *ficreseij;    probability to be observed in state j at the second wave
   char filerese[FILENAMELENGTH];    conditional to be observed in state i at the first wave. Therefore
  FILE  *ficresvij;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   char fileresv[FILENAMELENGTH];    'age' is age and 'sex' is a covariate. If you want to have a more
  FILE  *ficresvpl;    complex model than "constant and age", you should modify the program
   char fileresvpl[FILENAMELENGTH];    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
 #define NR_END 1    convergence.
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    The advantage of this computer programme, compared to a simple
     multinomial logistic model, is clear when the delay between waves is not
 #define NRANSI    identical for each individual. Also, if a individual missed an
 #define ITMAX 200    intermediate interview, the information is lost, but taken into
     account using an interpolation or extrapolation.  
 #define TOL 2.0e-4  
     hPijx is the probability to be observed in state i at age x+h
 #define CGOLD 0.3819660    conditional to the observed state i at age x. The delay 'h' can be
 #define ZEPS 1.0e-10    split into an exact number (nh*stepm) of unobserved intermediate
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    states. This elementary transition (by month, quarter,
     semester or year) is modelled as a multinomial logistic.  The hPx
 #define GOLD 1.618034    matrix is simply the matrix product of nh*stepm elementary matrices
 #define GLIMIT 100.0    and the contribution of each individual to the likelihood is simply
 #define TINY 1.0e-20    hPijx.
   
 static double maxarg1,maxarg2;    Also this programme outputs the covariance matrix of the parameters but also
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    of the life expectancies. It also computes the stable prevalence. 
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    
      Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))             Institut national d'études démographiques, Paris.
 #define rint(a) floor(a+0.5)    This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
 static double sqrarg;    It is copyrighted identically to a GNU software product, ie programme and
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    software can be distributed freely for non commercial use. Latest version
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    can be accessed at http://euroreves.ined.fr/imach .
   
 int imx;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 int stepm;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 /* Stepm, step in month: minimum step interpolation*/    
     **********************************************************************/
 int m,nb;  /*
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    main
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    read parameterfile
 double **pmmij, ***probs, ***mobaverage;    read datafile
 double dateintmean=0;    concatwav
     freqsummary
 double *weight;    if (mle >= 1)
 int **s; /* Status */      mlikeli
 double *agedc, **covar, idx;    print results files
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    if mle==1 
        computes hessian
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    read end of parameter file: agemin, agemax, bage, fage, estepm
 double ftolhess; /* Tolerance for computing hessian */        begin-prev-date,...
     open gnuplot file
 /**************** split *************************/    open html file
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    stable prevalence
 {     for age prevalim()
    char *s;                             /* pointer */    h Pij x
    int  l1, l2;                         /* length counters */    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
    l1 = strlen( path );                 /* length of path */    health expectancies
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Variance-covariance of DFLE
 #ifdef windows    prevalence()
    s = strrchr( path, '\\' );           /* find last / */     movingaverage()
 #else    varevsij() 
    s = strrchr( path, '/' );            /* find last / */    if popbased==1 varevsij(,popbased)
 #endif    total life expectancies
    if ( s == NULL ) {                   /* no directory, so use current */    Variance of stable prevalence
 #if     defined(__bsd__)                /* get current working directory */   end
       extern char       *getwd( );  */
   
       if ( getwd( dirc ) == NULL ) {  
 #else  
       extern char       *getcwd( );   
   #include <math.h>
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #include <stdio.h>
 #endif  #include <stdlib.h>
          return( GLOCK_ERROR_GETCWD );  #include <unistd.h>
       }  
       strcpy( name, path );             /* we've got it */  #include <sys/time.h>
    } else {                             /* strip direcotry from path */  #include <time.h>
       s++;                              /* after this, the filename */  #include "timeval.h"
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  /* #include <libintl.h> */
       strcpy( name, s );                /* save file name */  /* #define _(String) gettext (String) */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */  #define MAXLINE 256
    }  #define GNUPLOTPROGRAM "gnuplot"
    l1 = strlen( dirc );                 /* length of directory */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #ifdef windows  #define FILENAMELENGTH 132
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  /*#define DEBUG*/
 #else  /*#define windows*/
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #endif  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
    s = strrchr( name, '.' );            /* find last / */  
    s++;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
    strcpy(ext,s);                       /* save extension */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
    l1= strlen( name);  
    l2= strlen( s)+1;  #define NINTERVMAX 8
    strncpy( finame, name, l1-l2);  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
    finame[l1-l2]= 0;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
    return( 0 );                         /* we're done */  #define NCOVMAX 8 /* Maximum number of covariates */
 }  #define MAXN 20000
   #define YEARM 12. /* Number of months per year */
   #define AGESUP 130
 /******************************************/  #define AGEBASE 40
   #ifdef unix
 void replace(char *s, char*t)  #define DIRSEPARATOR '/'
 {  #define ODIRSEPARATOR '\\'
   int i;  #else
   int lg=20;  #define DIRSEPARATOR '\\'
   i=0;  #define ODIRSEPARATOR '/'
   lg=strlen(t);  #endif
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);  /* $Id$ */
     if (t[i]== '\\') s[i]='/';  /* $State$ */
   }  
 }  char version[]="Imach version 0.96d, February 2004, INED-EUROREVES ";
   char fullversion[]="$Revision$ $Date$"; 
 int nbocc(char *s, char occ)  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 {  int nvar;
   int i,j=0;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   int lg=20;  int npar=NPARMAX;
   i=0;  int nlstate=2; /* Number of live states */
   lg=strlen(s);  int ndeath=1; /* Number of dead states */
   for(i=0; i<= lg; i++) {  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   if  (s[i] == occ ) j++;  int popbased=0;
   }  
   return j;  int *wav; /* Number of waves for this individuual 0 is possible */
 }  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
 void cutv(char *u,char *v, char*t, char occ)  int gipmx, gsw; /* Global variables on the number of contributions 
 {                     to the likelihood and the sum of weights (done by funcone)*/
   int i,lg,j,p=0;  int mle, weightopt;
   i=0;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   for(j=0; j<=strlen(t)-1; j++) {  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   }             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
   lg=strlen(t);  double **oldm, **newm, **savm; /* Working pointers to matrices */
   for(j=0; j<p; j++) {  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     (u[j] = t[j]);  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   }  FILE *ficlog, *ficrespow;
      u[p]='\0';  int globpr; /* Global variable for printing or not */
   double fretone; /* Only one call to likelihood */
    for(j=0; j<= lg; j++) {  long ipmx; /* Number of contributions */
     if (j>=(p+1))(v[j-p-1] = t[j]);  double sw; /* Sum of weights */
   }  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 }  FILE *ficresilk;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 /********************** nrerror ********************/  FILE *ficresprobmorprev;
   FILE *fichtm, *fichtmcov; /* Html File */
 void nrerror(char error_text[])  FILE *ficreseij;
 {  char filerese[FILENAMELENGTH];
   fprintf(stderr,"ERREUR ...\n");  FILE  *ficresvij;
   fprintf(stderr,"%s\n",error_text);  char fileresv[FILENAMELENGTH];
   exit(1);  FILE  *ficresvpl;
 }  char fileresvpl[FILENAMELENGTH];
 /*********************** vector *******************/  char title[MAXLINE];
 double *vector(int nl, int nh)  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 {  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   double *v;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  char command[FILENAMELENGTH];
   if (!v) nrerror("allocation failure in vector");  int  outcmd=0;
   return v-nl+NR_END;  
 }  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   
 /************************ free vector ******************/  char filelog[FILENAMELENGTH]; /* Log file */
 void free_vector(double*v, int nl, int nh)  char filerest[FILENAMELENGTH];
 {  char fileregp[FILENAMELENGTH];
   free((FREE_ARG)(v+nl-NR_END));  char popfile[FILENAMELENGTH];
 }  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 {  struct timezone tzp;
   int *v;  extern int gettimeofday();
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   if (!v) nrerror("allocation failure in ivector");  long time_value;
   return v-nl+NR_END;  extern long time();
 }  char strcurr[80], strfor[80];
   
 /******************free ivector **************************/  #define NR_END 1
 void free_ivector(int *v, long nl, long nh)  #define FREE_ARG char*
 {  #define FTOL 1.0e-10
   free((FREE_ARG)(v+nl-NR_END));  
 }  #define NRANSI 
   #define ITMAX 200 
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #define TOL 2.0e-4 
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {  #define CGOLD 0.3819660 
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #define ZEPS 1.0e-10 
   int **m;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
    
   /* allocate pointers to rows */  #define GOLD 1.618034 
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #define GLIMIT 100.0 
   if (!m) nrerror("allocation failure 1 in matrix()");  #define TINY 1.0e-20 
   m += NR_END;  
   m -= nrl;  static double maxarg1,maxarg2;
    #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
    #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   /* allocate rows and set pointers to them */    
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define rint(a) floor(a+0.5)
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  static double sqrarg;
    #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
    
   /* return pointer to array of pointers to rows */  int imx; 
   return m;  int stepm;
 }  /* Stepm, step in month: minimum step interpolation*/
   
 /****************** free_imatrix *************************/  int estepm;
 void free_imatrix(m,nrl,nrh,ncl,nch)  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       int **m;  
       long nch,ncl,nrh,nrl;  int m,nb;
      /* free an int matrix allocated by imatrix() */  long *num;
 {  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   free((FREE_ARG) (m+nrl-NR_END));  double **pmmij, ***probs;
 }  double dateintmean=0;
   
 /******************* matrix *******************************/  double *weight;
 double **matrix(long nrl, long nrh, long ncl, long nch)  int **s; /* Status */
 {  double *agedc, **covar, idx;
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   double **m;  
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  double ftolhess; /* Tolerance for computing hessian */
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  /**************** split *************************/
   m -= nrl;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    char  *ss;                            /* pointer */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    int   l1, l2;                         /* length counters */
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   return m;    if ( ss == NULL ) {                   /* no directory, so use current */
 }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 /*************************free matrix ************************/      /* get current working directory */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)      /*    extern  char* getcwd ( char *buf , int len);*/
 {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   free((FREE_ARG)(m[nrl]+ncl-NR_END));        return( GLOCK_ERROR_GETCWD );
   free((FREE_ARG)(m+nrl-NR_END));      }
 }      strcpy( name, path );               /* we've got it */
     } else {                              /* strip direcotry from path */
 /******************* ma3x *******************************/      ss++;                               /* after this, the filename */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)      l2 = strlen( ss );                  /* length of filename */
 {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;      strcpy( name, ss );         /* save file name */
   double ***m;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    }
   if (!m) nrerror("allocation failure 1 in matrix()");    l1 = strlen( dirc );                  /* length of directory */
   m += NR_END;    /*#ifdef windows
   m -= nrl;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   #else
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #endif
   m[nrl] += NR_END;    */
   m[nrl] -= ncl;    ss = strrchr( name, '.' );            /* find last / */
     ss++;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    strcpy(ext,ss);                       /* save extension */
     l1= strlen( name);
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    l2= strlen(ss)+1;
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    strncpy( finame, name, l1-l2);
   m[nrl][ncl] += NR_END;    finame[l1-l2]= 0;
   m[nrl][ncl] -= nll;    return( 0 );                          /* we're done */
   for (j=ncl+1; j<=nch; j++)  }
     m[nrl][j]=m[nrl][j-1]+nlay;  
    
   for (i=nrl+1; i<=nrh; i++) {  /******************************************/
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  void replace_back_to_slash(char *s, char*t)
       m[i][j]=m[i][j-1]+nlay;  {
   }    int i;
   return m;    int lg=0;
 }    i=0;
     lg=strlen(t);
 /*************************free ma3x ************************/    for(i=0; i<= lg; i++) {
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)      (s[i] = t[i]);
 {      if (t[i]== '\\') s[i]='/';
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    }
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  }
   free((FREE_ARG)(m+nrl-NR_END));  
 }  int nbocc(char *s, char occ)
   {
 /***************** f1dim *************************/    int i,j=0;
 extern int ncom;    int lg=20;
 extern double *pcom,*xicom;    i=0;
 extern double (*nrfunc)(double []);    lg=strlen(s);
      for(i=0; i<= lg; i++) {
 double f1dim(double x)    if  (s[i] == occ ) j++;
 {    }
   int j;    return j;
   double f;  }
   double *xt;  
    void cutv(char *u,char *v, char*t, char occ)
   xt=vector(1,ncom);  {
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    /* cuts string t into u and v where u is ended by char occ excluding it
   f=(*nrfunc)(xt);       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   free_vector(xt,1,ncom);       gives u="abcedf" and v="ghi2j" */
   return f;    int i,lg,j,p=0;
 }    i=0;
     for(j=0; j<=strlen(t)-1; j++) {
 /*****************brent *************************/      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    }
 {  
   int iter;    lg=strlen(t);
   double a,b,d,etemp;    for(j=0; j<p; j++) {
   double fu,fv,fw,fx;      (u[j] = t[j]);
   double ftemp;    }
   double p,q,r,tol1,tol2,u,v,w,x,xm;       u[p]='\0';
   double e=0.0;  
       for(j=0; j<= lg; j++) {
   a=(ax < cx ? ax : cx);      if (j>=(p+1))(v[j-p-1] = t[j]);
   b=(ax > cx ? ax : cx);    }
   x=w=v=bx;  }
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {  /********************** nrerror ********************/
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  void nrerror(char error_text[])
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  {
     printf(".");fflush(stdout);    fprintf(stderr,"ERREUR ...\n");
 #ifdef DEBUG    fprintf(stderr,"%s\n",error_text);
     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);    exit(EXIT_FAILURE);
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  }
 #endif  /*********************** vector *******************/
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  double *vector(int nl, int nh)
       *xmin=x;  {
       return fx;    double *v;
     }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     ftemp=fu;    if (!v) nrerror("allocation failure in vector");
     if (fabs(e) > tol1) {    return v-nl+NR_END;
       r=(x-w)*(fx-fv);  }
       q=(x-v)*(fx-fw);  
       p=(x-v)*q-(x-w)*r;  /************************ free vector ******************/
       q=2.0*(q-r);  void free_vector(double*v, int nl, int nh)
       if (q > 0.0) p = -p;  {
       q=fabs(q);    free((FREE_ARG)(v+nl-NR_END));
       etemp=e;  }
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  /************************ivector *******************************/
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  int *ivector(long nl,long nh)
       else {  {
         d=p/q;    int *v;
         u=x+d;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
         if (u-a < tol2 || b-u < tol2)    if (!v) nrerror("allocation failure in ivector");
           d=SIGN(tol1,xm-x);    return v-nl+NR_END;
       }  }
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  /******************free ivector **************************/
     }  void free_ivector(int *v, long nl, long nh)
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  {
     fu=(*f)(u);    free((FREE_ARG)(v+nl-NR_END));
     if (fu <= fx) {  }
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)  /************************lvector *******************************/
         SHFT(fv,fw,fx,fu)  long *lvector(long nl,long nh)
         } else {  {
           if (u < x) a=u; else b=u;    long *v;
           if (fu <= fw || w == x) {    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
             v=w;    if (!v) nrerror("allocation failure in ivector");
             w=u;    return v-nl+NR_END;
             fv=fw;  }
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {  /******************free lvector **************************/
             v=u;  void free_lvector(long *v, long nl, long nh)
             fv=fu;  {
           }    free((FREE_ARG)(v+nl-NR_END));
         }  }
   }  
   nrerror("Too many iterations in brent");  /******************* imatrix *******************************/
   *xmin=x;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   return fx;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 }  { 
     long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 /****************** mnbrak ***********************/    int **m; 
     
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    /* allocate pointers to rows */ 
             double (*func)(double))    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 {    if (!m) nrerror("allocation failure 1 in matrix()"); 
   double ulim,u,r,q, dum;    m += NR_END; 
   double fu;    m -= nrl; 
      
   *fa=(*func)(*ax);    
   *fb=(*func)(*bx);    /* allocate rows and set pointers to them */ 
   if (*fb > *fa) {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     SHFT(dum,*ax,*bx,dum)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       SHFT(dum,*fb,*fa,dum)    m[nrl] += NR_END; 
       }    m[nrl] -= ncl; 
   *cx=(*bx)+GOLD*(*bx-*ax);    
   *fc=(*func)(*cx);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   while (*fb > *fc) {    
     r=(*bx-*ax)*(*fb-*fc);    /* return pointer to array of pointers to rows */ 
     q=(*bx-*cx)*(*fb-*fa);    return m; 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  } 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  
     ulim=(*bx)+GLIMIT*(*cx-*bx);  /****************** free_imatrix *************************/
     if ((*bx-u)*(u-*cx) > 0.0) {  void free_imatrix(m,nrl,nrh,ncl,nch)
       fu=(*func)(u);        int **m;
     } else if ((*cx-u)*(u-ulim) > 0.0) {        long nch,ncl,nrh,nrl; 
       fu=(*func)(u);       /* free an int matrix allocated by imatrix() */ 
       if (fu < *fc) {  { 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
           SHFT(*fb,*fc,fu,(*func)(u))    free((FREE_ARG) (m+nrl-NR_END)); 
           }  } 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  /******************* matrix *******************************/
       fu=(*func)(u);  double **matrix(long nrl, long nrh, long ncl, long nch)
     } else {  {
       u=(*cx)+GOLD*(*cx-*bx);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       fu=(*func)(u);    double **m;
     }  
     SHFT(*ax,*bx,*cx,u)    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       SHFT(*fa,*fb,*fc,fu)    if (!m) nrerror("allocation failure 1 in matrix()");
       }    m += NR_END;
 }    m -= nrl;
   
 /*************** linmin ************************/    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 int ncom;    m[nrl] += NR_END;
 double *pcom,*xicom;    m[nrl] -= ncl;
 double (*nrfunc)(double []);  
      for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    return m;
 {    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   double brent(double ax, double bx, double cx,     */
                double (*f)(double), double tol, double *xmin);  }
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  /*************************free matrix ************************/
               double *fc, double (*func)(double));  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   int j;  {
   double xx,xmin,bx,ax;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double fx,fb,fa;    free((FREE_ARG)(m+nrl-NR_END));
    }
   ncom=n;  
   pcom=vector(1,n);  /******************* ma3x *******************************/
   xicom=vector(1,n);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   nrfunc=func;  {
   for (j=1;j<=n;j++) {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     pcom[j]=p[j];    double ***m;
     xicom[j]=xi[j];  
   }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   ax=0.0;    if (!m) nrerror("allocation failure 1 in matrix()");
   xx=1.0;    m += NR_END;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    m -= nrl;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 #endif    m[nrl] += NR_END;
   for (j=1;j<=n;j++) {    m[nrl] -= ncl;
     xi[j] *= xmin;  
     p[j] += xi[j];    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   }  
   free_vector(xicom,1,n);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   free_vector(pcom,1,n);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 }    m[nrl][ncl] += NR_END;
     m[nrl][ncl] -= nll;
 /*************** powell ************************/    for (j=ncl+1; j<=nch; j++) 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      m[nrl][j]=m[nrl][j-1]+nlay;
             double (*func)(double []))    
 {    for (i=nrl+1; i<=nrh; i++) {
   void linmin(double p[], double xi[], int n, double *fret,      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
               double (*func)(double []));      for (j=ncl+1; j<=nch; j++) 
   int i,ibig,j;        m[i][j]=m[i][j-1]+nlay;
   double del,t,*pt,*ptt,*xit;    }
   double fp,fptt;    return m; 
   double *xits;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   pt=vector(1,n);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   ptt=vector(1,n);    */
   xit=vector(1,n);  }
   xits=vector(1,n);  
   *fret=(*func)(p);  /*************************free ma3x ************************/
   for (j=1;j<=n;j++) pt[j]=p[j];  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   for (*iter=1;;++(*iter)) {  {
     fp=(*fret);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     ibig=0;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     del=0.0;    free((FREE_ARG)(m+nrl-NR_END));
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  }
     for (i=1;i<=n;i++)  
       printf(" %d %.12f",i, p[i]);  /*************** function subdirf ***********/
     printf("\n");  char *subdirf(char fileres[])
     for (i=1;i<=n;i++) {  {
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    /* Caution optionfilefiname is hidden */
       fptt=(*fret);    strcpy(tmpout,optionfilefiname);
 #ifdef DEBUG    strcat(tmpout,"/"); /* Add to the right */
       printf("fret=%lf \n",*fret);    strcat(tmpout,fileres);
 #endif    return tmpout;
       printf("%d",i);fflush(stdout);  }
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {  /*************** function subdirf2 ***********/
         del=fabs(fptt-(*fret));  char *subdirf2(char fileres[], char *preop)
         ibig=i;  {
       }    
 #ifdef DEBUG    /* Caution optionfilefiname is hidden */
       printf("%d %.12e",i,(*fret));    strcpy(tmpout,optionfilefiname);
       for (j=1;j<=n;j++) {    strcat(tmpout,"/");
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    strcat(tmpout,preop);
         printf(" x(%d)=%.12e",j,xit[j]);    strcat(tmpout,fileres);
       }    return tmpout;
       for(j=1;j<=n;j++)  }
         printf(" p=%.12e",p[j]);  
       printf("\n");  /*************** function subdirf3 ***********/
 #endif  char *subdirf3(char fileres[], char *preop, char *preop2)
     }  {
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    
 #ifdef DEBUG    /* Caution optionfilefiname is hidden */
       int k[2],l;    strcpy(tmpout,optionfilefiname);
       k[0]=1;    strcat(tmpout,"/");
       k[1]=-1;    strcat(tmpout,preop);
       printf("Max: %.12e",(*func)(p));    strcat(tmpout,preop2);
       for (j=1;j<=n;j++)    strcat(tmpout,fileres);
         printf(" %.12e",p[j]);    return tmpout;
       printf("\n");  }
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {  /***************** f1dim *************************/
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  extern int ncom; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  extern double *pcom,*xicom;
         }  extern double (*nrfunc)(double []); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));   
       }  double f1dim(double x) 
 #endif  { 
     int j; 
     double f;
       free_vector(xit,1,n);    double *xt; 
       free_vector(xits,1,n);   
       free_vector(ptt,1,n);    xt=vector(1,ncom); 
       free_vector(pt,1,n);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       return;    f=(*nrfunc)(xt); 
     }    free_vector(xt,1,ncom); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    return f; 
     for (j=1;j<=n;j++) {  } 
       ptt[j]=2.0*p[j]-pt[j];  
       xit[j]=p[j]-pt[j];  /*****************brent *************************/
       pt[j]=p[j];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     }  { 
     fptt=(*func)(ptt);    int iter; 
     if (fptt < fp) {    double a,b,d,etemp;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    double fu,fv,fw,fx;
       if (t < 0.0) {    double ftemp;
         linmin(p,xit,n,fret,func);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
         for (j=1;j<=n;j++) {    double e=0.0; 
           xi[j][ibig]=xi[j][n];   
           xi[j][n]=xit[j];    a=(ax < cx ? ax : cx); 
         }    b=(ax > cx ? ax : cx); 
 #ifdef DEBUG    x=w=v=bx; 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    fw=fv=fx=(*f)(x); 
         for(j=1;j<=n;j++)    for (iter=1;iter<=ITMAX;iter++) { 
           printf(" %.12e",xit[j]);      xm=0.5*(a+b); 
         printf("\n");      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 #endif      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       }      printf(".");fflush(stdout);
     }      fprintf(ficlog,".");fflush(ficlog);
   }  #ifdef DEBUG
 }      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 /**** Prevalence limit ****************/      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   #endif
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 {        *xmin=x; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        return fx; 
      matrix by transitions matrix until convergence is reached */      } 
       ftemp=fu;
   int i, ii,j,k;      if (fabs(e) > tol1) { 
   double min, max, maxmin, maxmax,sumnew=0.;        r=(x-w)*(fx-fv); 
   double **matprod2();        q=(x-v)*(fx-fw); 
   double **out, cov[NCOVMAX], **pmij();        p=(x-v)*q-(x-w)*r; 
   double **newm;        q=2.0*(q-r); 
   double agefin, delaymax=50 ; /* Max number of years to converge */        if (q > 0.0) p = -p; 
         q=fabs(q); 
   for (ii=1;ii<=nlstate+ndeath;ii++)        etemp=e; 
     for (j=1;j<=nlstate+ndeath;j++){        e=d; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     }          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         else { 
    cov[1]=1.;          d=p/q; 
            u=x+d; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */          if (u-a < tol2 || b-u < tol2) 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){            d=SIGN(tol1,xm-x); 
     newm=savm;        } 
     /* Covariates have to be included here again */      } else { 
      cov[2]=agefin;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
        } 
       for (k=1; k<=cptcovn;k++) {      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      fu=(*f)(u); 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/      if (fu <= fx) { 
       }        if (u >= x) a=x; else b=x; 
       for (k=1; k<=cptcovage;k++)        SHFT(v,w,x,u) 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          SHFT(fv,fw,fx,fu) 
       for (k=1; k<=cptcovprod;k++)          } else { 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];            if (u < x) a=u; else b=u; 
             if (fu <= fw || w == x) { 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/              v=w; 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/              w=u; 
               fv=fw; 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);              fw=fu; 
             } else if (fu <= fv || v == x || v == w) { 
     savm=oldm;              v=u; 
     oldm=newm;              fv=fu; 
     maxmax=0.;            } 
     for(j=1;j<=nlstate;j++){          } 
       min=1.;    } 
       max=0.;    nrerror("Too many iterations in brent"); 
       for(i=1; i<=nlstate; i++) {    *xmin=x; 
         sumnew=0;    return fx; 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  } 
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);  /****************** mnbrak ***********************/
         min=FMIN(min,prlim[i][j]);  
       }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       maxmin=max-min;              double (*func)(double)) 
       maxmax=FMAX(maxmax,maxmin);  { 
     }    double ulim,u,r,q, dum;
     if(maxmax < ftolpl){    double fu; 
       return prlim;   
     }    *fa=(*func)(*ax); 
   }    *fb=(*func)(*bx); 
 }    if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
 /*************** transition probabilities ***************/        SHFT(dum,*fb,*fa,dum) 
         } 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    *cx=(*bx)+GOLD*(*bx-*ax); 
 {    *fc=(*func)(*cx); 
   double s1, s2;    while (*fb > *fc) { 
   /*double t34;*/      r=(*bx-*ax)*(*fb-*fc); 
   int i,j,j1, nc, ii, jj;      q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     for(i=1; i<= nlstate; i++){        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     for(j=1; j<i;j++){      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      if ((*bx-u)*(u-*cx) > 0.0) { 
         /*s2 += param[i][j][nc]*cov[nc];*/        fu=(*func)(u); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/        fu=(*func)(u); 
       }        if (fu < *fc) { 
       ps[i][j]=s2;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/            SHFT(*fb,*fc,fu,(*func)(u)) 
     }            } 
     for(j=i+1; j<=nlstate+ndeath;j++){      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        u=ulim; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        fu=(*func)(u); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      } else { 
       }        u=(*cx)+GOLD*(*cx-*bx); 
       ps[i][j]=s2;        fu=(*func)(u); 
     }      } 
   }      SHFT(*ax,*bx,*cx,u) 
     /*ps[3][2]=1;*/        SHFT(*fa,*fb,*fc,fu) 
         } 
   for(i=1; i<= nlstate; i++){  } 
      s1=0;  
     for(j=1; j<i; j++)  /*************** linmin ************************/
       s1+=exp(ps[i][j]);  
     for(j=i+1; j<=nlstate+ndeath; j++)  int ncom; 
       s1+=exp(ps[i][j]);  double *pcom,*xicom;
     ps[i][i]=1./(s1+1.);  double (*nrfunc)(double []); 
     for(j=1; j<i; j++)   
       ps[i][j]= exp(ps[i][j])*ps[i][i];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     for(j=i+1; j<=nlstate+ndeath; j++)  { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    double brent(double ax, double bx, double cx, 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */                 double (*f)(double), double tol, double *xmin); 
   } /* end i */    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){                double *fc, double (*func)(double)); 
     for(jj=1; jj<= nlstate+ndeath; jj++){    int j; 
       ps[ii][jj]=0;    double xx,xmin,bx,ax; 
       ps[ii][ii]=1;    double fx,fb,fa;
     }   
   }    ncom=n; 
     pcom=vector(1,n); 
     xicom=vector(1,n); 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    nrfunc=func; 
     for(jj=1; jj<= nlstate+ndeath; jj++){    for (j=1;j<=n;j++) { 
      printf("%lf ",ps[ii][jj]);      pcom[j]=p[j]; 
    }      xicom[j]=xi[j]; 
     printf("\n ");    } 
     }    ax=0.0; 
     printf("\n ");printf("%lf ",cov[2]);*/    xx=1.0; 
 /*    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   goto end;*/  #ifdef DEBUG
     return ps;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   #endif
 /**************** Product of 2 matrices ******************/    for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      p[j] += xi[j]; 
 {    } 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    free_vector(xicom,1,n); 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    free_vector(pcom,1,n); 
   /* in, b, out are matrice of pointers which should have been initialized  } 
      before: only the contents of out is modified. The function returns  
      a pointer to pointers identical to out */  char *asc_diff_time(long time_sec, char ascdiff[])
   long i, j, k;  {
   for(i=nrl; i<= nrh; i++)    long sec_left, days, hours, minutes;
     for(k=ncolol; k<=ncoloh; k++)    days = (time_sec) / (60*60*24);
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    sec_left = (time_sec) % (60*60*24);
         out[i][k] +=in[i][j]*b[j][k];    hours = (sec_left) / (60*60) ;
     sec_left = (sec_left) %(60*60);
   return out;    minutes = (sec_left) /60;
 }    sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     return ascdiff;
 /************* Higher Matrix Product ***************/  }
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  /*************** powell ************************/
 {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month              double (*func)(double [])) 
      duration (i.e. until  { 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    void linmin(double p[], double xi[], int n, double *fret, 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step                double (*func)(double [])); 
      (typically every 2 years instead of every month which is too big).    int i,ibig,j; 
      Model is determined by parameters x and covariates have to be    double del,t,*pt,*ptt,*xit;
      included manually here.    double fp,fptt;
     double *xits;
      */    int niterf, itmp;
   
   int i, j, d, h, k;    pt=vector(1,n); 
   double **out, cov[NCOVMAX];    ptt=vector(1,n); 
   double **newm;    xit=vector(1,n); 
     xits=vector(1,n); 
   /* Hstepm could be zero and should return the unit matrix */    *fret=(*func)(p); 
   for (i=1;i<=nlstate+ndeath;i++)    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (j=1;j<=nlstate+ndeath;j++){    for (*iter=1;;++(*iter)) { 
       oldm[i][j]=(i==j ? 1.0 : 0.0);      fp=(*fret); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);      ibig=0; 
     }      del=0.0; 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      last_time=curr_time;
   for(h=1; h <=nhstepm; h++){      (void) gettimeofday(&curr_time,&tzp);
     for(d=1; d <=hstepm; d++){      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);
       newm=savm;      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);
       /* Covariates have to be included here again */      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       cov[1]=1.;      for (i=1;i<=n;i++) {
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        printf(" %d %.12f",i, p[i]);
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        fprintf(ficlog," %d %.12lf",i, p[i]);
       for (k=1; k<=cptcovage;k++)        fprintf(ficrespow," %.12lf", p[i]);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      }
       for (k=1; k<=cptcovprod;k++)      printf("\n");
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");fflush(ficrespow);
       if(*iter <=3){
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        tm = *localtime(&curr_time.tv_sec);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        strcpy(strcurr,asctime(&tmf));
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  /*       asctime_r(&tm,strcurr); */
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        forecast_time=curr_time;
       savm=oldm;        itmp = strlen(strcurr);
       oldm=newm;        if(strcurr[itmp-1]=='\n')
     }          strcurr[itmp-1]='\0';
     for(i=1; i<=nlstate+ndeath; i++)        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       for(j=1;j<=nlstate+ndeath;j++) {        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         po[i][j][h]=newm[i][j];        for(niterf=10;niterf<=30;niterf+=10){
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
          */          tmf = *localtime(&forecast_time.tv_sec);
       }  /*      asctime_r(&tmf,strfor); */
   } /* end h */          strcpy(strfor,asctime(&tmf));
   return po;          itmp = strlen(strfor);
 }          if(strfor[itmp-1]=='\n')
           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);
 /*************** log-likelihood *************/          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);
 double func( double *x)        }
 {      }
   int i, ii, j, k, mi, d, kk;      for (i=1;i<=n;i++) { 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   double **out;        fptt=(*fret); 
   double sw; /* Sum of weights */  #ifdef DEBUG
   double lli; /* Individual log likelihood */        printf("fret=%lf \n",*fret);
   long ipmx;        fprintf(ficlog,"fret=%lf \n",*fret);
   /*extern weight */  #endif
   /* We are differentiating ll according to initial status */        printf("%d",i);fflush(stdout);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        fprintf(ficlog,"%d",i);fflush(ficlog);
   /*for(i=1;i<imx;i++)        linmin(p,xit,n,fret,func); 
     printf(" %d\n",s[4][i]);        if (fabs(fptt-(*fret)) > del) { 
   */          del=fabs(fptt-(*fret)); 
   cov[1]=1.;          ibig=i; 
         } 
   for(k=1; k<=nlstate; k++) ll[k]=0.;  #ifdef DEBUG
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        printf("%d %.12e",i,(*fret));
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        fprintf(ficlog,"%d %.12e",i,(*fret));
     for(mi=1; mi<= wav[i]-1; mi++){        for (j=1;j<=n;j++) {
       for (ii=1;ii<=nlstate+ndeath;ii++)          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          printf(" x(%d)=%.12e",j,xit[j]);
       for(d=0; d<dh[mi][i]; d++){          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         newm=savm;        }
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        for(j=1;j<=n;j++) {
         for (kk=1; kk<=cptcovage;kk++) {          printf(" p=%.12e",p[j]);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];          fprintf(ficlog," p=%.12e",p[j]);
         }        }
                printf("\n");
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        fprintf(ficlog,"\n");
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  #endif
         savm=oldm;      } 
         oldm=newm;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
          #ifdef DEBUG
                int k[2],l;
       } /* end mult */        k[0]=1;
              k[1]=-1;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        printf("Max: %.12e",(*func)(p));
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        fprintf(ficlog,"Max: %.12e",(*func)(p));
       ipmx +=1;        for (j=1;j<=n;j++) {
       sw += weight[i];          printf(" %.12e",p[j]);
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          fprintf(ficlog," %.12e",p[j]);
     } /* end of wave */        }
   } /* end of individual */        printf("\n");
         fprintf(ficlog,"\n");
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        for(l=0;l<=1;l++) {
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */          for (j=1;j<=n;j++) {
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   return -l;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 /*********** Maximum Likelihood Estimation ***************/          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  #endif
 {  
   int i,j, iter;  
   double **xi,*delti;        free_vector(xit,1,n); 
   double fret;        free_vector(xits,1,n); 
   xi=matrix(1,npar,1,npar);        free_vector(ptt,1,n); 
   for (i=1;i<=npar;i++)        free_vector(pt,1,n); 
     for (j=1;j<=npar;j++)        return; 
       xi[i][j]=(i==j ? 1.0 : 0.0);      } 
   printf("Powell\n");      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   powell(p,xi,npar,ftol,&iter,&fret,func);      for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        xit[j]=p[j]-pt[j]; 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        pt[j]=p[j]; 
       } 
 }      fptt=(*func)(ptt); 
       if (fptt < fp) { 
 /**** Computes Hessian and covariance matrix ***/        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        if (t < 0.0) { 
 {          linmin(p,xit,n,fret,func); 
   double  **a,**y,*x,pd;          for (j=1;j<=n;j++) { 
   double **hess;            xi[j][ibig]=xi[j][n]; 
   int i, j,jk;            xi[j][n]=xit[j]; 
   int *indx;          }
   #ifdef DEBUG
   double hessii(double p[], double delta, int theta, double delti[]);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   double hessij(double p[], double delti[], int i, int j);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   void lubksb(double **a, int npar, int *indx, double b[]) ;          for(j=1;j<=n;j++){
   void ludcmp(double **a, int npar, int *indx, double *d) ;            printf(" %.12e",xit[j]);
             fprintf(ficlog," %.12e",xit[j]);
   hess=matrix(1,npar,1,npar);          }
           printf("\n");
   printf("\nCalculation of the hessian matrix. Wait...\n");          fprintf(ficlog,"\n");
   for (i=1;i<=npar;i++){  #endif
     printf("%d",i);fflush(stdout);        }
     hess[i][i]=hessii(p,ftolhess,i,delti);      } 
     /*printf(" %f ",p[i]);*/    } 
     /*printf(" %lf ",hess[i][i]);*/  } 
   }  
    /**** Prevalence limit (stable prevalence)  ****************/
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++)  {  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       if (j>i) {  {
         printf(".%d%d",i,j);fflush(stdout);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         hess[i][j]=hessij(p,delti,i,j);       matrix by transitions matrix until convergence is reached */
         hess[j][i]=hess[i][j];      
         /*printf(" %lf ",hess[i][j]);*/    int i, ii,j,k;
       }    double min, max, maxmin, maxmax,sumnew=0.;
     }    double **matprod2();
   }    double **out, cov[NCOVMAX], **pmij();
   printf("\n");    double **newm;
     double agefin, delaymax=50 ; /* Max number of years to converge */
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  
      for (ii=1;ii<=nlstate+ndeath;ii++)
   a=matrix(1,npar,1,npar);      for (j=1;j<=nlstate+ndeath;j++){
   y=matrix(1,npar,1,npar);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   x=vector(1,npar);      }
   indx=ivector(1,npar);  
   for (i=1;i<=npar;i++)     cov[1]=1.;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];   
   ludcmp(a,npar,indx,&pd);   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   for (j=1;j<=npar;j++) {      newm=savm;
     for (i=1;i<=npar;i++) x[i]=0;      /* Covariates have to be included here again */
     x[j]=1;       cov[2]=agefin;
     lubksb(a,npar,indx,x);    
     for (i=1;i<=npar;i++){        for (k=1; k<=cptcovn;k++) {
       matcov[i][j]=x[i];          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];
   printf("\n#Hessian matrix#\n");        for (k=1; k<=cptcovprod;k++)
   for (i=1;i<=npar;i++) {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     }        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     printf("\n");        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   }      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
   /* Recompute Inverse */      savm=oldm;
   for (i=1;i<=npar;i++)      oldm=newm;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      maxmax=0.;
   ludcmp(a,npar,indx,&pd);      for(j=1;j<=nlstate;j++){
         min=1.;
   /*  printf("\n#Hessian matrix recomputed#\n");        max=0.;
         for(i=1; i<=nlstate; i++) {
   for (j=1;j<=npar;j++) {          sumnew=0;
     for (i=1;i<=npar;i++) x[i]=0;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     x[j]=1;          prlim[i][j]= newm[i][j]/(1-sumnew);
     lubksb(a,npar,indx,x);          max=FMAX(max,prlim[i][j]);
     for (i=1;i<=npar;i++){          min=FMIN(min,prlim[i][j]);
       y[i][j]=x[i];        }
       printf("%.3e ",y[i][j]);        maxmin=max-min;
     }        maxmax=FMAX(maxmax,maxmin);
     printf("\n");      }
   }      if(maxmax < ftolpl){
   */        return prlim;
       }
   free_matrix(a,1,npar,1,npar);    }
   free_matrix(y,1,npar,1,npar);  }
   free_vector(x,1,npar);  
   free_ivector(indx,1,npar);  /*************** transition probabilities ***************/ 
   free_matrix(hess,1,npar,1,npar);  
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
 }    double s1, s2;
     /*double t34;*/
 /*************** hessian matrix ****************/    int i,j,j1, nc, ii, jj;
 double hessii( double x[], double delta, int theta, double delti[])  
 {      for(i=1; i<= nlstate; i++){
   int i;      for(j=1; j<i;j++){
   int l=1, lmax=20;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   double k1,k2;          /*s2 += param[i][j][nc]*cov[nc];*/
   double p2[NPARMAX+1];          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   double res;          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        }
   double fx;        ps[i][j]=s2;
   int k=0,kmax=10;        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   double l1;      }
       for(j=i+1; j<=nlstate+ndeath;j++){
   fx=func(x);        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   for (i=1;i<=npar;i++) p2[i]=x[i];          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   for(l=0 ; l <=lmax; l++){          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
     l1=pow(10,l);        }
     delts=delt;        ps[i][j]=s2;
     for(k=1 ; k <kmax; k=k+1){      }
       delt = delta*(l1*k);    }
       p2[theta]=x[theta] +delt;      /*ps[3][2]=1;*/
       k1=func(p2)-fx;  
       p2[theta]=x[theta]-delt;    for(i=1; i<= nlstate; i++){
       k2=func(p2)-fx;       s1=0;
       /*res= (k1-2.0*fx+k2)/delt/delt; */      for(j=1; j<i; j++)
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        s1+=exp(ps[i][j]);
            for(j=i+1; j<=nlstate+ndeath; j++)
 #ifdef DEBUG        s1+=exp(ps[i][j]);
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);      ps[i][i]=1./(s1+1.);
 #endif      for(j=1; j<i; j++)
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        ps[i][j]= exp(ps[i][j])*ps[i][i];
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      for(j=i+1; j<=nlstate+ndeath; j++)
         k=kmax;        ps[i][j]= exp(ps[i][j])*ps[i][i];
       }      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    } /* end i */
         k=kmax; l=lmax*10.;  
       }    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      for(jj=1; jj<= nlstate+ndeath; jj++){
         delts=delt;        ps[ii][jj]=0;
       }        ps[ii][ii]=1;
     }      }
   }    }
   delti[theta]=delts;  
   return res;  
      /*   for(ii=1; ii<= nlstate+ndeath; ii++){
 }      for(jj=1; jj<= nlstate+ndeath; jj++){
        printf("%lf ",ps[ii][jj]);
 double hessij( double x[], double delti[], int thetai,int thetaj)     }
 {      printf("\n ");
   int i;      }
   int l=1, l1, lmax=20;      printf("\n ");printf("%lf ",cov[2]);*/
   double k1,k2,k3,k4,res,fx;  /*
   double p2[NPARMAX+1];    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   int k;    goto end;*/
       return ps;
   fx=func(x);  }
   for (k=1; k<=2; k++) {  
     for (i=1;i<=npar;i++) p2[i]=x[i];  /**************** Product of 2 matrices ******************/
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     k1=func(p2)-fx;  {
      /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     p2[thetai]=x[thetai]+delti[thetai]/k;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    /* in, b, out are matrice of pointers which should have been initialized 
     k2=func(p2)-fx;       before: only the contents of out is modified. The function returns
         a pointer to pointers identical to out */
     p2[thetai]=x[thetai]-delti[thetai]/k;    long i, j, k;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    for(i=nrl; i<= nrh; i++)
     k3=func(p2)-fx;      for(k=ncolol; k<=ncoloh; k++)
          for(j=ncl,out[i][k]=0.; j<=nch; j++)
     p2[thetai]=x[thetai]-delti[thetai]/k;          out[i][k] +=in[i][j]*b[j][k];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k4=func(p2)-fx;    return out;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  }
 #ifdef DEBUG  
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  
 #endif  /************* Higher Matrix Product ***************/
   }  
   return res;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
 }  {
     /* Computes the transition matrix starting at age 'age' over 
 /************** Inverse of matrix **************/       'nhstepm*hstepm*stepm' months (i.e. until
 void ludcmp(double **a, int n, int *indx, double *d)       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
 {       nhstepm*hstepm matrices. 
   int i,imax,j,k;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   double big,dum,sum,temp;       (typically every 2 years instead of every month which is too big 
   double *vv;       for the memory).
         Model is determined by parameters x and covariates have to be 
   vv=vector(1,n);       included manually here. 
   *d=1.0;  
   for (i=1;i<=n;i++) {       */
     big=0.0;  
     for (j=1;j<=n;j++)    int i, j, d, h, k;
       if ((temp=fabs(a[i][j])) > big) big=temp;    double **out, cov[NCOVMAX];
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    double **newm;
     vv[i]=1.0/big;  
   }    /* Hstepm could be zero and should return the unit matrix */
   for (j=1;j<=n;j++) {    for (i=1;i<=nlstate+ndeath;i++)
     for (i=1;i<j;i++) {      for (j=1;j<=nlstate+ndeath;j++){
       sum=a[i][j];        oldm[i][j]=(i==j ? 1.0 : 0.0);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        po[i][j][0]=(i==j ? 1.0 : 0.0);
       a[i][j]=sum;      }
     }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     big=0.0;    for(h=1; h <=nhstepm; h++){
     for (i=j;i<=n;i++) {      for(d=1; d <=hstepm; d++){
       sum=a[i][j];        newm=savm;
       for (k=1;k<j;k++)        /* Covariates have to be included here again */
         sum -= a[i][k]*a[k][j];        cov[1]=1.;
       a[i][j]=sum;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       if ( (dum=vv[i]*fabs(sum)) >= big) {        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         big=dum;        for (k=1; k<=cptcovage;k++)
         imax=i;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       }        for (k=1; k<=cptcovprod;k++)
     }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     if (j != imax) {  
       for (k=1;k<=n;k++) {  
         dum=a[imax][k];        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         a[imax][k]=a[j][k];        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         a[j][k]=dum;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
       *d = -(*d);        savm=oldm;
       vv[imax]=vv[j];        oldm=newm;
     }      }
     indx[j]=imax;      for(i=1; i<=nlstate+ndeath; i++)
     if (a[j][j] == 0.0) a[j][j]=TINY;        for(j=1;j<=nlstate+ndeath;j++) {
     if (j != n) {          po[i][j][h]=newm[i][j];
       dum=1.0/(a[j][j]);          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       for (i=j+1;i<=n;i++) a[i][j] *= dum;           */
     }        }
   }    } /* end h */
   free_vector(vv,1,n);  /* Doesn't work */    return po;
 ;  }
 }  
   
 void lubksb(double **a, int n, int *indx, double b[])  /*************** log-likelihood *************/
 {  double func( double *x)
   int i,ii=0,ip,j;  {
   double sum;    int i, ii, j, k, mi, d, kk;
      double l, ll[NLSTATEMAX], cov[NCOVMAX];
   for (i=1;i<=n;i++) {    double **out;
     ip=indx[i];    double sw; /* Sum of weights */
     sum=b[ip];    double lli; /* Individual log likelihood */
     b[ip]=b[i];    int s1, s2;
     if (ii)    double bbh, survp;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    long ipmx;
     else if (sum) ii=i;    /*extern weight */
     b[i]=sum;    /* We are differentiating ll according to initial status */
   }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   for (i=n;i>=1;i--) {    /*for(i=1;i<imx;i++) 
     sum=b[i];      printf(" %d\n",s[4][i]);
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    */
     b[i]=sum/a[i][i];    cov[1]=1.;
   }  
 }    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
 /************ Frequencies ********************/    if(mle==1){
 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)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 {  /* Some frequencies */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double ***freq; /* Frequencies */            for (j=1;j<=nlstate+ndeath;j++){
   double *pp;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double pos, k2, dateintsum=0,k2cpt=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   FILE *ficresp;            }
   char fileresp[FILENAMELENGTH];          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   pp=vector(1,nlstate);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            for (kk=1; kk<=cptcovage;kk++) {
   strcpy(fileresp,"p");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   strcat(fileresp,fileres);            }
   if((ficresp=fopen(fileresp,"w"))==NULL) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     printf("Problem with prevalence resultfile: %s\n", fileresp);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     exit(0);            savm=oldm;
   }            oldm=newm;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          } /* end mult */
   j1=0;        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   j=cptcoveff;          /* But now since version 0.9 we anticipate for bias and large stepm.
   if (cptcovn<1) {j=1;ncodemax[1]=1;}           * If stepm is larger than one month (smallest stepm) and if the exact delay 
            * (in months) between two waves is not a multiple of stepm, we rounded to 
   for(k1=1; k1<=j;k1++){           * the nearest (and in case of equal distance, to the lowest) interval but now
    for(i1=1; i1<=ncodemax[k1];i1++){           * we keep into memory the bias bh[mi][i] and also the previous matrix product
        j1++;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);           * probability in order to take into account the bias as a fraction of the way
          scanf("%d", i);*/           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
         for (i=-1; i<=nlstate+ndeath; i++)             * -stepm/2 to stepm/2 .
          for (jk=-1; jk<=nlstate+ndeath; jk++)             * For stepm=1 the results are the same as for previous versions of Imach.
            for(m=agemin; m <= agemax+3; m++)           * For stepm > 1 the results are less biased than in previous versions. 
              freq[i][jk][m]=0;           */
           s1=s[mw[mi][i]][i];
         dateintsum=0;          s2=s[mw[mi+1][i]][i];
         k2cpt=0;          bbh=(double)bh[mi][i]/(double)stepm; 
        for (i=1; i<=imx; i++) {          /* bias is positive if real duration
          bool=1;           * is higher than the multiple of stepm and negative otherwise.
          if  (cptcovn>0) {           */
            for (z1=1; z1<=cptcoveff; z1++)          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          if( s2 > nlstate){ 
                bool=0;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
          }               to the likelihood is the probability to die between last step unit time and current 
          if (bool==1) {               step unit time, which is also the differences between probability to die before dh 
            for(m=firstpass; m<=lastpass; m++){               and probability to die before dh-stepm . 
              k2=anint[m][i]+(mint[m][i]/12.);               In version up to 0.92 likelihood was computed
              if ((k2>=dateprev1) && (k2<=dateprev2)) {          as if date of death was unknown. Death was treated as any other
                if(agev[m][i]==0) agev[m][i]=agemax+1;          health state: the date of the interview describes the actual state
                if(agev[m][i]==1) agev[m][i]=agemax+2;          and not the date of a change in health state. The former idea was
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          to consider that at each interview the state was recorded
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          (healthy, disable or death) and IMaCh was corrected; but when we
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          introduced the exact date of death then we should have modified
                  dateintsum=dateintsum+k2;          the contribution of an exact death to the likelihood. This new
                  k2cpt++;          contribution is smaller and very dependent of the step unit
                }          stepm. It is no more the probability to die between last interview
           and month of death but the probability to survive from last
              }          interview up to one month before death multiplied by the
            }          probability to die within a month. Thanks to Chris
          }          Jackson for correcting this bug.  Former versions increased
        }          mortality artificially. The bad side is that we add another loop
         if  (cptcovn>0) {          which slows down the processing. The difference can be up to 10%
          fprintf(ficresp, "\n#********** Variable ");          lower mortality.
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            */
        fprintf(ficresp, "**********\n#");            lli=log(out[s1][s2] - savm[s1][s2]);
         }          }else{
        for(i=1; i<=nlstate;i++)            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
        fprintf(ficresp, "\n");          } 
                  /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   for(i=(int)agemin; i <= (int)agemax+3; i++){          /*if(lli ==000.0)*/
     if(i==(int)agemax+3)          /*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); */
       printf("Total");          ipmx +=1;
     else          sw += weight[i];
       printf("Age %d", i);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(jk=1; jk <=nlstate ; jk++){        } /* end of wave */
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      } /* end of individual */
         pp[jk] += freq[jk][m][i];    }  else if(mle==2){
     }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(jk=1; jk <=nlstate ; jk++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(m=-1, pos=0; m <=0 ; m++)        for(mi=1; mi<= wav[i]-1; mi++){
         pos += freq[jk][m][i];          for (ii=1;ii<=nlstate+ndeath;ii++)
       if(pp[jk]>=1.e-10)            for (j=1;j<=nlstate+ndeath;j++){
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       else              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            }
     }          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
      for(jk=1; jk <=nlstate ; jk++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            for (kk=1; kk<=cptcovage;kk++) {
         pp[jk] += freq[jk][m][i];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      }            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for(jk=1,pos=0; jk <=nlstate ; jk++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       pos += pp[jk];            savm=oldm;
     for(jk=1; jk <=nlstate ; jk++){            oldm=newm;
       if(pos>=1.e-5)          } /* end mult */
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        
       else          s1=s[mw[mi][i]][i];
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          s2=s[mw[mi+1][i]][i];
       if( i <= (int) agemax){          bbh=(double)bh[mi][i]/(double)stepm; 
         if(pos>=1.e-5){          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          ipmx +=1;
           probs[i][jk][j1]= pp[jk]/pos;          sw += weight[i];
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         }        } /* end of wave */
       else      } /* end of individual */
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    }  else if(mle==3){  /* exponential inter-extrapolation */
       }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for(jk=-1; jk <=nlstate+ndeath; jk++)        for(mi=1; mi<= wav[i]-1; mi++){
       for(m=-1; m <=nlstate+ndeath; m++)          for (ii=1;ii<=nlstate+ndeath;ii++)
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            for (j=1;j<=nlstate+ndeath;j++){
     if(i <= (int) agemax)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficresp,"\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     printf("\n");            }
     }          for(d=0; d<dh[mi][i]; d++){
     }            newm=savm;
  }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   dateintmean=dateintsum/k2cpt;            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   fclose(ficresp);            }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   free_vector(pp,1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   /* End of Freq */            oldm=newm;
 }          } /* end mult */
         
 /************ Prevalence ********************/          s1=s[mw[mi][i]][i];
 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)          s2=s[mw[mi+1][i]][i];
 {  /* Some frequencies */          bbh=(double)bh[mi][i]/(double)stepm; 
            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 */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          ipmx +=1;
   double ***freq; /* Frequencies */          sw += weight[i];
   double *pp;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double pos, k2;        } /* end of wave */
       } /* end of individual */
   pp=vector(1,nlstate);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        for(mi=1; mi<= wav[i]-1; mi++){
   j1=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   j=cptcoveff;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
  for(k1=1; k1<=j;k1++){          for(d=0; d<dh[mi][i]; d++){
     for(i1=1; i1<=ncodemax[k1];i1++){            newm=savm;
       j1++;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
       for (i=-1; i<=nlstate+ndeath; i++)                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for (jk=-1; jk<=nlstate+ndeath; jk++)              }
           for(m=agemin; m <= agemax+3; m++)          
             freq[i][jk][m]=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                               1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for (i=1; i<=imx; i++) {            savm=oldm;
         bool=1;            oldm=newm;
         if  (cptcovn>0) {          } /* end mult */
           for (z1=1; z1<=cptcoveff; z1++)        
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          s1=s[mw[mi][i]][i];
               bool=0;          s2=s[mw[mi+1][i]][i];
         }          if( s2 > nlstate){ 
         if (bool==1) {            lli=log(out[s1][s2] - savm[s1][s2]);
           for(m=firstpass; m<=lastpass; m++){          }else{
             k2=anint[m][i]+(mint[m][i]/12.);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          }
               if(agev[m][i]==0) agev[m][i]=agemax+1;          ipmx +=1;
               if(agev[m][i]==1) agev[m][i]=agemax+2;          sw += weight[i];
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[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 */
         }    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
              for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(i=(int)agemin; i <= (int)agemax+3; i++){        for(mi=1; mi<= wav[i]-1; mi++){
           for(jk=1; jk <=nlstate ; jk++){          for (ii=1;ii<=nlstate+ndeath;ii++)
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            for (j=1;j<=nlstate+ndeath;j++){
               pp[jk] += freq[jk][m][i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(jk=1; jk <=nlstate ; jk++){            }
             for(m=-1, pos=0; m <=0 ; m++)          for(d=0; d<dh[mi][i]; d++){
             pos += freq[jk][m][i];            newm=savm;
         }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                    for (kk=1; kk<=cptcovage;kk++) {
          for(jk=1; jk <=nlstate ; jk++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            }
              pp[jk] += freq[jk][m][i];          
          }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                                   1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];            savm=oldm;
             oldm=newm;
          for(jk=1; jk <=nlstate ; jk++){                    } /* end mult */
            if( i <= (int) agemax){        
              if(pos>=1.e-5){          s1=s[mw[mi][i]][i];
                probs[i][jk][j1]= pp[jk]/pos;          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;
          }          sw += weight[i];
                    ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         }          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
     }        } /* end of wave */
   }      } /* end of individual */
      } /* End of if */
      for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   free_vector(pp,1,nlstate);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
      return -l;
 }  /* End of Freq */  }
   
 /************* Waves Concatenation ***************/  /*************** log-likelihood *************/
   double funcone( double *x)
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  {
 {    /* Same as likeli but slower because of a lot of printf and if */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    int i, ii, j, k, mi, d, kk;
      Death is a valid wave (if date is known).    double l, ll[NLSTATEMAX], cov[NCOVMAX];
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    double **out;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    double lli; /* Individual log likelihood */
      and mw[mi+1][i]. dh depends on stepm.    double llt;
      */    int s1, s2;
     double bbh, survp;
   int i, mi, m;    /*extern weight */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    /* We are differentiating ll according to initial status */
      double sum=0., jmean=0.;*/    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
   int j, k=0,jk, ju, jl;      printf(" %d\n",s[4][i]);
   double sum=0.;    */
   jmin=1e+5;    cov[1]=1.;
   jmax=-1;  
   jmean=0.;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   for(i=1; i<=imx; i++){  
     mi=0;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     m=firstpass;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     while(s[m][i] <= nlstate){      for(mi=1; mi<= wav[i]-1; mi++){
       if(s[m][i]>=1)        for (ii=1;ii<=nlstate+ndeath;ii++)
         mw[++mi][i]=m;          for (j=1;j<=nlstate+ndeath;j++){
       if(m >=lastpass)            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         break;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
       else          }
         m++;        for(d=0; d<dh[mi][i]; d++){
     }/* end while */          newm=savm;
     if (s[m][i] > nlstate){          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       mi++;     /* Death is another wave */          for (kk=1; kk<=cptcovage;kk++) {
       /* if(mi==0)  never been interviewed correctly before death */            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
          /* Only death is a correct wave */          }
       mw[mi][i]=m;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     }                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;
     wav[i]=mi;          oldm=newm;
     if(mi==0)        } /* end mult */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        
   }        s1=s[mw[mi][i]][i];
         s2=s[mw[mi+1][i]][i];
   for(i=1; i<=imx; i++){        bbh=(double)bh[mi][i]/(double)stepm; 
     for(mi=1; mi<wav[i];mi++){        /* bias is positive if real duration
       if (stepm <=0)         * is higher than the multiple of stepm and negative otherwise.
         dh[mi][i]=1;         */
       else{        if( s2 > nlstate && (mle <5) ){  /* Jackson */
         if (s[mw[mi+1][i]][i] > nlstate) {          lli=log(out[s1][s2] - savm[s1][s2]);
           if (agedc[i] < 2*AGESUP) {        } else if (mle==1){
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           if(j==0) j=1;  /* Survives at least one month after exam */        } else if(mle==2){
           k=k+1;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           if (j >= jmax) jmax=j;        } else if(mle==3){  /* exponential inter-extrapolation */
           if (j <= jmin) jmin=j;          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 */
           sum=sum+j;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           /* if (j<10) printf("j=%d num=%d ",j,i); */          lli=log(out[s1][s2]); /* Original formula */
           }        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
         }          lli=log(out[s1][s2]); /* Original formula */
         else{        } /* End of if */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        ipmx +=1;
           k=k+1;        sw += weight[i];
           if (j >= jmax) jmax=j;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           else if (j <= jmin)jmin=j;  /*       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<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        if(globpr){
           sum=sum+j;          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
         }   %10.6f %10.6f %10.6f ", \
         jk= j/stepm;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
         jl= j -jk*stepm;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         ju= j -(jk+1)*stepm;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
         if(jl <= -ju)            llt +=ll[k]*gipmx/gsw;
           dh[mi][i]=jk;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
         else          }
           dh[mi][i]=jk+1;          fprintf(ficresilk," %10.6f\n", -llt);
         if(dh[mi][i]==0)        }
           dh[mi][i]=1; /* At least one step */      } /* end of wave */
       }    } /* end of individual */
     }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   jmean=sum/k;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    if(globpr==0){ /* First time we count the contributions and weights */
  }      gipmx=ipmx;
 /*********** Tricode ****************************/      gsw=sw;
 void tricode(int *Tvar, int **nbcode, int imx)    }
 {    return -l;
   int Ndum[20],ij=1, k, j, i;  }
   int cptcode=0;  
   cptcoveff=0;  
    /*************** function likelione ***********/
   for (k=0; k<19; k++) Ndum[k]=0;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   for (k=1; k<=7; k++) ncodemax[k]=0;  {
     /* This routine should help understanding what is done with 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {       the selection of individuals/waves and
     for (i=1; i<=imx; i++) {       to check the exact contribution to the likelihood.
       ij=(int)(covar[Tvar[j]][i]);       Plotting could be done.
       Ndum[ij]++;     */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    int k;
       if (ij > cptcode) cptcode=ij;  
     }    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
     for (i=0; i<=cptcode; i++) {      strcat(fileresilk,fileres);
       if(Ndum[i]!=0) ncodemax[j]++;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     }        printf("Problem with resultfile: %s\n", fileresilk);
     ij=1;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
       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");
     for (i=1; i<=ncodemax[j]; i++) {      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       for (k=0; k<=19; k++) {      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
         if (Ndum[k] != 0) {      for(k=1; k<=nlstate; k++) 
           nbcode[Tvar[j]][ij]=k;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
           ij++;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
         }    }
         if (ij > ncodemax[j]) break;  
       }      *fretone=(*funcone)(p);
     }    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));
  for (k=0; k<19; k++) Ndum[k]=0;      fflush(fichtm); 
     } 
  for (i=1; i<=ncovmodel-2; i++) {    return;
       ij=Tvar[i];  }
       Ndum[ij]++;  
     }  
   /*********** Maximum Likelihood Estimation ***************/
  ij=1;  
  for (i=1; i<=10; i++) {  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
    if((Ndum[i]!=0) && (i<=ncov)){  {
      Tvaraff[ij]=i;    int i,j, iter;
      ij++;    double **xi;
    }    double fret;
  }    double fretone; /* Only one call to likelihood */
      char filerespow[FILENAMELENGTH];
     cptcoveff=ij-1;    xi=matrix(1,npar,1,npar);
 }    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
 /*********** Health Expectancies ****************/        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    strcpy(filerespow,"pow"); 
 {    strcat(filerespow,fileres);
   /* Health expectancies */    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   int i, j, nhstepm, hstepm, h;      printf("Problem with resultfile: %s\n", filerespow);
   double age, agelim,hf;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   double ***p3mat;    }
      fprintf(ficrespow,"# Powell\n# iter -2*LL");
   fprintf(ficreseij,"# Health expectancies\n");    for (i=1;i<=nlstate;i++)
   fprintf(ficreseij,"# Age");      for(j=1;j<=nlstate+ndeath;j++)
   for(i=1; i<=nlstate;i++)        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     for(j=1; j<=nlstate;j++)    fprintf(ficrespow,"\n");
       fprintf(ficreseij," %1d-%1d",i,j);  
   fprintf(ficreseij,"\n");    powell(p,xi,npar,ftol,&iter,&fret,func);
   
   hstepm=1*YEARM; /*  Every j years of age (in month) */    fclose(ficrespow);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   agelim=AGESUP;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     /* nhstepm age range expressed in number of stepm */  }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years = 20*12/6=40 stepm */  /**** Computes Hessian and covariance matrix ***/
     if (stepm >= YEARM) hstepm=1;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */  {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double  **a,**y,*x,pd;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    double **hess;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    int i, j,jk;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      int *indx;
   
     double hessii(double p[], double delta, int theta, double delti[]);
     for(i=1; i<=nlstate;i++)    double hessij(double p[], double delti[], int i, int j);
       for(j=1; j<=nlstate;j++)    void lubksb(double **a, int npar, int *indx, double b[]) ;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){    void ludcmp(double **a, int npar, int *indx, double *d) ;
           eij[i][j][(int)age] +=p3mat[i][j][h];  
         }    hess=matrix(1,npar,1,npar);
      
     hf=1;    printf("\nCalculation of the hessian matrix. Wait...\n");
     if (stepm >= YEARM) hf=stepm/YEARM;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficreseij,"%.0f",age );    for (i=1;i<=npar;i++){
     for(i=1; i<=nlstate;i++)      printf("%d",i);fflush(stdout);
       for(j=1; j<=nlstate;j++){      fprintf(ficlog,"%d",i);fflush(ficlog);
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);      hess[i][i]=hessii(p,ftolhess,i,delti);
       }      /*printf(" %f ",p[i]);*/
     fprintf(ficreseij,"\n");      /*printf(" %lf ",hess[i][i]);*/
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
   }    
 }    for (i=1;i<=npar;i++) {
       for (j=1;j<=npar;j++)  {
 /************ Variance ******************/        if (j>i) { 
 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(".%d%d",i,j);fflush(stdout);
 {          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   /* Variance of health expectancies */          hess[i][j]=hessij(p,delti,i,j);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          hess[j][i]=hess[i][j];    
   double **newm;          /*printf(" %lf ",hess[i][j]);*/
   double **dnewm,**doldm;        }
   int i, j, nhstepm, hstepm, h;      }
   int k, cptcode;    }
   double *xp;    printf("\n");
   double **gp, **gm;    fprintf(ficlog,"\n");
   double ***gradg, ***trgradg;  
   double ***p3mat;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   double age,agelim;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   int theta;    
     a=matrix(1,npar,1,npar);
    fprintf(ficresvij,"# Covariances of life expectancies\n");    y=matrix(1,npar,1,npar);
   fprintf(ficresvij,"# Age");    x=vector(1,npar);
   for(i=1; i<=nlstate;i++)    indx=ivector(1,npar);
     for(j=1; j<=nlstate;j++)    for (i=1;i<=npar;i++)
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   fprintf(ficresvij,"\n");    ludcmp(a,npar,indx,&pd);
   
   xp=vector(1,npar);    for (j=1;j<=npar;j++) {
   dnewm=matrix(1,nlstate,1,npar);      for (i=1;i<=npar;i++) x[i]=0;
   doldm=matrix(1,nlstate,1,nlstate);      x[j]=1;
        lubksb(a,npar,indx,x);
   hstepm=1*YEARM; /* Every year of age */      for (i=1;i<=npar;i++){ 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        matcov[i][j]=x[i];
   agelim = AGESUP;      }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
     if (stepm >= YEARM) hstepm=1;    printf("\n#Hessian matrix#\n");
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    fprintf(ficlog,"\n#Hessian matrix#\n");
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (i=1;i<=npar;i++) { 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      for (j=1;j<=npar;j++) { 
     gp=matrix(0,nhstepm,1,nlstate);        printf("%.3e ",hess[i][j]);
     gm=matrix(0,nhstepm,1,nlstate);        fprintf(ficlog,"%.3e ",hess[i][j]);
       }
     for(theta=1; theta <=npar; theta++){      printf("\n");
       for(i=1; i<=npar; i++){ /* Computes gradient */      fprintf(ficlog,"\n");
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    }
       }  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      /* Recompute Inverse */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
       if (popbased==1) {    ludcmp(a,npar,indx,&pd);
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];    /*  printf("\n#Hessian matrix recomputed#\n");
       }  
          for (j=1;j<=npar;j++) {
       for(j=1; j<= nlstate; j++){      for (i=1;i<=npar;i++) x[i]=0;
         for(h=0; h<=nhstepm; h++){      x[j]=1;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      lubksb(a,npar,indx,x);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      for (i=1;i<=npar;i++){ 
         }        y[i][j]=x[i];
       }        printf("%.3e ",y[i][j]);
            fprintf(ficlog,"%.3e ",y[i][j]);
       for(i=1; i<=npar; i++) /* Computes gradient */      }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      printf("\n");
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        fprintf(ficlog,"\n");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    }
     */
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)    free_matrix(a,1,npar,1,npar);
           prlim[i][i]=probs[(int)age][i][ij];    free_matrix(y,1,npar,1,npar);
       }    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
       for(j=1; j<= nlstate; j++){    free_matrix(hess,1,npar,1,npar);
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  }
         }  
       }  /*************** hessian matrix ****************/
   double hessii( double x[], double delta, int theta, double delti[])
       for(j=1; j<= nlstate; j++)  {
         for(h=0; h<=nhstepm; h++){    int i;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    int l=1, lmax=20;
         }    double k1,k2;
     } /* End theta */    double p2[NPARMAX+1];
     double res;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     double fx;
     for(h=0; h<=nhstepm; h++)    int k=0,kmax=10;
       for(j=1; j<=nlstate;j++)    double l1;
         for(theta=1; theta <=npar; theta++)  
           trgradg[h][j][theta]=gradg[h][theta][j];    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
     for(i=1;i<=nlstate;i++)    for(l=0 ; l <=lmax; l++){
       for(j=1;j<=nlstate;j++)      l1=pow(10,l);
         vareij[i][j][(int)age] =0.;      delts=delt;
     for(h=0;h<=nhstepm;h++){      for(k=1 ; k <kmax; k=k+1){
       for(k=0;k<=nhstepm;k++){        delt = delta*(l1*k);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        p2[theta]=x[theta] +delt;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        k1=func(p2)-fx;
         for(i=1;i<=nlstate;i++)        p2[theta]=x[theta]-delt;
           for(j=1;j<=nlstate;j++)        k2=func(p2)-fx;
             vareij[i][j][(int)age] += doldm[i][j];        /*res= (k1-2.0*fx+k2)/delt/delt; */
       }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     }        
     h=1;  #ifdef DEBUG
     if (stepm >= YEARM) h=stepm/YEARM;        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     fprintf(ficresvij,"%.0f ",age );        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     for(i=1; i<=nlstate;i++)  #endif
       for(j=1; j<=nlstate;j++){        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       }          k=kmax;
     fprintf(ficresvij,"\n");        }
     free_matrix(gp,0,nhstepm,1,nlstate);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     free_matrix(gm,0,nhstepm,1,nlstate);          k=kmax; l=lmax*10.;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        }
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          delts=delt;
   } /* End age */        }
        }
   free_vector(xp,1,npar);    }
   free_matrix(doldm,1,nlstate,1,npar);    delti[theta]=delts;
   free_matrix(dnewm,1,nlstate,1,nlstate);    return res; 
     
 }  }
   
 /************ Variance of prevlim ******************/  double hessij( double x[], double delti[], int thetai,int thetaj)
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)  {
 {    int i;
   /* Variance of prevalence limit */    int l=1, l1, lmax=20;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    double k1,k2,k3,k4,res,fx;
   double **newm;    double p2[NPARMAX+1];
   double **dnewm,**doldm;    int k;
   int i, j, nhstepm, hstepm;  
   int k, cptcode;    fx=func(x);
   double *xp;    for (k=1; k<=2; k++) {
   double *gp, *gm;      for (i=1;i<=npar;i++) p2[i]=x[i];
   double **gradg, **trgradg;      p2[thetai]=x[thetai]+delti[thetai]/k;
   double age,agelim;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   int theta;      k1=func(p2)-fx;
        
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      p2[thetai]=x[thetai]+delti[thetai]/k;
   fprintf(ficresvpl,"# Age");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   for(i=1; i<=nlstate;i++)      k2=func(p2)-fx;
       fprintf(ficresvpl," %1d-%1d",i,i);    
   fprintf(ficresvpl,"\n");      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   xp=vector(1,npar);      k3=func(p2)-fx;
   dnewm=matrix(1,nlstate,1,npar);    
   doldm=matrix(1,nlstate,1,nlstate);      p2[thetai]=x[thetai]-delti[thetai]/k;
        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   hstepm=1*YEARM; /* Every year of age */      k4=func(p2)-fx;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   agelim = AGESUP;  #ifdef DEBUG
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      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);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      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);
     if (stepm >= YEARM) hstepm=1;  #endif
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    }
     gradg=matrix(1,npar,1,nlstate);    return res;
     gp=vector(1,nlstate);  }
     gm=vector(1,nlstate);  
   /************** Inverse of matrix **************/
     for(theta=1; theta <=npar; theta++){  void ludcmp(double **a, int n, int *indx, double *d) 
       for(i=1; i<=npar; i++){ /* Computes gradient */  { 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    int i,imax,j,k; 
       }    double big,dum,sum,temp; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double *vv; 
       for(i=1;i<=nlstate;i++)   
         gp[i] = prlim[i][i];    vv=vector(1,n); 
        *d=1.0; 
       for(i=1; i<=npar; i++) /* Computes gradient */    for (i=1;i<=n;i++) { 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      big=0.0; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      for (j=1;j<=n;j++) 
       for(i=1;i<=nlstate;i++)        if ((temp=fabs(a[i][j])) > big) big=temp; 
         gm[i] = prlim[i][i];      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
       for(i=1;i<=nlstate;i++)    } 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    for (j=1;j<=n;j++) { 
     } /* End theta */      for (i=1;i<j;i++) { 
         sum=a[i][j]; 
     trgradg =matrix(1,nlstate,1,npar);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
     for(j=1; j<=nlstate;j++)      } 
       for(theta=1; theta <=npar; theta++)      big=0.0; 
         trgradg[j][theta]=gradg[theta][j];      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
     for(i=1;i<=nlstate;i++)        for (k=1;k<j;k++) 
       varpl[i][(int)age] =0.;          sum -= a[i][k]*a[k][j]; 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        a[i][j]=sum; 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     for(i=1;i<=nlstate;i++)          big=dum; 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          imax=i; 
         } 
     fprintf(ficresvpl,"%.0f ",age );      } 
     for(i=1; i<=nlstate;i++)      if (j != imax) { 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        for (k=1;k<=n;k++) { 
     fprintf(ficresvpl,"\n");          dum=a[imax][k]; 
     free_vector(gp,1,nlstate);          a[imax][k]=a[j][k]; 
     free_vector(gm,1,nlstate);          a[j][k]=dum; 
     free_matrix(gradg,1,npar,1,nlstate);        } 
     free_matrix(trgradg,1,nlstate,1,npar);        *d = -(*d); 
   } /* End age */        vv[imax]=vv[j]; 
       } 
   free_vector(xp,1,npar);      indx[j]=imax; 
   free_matrix(doldm,1,nlstate,1,npar);      if (a[j][j] == 0.0) a[j][j]=TINY; 
   free_matrix(dnewm,1,nlstate,1,nlstate);      if (j != n) { 
         dum=1.0/(a[j][j]); 
 }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       } 
 /************ Variance of one-step probabilities  ******************/    } 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    free_vector(vv,1,n);  /* Doesn't work */
 {  ;
   int i, j;  } 
   int k=0, cptcode;  
   double **dnewm,**doldm;  void lubksb(double **a, int n, int *indx, double b[]) 
   double *xp;  { 
   double *gp, *gm;    int i,ii=0,ip,j; 
   double **gradg, **trgradg;    double sum; 
   double age,agelim, cov[NCOVMAX];   
   int theta;    for (i=1;i<=n;i++) { 
   char fileresprob[FILENAMELENGTH];      ip=indx[i]; 
       sum=b[ip]; 
   strcpy(fileresprob,"prob");      b[ip]=b[i]; 
   strcat(fileresprob,fileres);      if (ii) 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     printf("Problem with resultfile: %s\n", fileresprob);      else if (sum) ii=i; 
   }      b[i]=sum; 
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    } 
      for (i=n;i>=1;i--) { 
       sum=b[i]; 
   xp=vector(1,npar);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      b[i]=sum/a[i][i]; 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    } 
    } 
   cov[1]=1;  
   for (age=bage; age<=fage; age ++){  /************ Frequencies ********************/
     cov[2]=age;  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)
     gradg=matrix(1,npar,1,9);  {  /* Some frequencies */
     trgradg=matrix(1,9,1,npar);    
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    int first;
        double ***freq; /* Frequencies */
     for(theta=1; theta <=npar; theta++){    double *pp, **prop;
       for(i=1; i<=npar; i++)    double pos,posprop, k2, dateintsum=0,k2cpt=0;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    FILE *ficresp;
          char fileresp[FILENAMELENGTH];
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    
        pp=vector(1,nlstate);
       k=0;    prop=matrix(1,nlstate,iagemin,iagemax+3);
       for(i=1; i<= (nlstate+ndeath); i++){    strcpy(fileresp,"p");
         for(j=1; j<=(nlstate+ndeath);j++){    strcat(fileresp,fileres);
            k=k+1;    if((ficresp=fopen(fileresp,"w"))==NULL) {
           gp[k]=pmmij[i][j];      printf("Problem with prevalence resultfile: %s\n", fileresp);
         }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       }      exit(0);
     }
       for(i=1; i<=npar; i++)    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    j1=0;
        
     j=cptcoveff;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       k=0;  
       for(i=1; i<=(nlstate+ndeath); i++){    first=1;
         for(j=1; j<=(nlstate+ndeath);j++){  
           k=k+1;    for(k1=1; k1<=j;k1++){
           gm[k]=pmmij[i][j];      for(i1=1; i1<=ncodemax[k1];i1++){
         }        j1++;
       }        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
                scanf("%d", i);*/
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        for (i=-1; i<=nlstate+ndeath; i++)  
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            for (jk=-1; jk<=nlstate+ndeath; jk++)  
     }            for(m=iagemin; m <= iagemax+3; m++)
               freq[i][jk][m]=0;
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  
       for(theta=1; theta <=npar; theta++)      for (i=1; i<=nlstate; i++)  
       trgradg[j][theta]=gradg[theta][j];        for(m=iagemin; m <= iagemax+3; m++)
            prop[i][m]=0;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);        dateintsum=0;
         k2cpt=0;
      pmij(pmmij,cov,ncovmodel,x,nlstate);        for (i=1; i<=imx; i++) {
           bool=1;
      k=0;          if  (cptcovn>0) {
      for(i=1; i<=(nlstate+ndeath); i++){            for (z1=1; z1<=cptcoveff; z1++) 
        for(j=1; j<=(nlstate+ndeath);j++){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
          k=k+1;                bool=0;
          gm[k]=pmmij[i][j];          }
         }          if (bool==1){
      }            for(m=firstpass; m<=lastpass; m++){
                    k2=anint[m][i]+(mint[m][i]/12.);
      /*printf("\n%d ",(int)age);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                        if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));                if (m<lastpass) {
      }*/                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                   freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   fprintf(ficresprob,"\n%d ",(int)age);                }
                 
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);                  dateintsum=dateintsum+k2;
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);                  k2cpt++;
   }                }
                 /*}*/
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));            }
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          }
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        }
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);         
 }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
  free_vector(xp,1,npar);  
 fclose(ficresprob);        if  (cptcovn>0) {
  exit(0);          fprintf(ficresp, "\n#********** Variable "); 
 }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresp, "**********\n#");
 /***********************************************/        }
 /**************** Main Program *****************/        for(i=1; i<=nlstate;i++) 
 /***********************************************/          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficresp, "\n");
 int main(int argc, char *argv[])        
 {        for(i=iagemin; i <= iagemax+3; i++){
           if(i==iagemax+3){
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;            fprintf(ficlog,"Total");
   double agedeb, agefin,hf;          }else{
   double agemin=1.e20, agemax=-1.e20;            if(first==1){
               first=0;
   double fret;              printf("See log file for details...\n");
   double **xi,tmp,delta;            }
             fprintf(ficlog,"Age %d", i);
   double dum; /* Dummy variable */          }
   double ***p3mat;          for(jk=1; jk <=nlstate ; jk++){
   int *indx;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   char line[MAXLINE], linepar[MAXLINE];              pp[jk] += freq[jk][m][i]; 
   char title[MAXLINE];          }
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];          for(jk=1; jk <=nlstate ; jk++){
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];            for(m=-1, pos=0; m <=0 ; m++)
                pos += freq[jk][m][i];
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];;            if(pp[jk]>=1.e-10){
               if(first==1){
   char filerest[FILENAMELENGTH];              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   char fileregp[FILENAMELENGTH];              }
   char popfile[FILENAMELENGTH];              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];            }else{
   int firstobs=1, lastobs=10;              if(first==1)
   int sdeb, sfin; /* Status at beginning and end */                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   int c,  h , cpt,l;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   int ju,jl, mi;            }
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          }
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  
   int mobilav=0,popforecast=0;          for(jk=1; jk <=nlstate ; jk++){
   int hstepm, nhstepm;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   int *popage;/*boolprev=0 if date and zero if wave*/              pp[jk] += freq[jk][m][i];
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;          }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   double bage, fage, age, agelim, agebase;            pos += pp[jk];
   double ftolpl=FTOL;            posprop += prop[jk][i];
   double **prlim;          }
   double *severity;          for(jk=1; jk <=nlstate ; jk++){
   double ***param; /* Matrix of parameters */            if(pos>=1.e-5){
   double  *p;              if(first==1)
   double **matcov; /* Matrix of covariance */                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   double ***delti3; /* Scale */              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   double *delti; /* Scale */            }else{
   double ***eij, ***vareij;              if(first==1)
   double **varpl; /* Variances of prevalence limits by age */                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   double *epj, vepp;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   double kk1, kk2;            }
   double *popeffectif,*popcount;            if( i <= iagemax){
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;              if(pos>=1.e-5){
   double yp,yp1,yp2;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   char *alph[]={"a","a","b","c","d","e"}, str[4];              }
               else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   char z[1]="c", occ;            }
 #include <sys/time.h>          }
 #include <time.h>          
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          for(jk=-1; jk <=nlstate+ndeath; jk++)
              for(m=-1; m <=nlstate+ndeath; m++)
   /* long total_usecs;              if(freq[jk][m][i] !=0 ) {
   struct timeval start_time, end_time;              if(first==1)
                  printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
           if(i <= iagemax)
   printf("\n%s",version);            fprintf(ficresp,"\n");
   if(argc <=1){          if(first==1)
     printf("\nEnter the parameter file name: ");            printf("Others in log...\n");
     scanf("%s",pathtot);          fprintf(ficlog,"\n");
   }        }
   else{      }
     strcpy(pathtot,argv[1]);    }
   }    dateintmean=dateintsum/k2cpt; 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/   
   /*cygwin_split_path(pathtot,path,optionfile);    fclose(ficresp);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
   /* cutv(path,optionfile,pathtot,'\\');*/    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    /* End of Freq */
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  }
   chdir(path);  
   replace(pathc,path);  /************ Prevalence ********************/
   void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
 /*-------- arguments in the command line --------*/  {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   strcpy(fileres,"r");       in each health status at the date of interview (if between dateprev1 and dateprev2).
   strcat(fileres, optionfilefiname);       We still use firstpass and lastpass as another selection.
   strcat(fileres,".txt");    /* Other files have txt extension */    */
    
   /*---------arguments file --------*/    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     double ***freq; /* Frequencies */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    double *pp, **prop;
     printf("Problem with optionfile %s\n",optionfile);    double pos,posprop; 
     goto end;    double  y2; /* in fractional years */
   }    int iagemin, iagemax;
   
   strcpy(filereso,"o");    iagemin= (int) agemin;
   strcat(filereso,fileres);    iagemax= (int) agemax;
   if((ficparo=fopen(filereso,"w"))==NULL) {    /*pp=vector(1,nlstate);*/
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j1=0;
   /* Reads comments: lines beginning with '#' */    
   while((c=getc(ficpar))=='#' && c!= EOF){    j=cptcoveff;
     ungetc(c,ficpar);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     fgets(line, MAXLINE, ficpar);    
     puts(line);    for(k1=1; k1<=j;k1++){
     fputs(line,ficparo);      for(i1=1; i1<=ncodemax[k1];i1++){
   }        j1++;
   ungetc(c,ficpar);        
         for (i=1; i<=nlstate; i++)  
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);          for(m=iagemin; m <= iagemax+3; m++)
   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);            prop[i][m]=0.0;
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);       
 while((c=getc(ficpar))=='#' && c!= EOF){        for (i=1; i<=imx; i++) { /* Each individual */
     ungetc(c,ficpar);          bool=1;
     fgets(line, MAXLINE, ficpar);          if  (cptcovn>0) {
     puts(line);            for (z1=1; z1<=cptcoveff; z1++) 
     fputs(line,ficparo);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   }                bool=0;
   ungetc(c,ficpar);          } 
            if (bool==1) { 
                for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   covar=matrix(0,NCOVMAX,1,n);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   cptcovn=0;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
   ncovmodel=2+cptcovn;                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); 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                    /*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]]);*/
   /* Read guess parameters */                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   /* Reads comments: lines beginning with '#' */                  prop[s[m][i]][iagemax+3] += weight[i]; 
   while((c=getc(ficpar))=='#' && c!= EOF){                } 
     ungetc(c,ficpar);              }
     fgets(line, MAXLINE, ficpar);            } /* end selection of waves */
     puts(line);          }
     fputs(line,ficparo);        }
   }        for(i=iagemin; i <= iagemax+3; i++){  
   ungetc(c,ficpar);          
            for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            posprop += prop[jk][i]; 
     for(i=1; i <=nlstate; i++)          } 
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);          for(jk=1; jk <=nlstate ; jk++){     
       fprintf(ficparo,"%1d%1d",i1,j1);            if( i <=  iagemax){ 
       printf("%1d%1d",i,j);              if(posprop>=1.e-5){ 
       for(k=1; k<=ncovmodel;k++){                probs[i][jk][j1]= prop[jk][i]/posprop;
         fscanf(ficpar," %lf",&param[i][j][k]);              } 
         printf(" %lf",param[i][j][k]);            } 
         fprintf(ficparo," %lf",param[i][j][k]);          }/* end jk */ 
       }        }/* end i */ 
       fscanf(ficpar,"\n");      } /* end i1 */
       printf("\n");    } /* end k1 */
       fprintf(ficparo,"\n");    
     }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
      /*free_vector(pp,1,nlstate);*/
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
   p=param[1][1];  
    /************* Waves Concatenation ***************/
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){  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)
     ungetc(c,ficpar);  {
     fgets(line, MAXLINE, ficpar);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     puts(line);       Death is a valid wave (if date is known).
     fputs(line,ficparo);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   ungetc(c,ficpar);       and mw[mi+1][i]. dh depends on stepm.
        */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    int i, mi, m;
   for(i=1; i <=nlstate; i++){    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     for(j=1; j <=nlstate+ndeath-1; j++){       double sum=0., jmean=0.;*/
       fscanf(ficpar,"%1d%1d",&i1,&j1);    int first;
       printf("%1d%1d",i,j);    int j, k=0,jk, ju, jl;
       fprintf(ficparo,"%1d%1d",i1,j1);    double sum=0.;
       for(k=1; k<=ncovmodel;k++){    first=0;
         fscanf(ficpar,"%le",&delti3[i][j][k]);    jmin=1e+5;
         printf(" %le",delti3[i][j][k]);    jmax=-1;
         fprintf(ficparo," %le",delti3[i][j][k]);    jmean=0.;
       }    for(i=1; i<=imx; i++){
       fscanf(ficpar,"\n");      mi=0;
       printf("\n");      m=firstpass;
       fprintf(ficparo,"\n");      while(s[m][i] <= nlstate){
     }        if(s[m][i]>=1)
   }          mw[++mi][i]=m;
   delti=delti3[1][1];        if(m >=lastpass)
            break;
   /* Reads comments: lines beginning with '#' */        else
   while((c=getc(ficpar))=='#' && c!= EOF){          m++;
     ungetc(c,ficpar);      }/* end while */
     fgets(line, MAXLINE, ficpar);      if (s[m][i] > nlstate){
     puts(line);        mi++;     /* Death is another wave */
     fputs(line,ficparo);        /* if(mi==0)  never been interviewed correctly before death */
   }           /* Only death is a correct wave */
   ungetc(c,ficpar);        mw[mi][i]=m;
        }
   matcov=matrix(1,npar,1,npar);  
   for(i=1; i <=npar; i++){      wav[i]=mi;
     fscanf(ficpar,"%s",&str);      if(mi==0){
     printf("%s",str);        nbwarn++;
     fprintf(ficparo,"%s",str);        if(first==0){
     for(j=1; j <=i; j++){          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       fscanf(ficpar," %le",&matcov[i][j]);          first=1;
       printf(" %.5le",matcov[i][j]);        }
       fprintf(ficparo," %.5le",matcov[i][j]);        if(first==1){
     }          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
     fscanf(ficpar,"\n");        }
     printf("\n");      } /* end mi==0 */
     fprintf(ficparo,"\n");    } /* End individuals */
   }  
   for(i=1; i <=npar; i++)    for(i=1; i<=imx; i++){
     for(j=i+1;j<=npar;j++)      for(mi=1; mi<wav[i];mi++){
       matcov[i][j]=matcov[j][i];        if (stepm <=0)
              dh[mi][i]=1;
   printf("\n");        else{
           if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             if (agedc[i] < 2*AGESUP) {
     /*-------- data file ----------*/              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     if((ficres =fopen(fileres,"w"))==NULL) {              if(j==0) j=1;  /* Survives at least one month after exam */
       printf("Problem with resultfile: %s\n", fileres);goto end;              else if(j<0){
     }                nberr++;
     fprintf(ficres,"#%s\n",version);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                    j=1; /* Temporary Dangerous patch */
     if((fic=fopen(datafile,"r"))==NULL)    {                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);
       printf("Problem with datafile: %s\n", datafile);goto end;                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     }                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
               }
     n= lastobs;              k=k+1;
     severity = vector(1,maxwav);              if (j >= jmax) jmax=j;
     outcome=imatrix(1,maxwav+1,1,n);              if (j <= jmin) jmin=j;
     num=ivector(1,n);              sum=sum+j;
     moisnais=vector(1,n);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     annais=vector(1,n);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     moisdc=vector(1,n);            }
     andc=vector(1,n);          }
     agedc=vector(1,n);          else{
     cod=ivector(1,n);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     weight=vector(1,n);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */            k=k+1;
     mint=matrix(1,maxwav,1,n);            if (j >= jmax) jmax=j;
     anint=matrix(1,maxwav,1,n);            else if (j <= jmin)jmin=j;
     s=imatrix(1,maxwav+1,1,n);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     adl=imatrix(1,maxwav+1,1,n);                /*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]);*/
     tab=ivector(1,NCOVMAX);            if(j<0){
     ncodemax=ivector(1,8);              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]);
     i=1;              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]);
     while (fgets(line, MAXLINE, fic) != NULL)    {            }
       if ((i >= firstobs) && (i <=lastobs)) {            sum=sum+j;
                  }
         for (j=maxwav;j>=1;j--){          jk= j/stepm;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          jl= j -jk*stepm;
           strcpy(line,stra);          ju= j -(jk+1)*stepm;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            if(jl==0){
         }              dh[mi][i]=jk;
                      bh[mi][i]=0;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);            }else{ /* We want a negative bias in order to only have interpolation ie
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);                    * at the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);              bh[mi][i]=ju;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);            }
           }else{
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);            if(jl <= -ju){
         for (j=ncov;j>=1;j--){              dh[mi][i]=jk;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);              bh[mi][i]=jl;       /* bias is positive if real duration
         }                                   * is higher than the multiple of stepm and negative otherwise.
         num[i]=atol(stra);                                   */
                    }
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){            else{
           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;}*/              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
         i=i+1;            }
       }            if(dh[mi][i]==0){
     }              dh[mi][i]=1; /* At least one step */
     /* printf("ii=%d", ij);              bh[mi][i]=ju; /* At least one step */
        scanf("%d",i);*/              /*  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);*/
   imx=i-1; /* Number of individuals */            }
           } /* end if mle */
   /* for (i=1; i<=imx; i++){        }
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      } /* end wave */
     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;    jmean=sum/k;
     }    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     for (i=1; i<=imx; i++)   }
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/  
   /*********** Tricode ****************************/
   /* Calculation of the number of parameter from char model*/  void tricode(int *Tvar, int **nbcode, int imx)
   Tvar=ivector(1,15);  {
   Tprod=ivector(1,15);    
   Tvaraff=ivector(1,15);    int Ndum[20],ij=1, k, j, i, maxncov=19;
   Tvard=imatrix(1,15,1,2);    int cptcode=0;
   Tage=ivector(1,15);          cptcoveff=0; 
       
   if (strlen(model) >1){    for (k=0; k<maxncov; k++) Ndum[k]=0;
     j=0, j1=0, k1=1, k2=1;    for (k=1; k<=7; k++) ncodemax[k]=0;
     j=nbocc(model,'+');  
     j1=nbocc(model,'*');    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     cptcovn=j+1;      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     cptcovprod=j1;                                 modality*/ 
            ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
            Ndum[ij]++; /*store the modality */
     strcpy(modelsav,model);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
       printf("Error. Non available option model=%s ",model);                                         Tvar[j]. If V=sex and male is 0 and 
       goto end;                                         female is 1, then  cptcode=1.*/
     }      }
      
     for(i=(j+1); i>=1;i--){      for (i=0; i<=cptcode; i++) {
       cutv(stra,strb,modelsav,'+');        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      }
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  
       /*scanf("%d",i);*/      ij=1; 
       if (strchr(strb,'*')) {      for (i=1; i<=ncodemax[j]; i++) {
         cutv(strd,strc,strb,'*');        for (k=0; k<= maxncov; k++) {
         if (strcmp(strc,"age")==0) {          if (Ndum[k] != 0) {
           cptcovprod--;            nbcode[Tvar[j]][ij]=k; 
           cutv(strb,stre,strd,'V');            /* 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; */
           Tvar[i]=atoi(stre);            
           cptcovage++;            ij++;
             Tage[cptcovage]=i;          }
             /*printf("stre=%s ", stre);*/          if (ij > ncodemax[j]) break; 
         }        }  
         else if (strcmp(strd,"age")==0) {      } 
           cptcovprod--;    }  
           cutv(strb,stre,strc,'V');  
           Tvar[i]=atoi(stre);   for (k=0; k< maxncov; k++) Ndum[k]=0;
           cptcovage++;  
           Tage[cptcovage]=i;   for (i=1; i<=ncovmodel-2; i++) { 
         }     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
         else {     ij=Tvar[i];
           cutv(strb,stre,strc,'V');     Ndum[ij]++;
           Tvar[i]=ncov+k1;   }
           cutv(strb,strc,strd,'V');  
           Tprod[k1]=i;   ij=1;
           Tvard[k1][1]=atoi(strc);   for (i=1; i<= maxncov; i++) {
           Tvard[k1][2]=atoi(stre);     if((Ndum[i]!=0) && (i<=ncovcol)){
           Tvar[cptcovn+k2]=Tvard[k1][1];       Tvaraff[ij]=i; /*For printing */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];       ij++;
           for (k=1; k<=lastobs;k++)     }
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];   }
           k1++;   
           k2=k2+2;   cptcoveff=ij-1; /*Number of simple covariates*/
         }  }
       }  
       else {  /*********** Health Expectancies ****************/
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  
        /*  scanf("%d",i);*/  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
       cutv(strd,strc,strb,'V');  
       Tvar[i]=atoi(strc);  {
       }    /* Health expectancies */
       strcpy(modelsav,stra);      int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    double age, agelim, hf;
         scanf("%d",i);*/    double ***p3mat,***varhe;
     }    double **dnewm,**doldm;
 }    double *xp;
      double **gp, **gm;
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    double ***gradg, ***trgradg;
   printf("cptcovprod=%d ", cptcovprod);    int theta;
   scanf("%d ",i);*/  
     fclose(fic);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
     /*  if(mle==1){*/    dnewm=matrix(1,nlstate*nlstate,1,npar);
     if (weightopt != 1) { /* Maximisation without weights*/    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       for(i=1;i<=n;i++) weight[i]=1.0;    
     }    fprintf(ficreseij,"# Health expectancies\n");
     /*-calculation of age at interview from date of interview and age at death -*/    fprintf(ficreseij,"# Age");
     agev=matrix(1,maxwav,1,imx);    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
    for (i=1; i<=imx; i++)        fprintf(ficreseij," %1d-%1d (SE)",i,j);
      for(m=2; (m<= maxwav); m++)    fprintf(ficreseij,"\n");
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  
          anint[m][i]=9999;    if(estepm < stepm){
          s[m][i]=-1;      printf ("Problem %d lower than %d\n",estepm, stepm);
        }    }
        else  hstepm=estepm;   
     for (i=1; i<=imx; i++)  {    /* We compute the life expectancy from trapezoids spaced every estepm months
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);     * This is mainly to measure the difference between two models: for example
       for(m=1; (m<= maxwav); m++){     * if stepm=24 months pijx are given only every 2 years and by summing them
         if(s[m][i] >0){     * we are calculating an estimate of the Life Expectancy assuming a linear 
           if (s[m][i] == nlstate+1) {     * progression in between and thus overestimating or underestimating according
             if(agedc[i]>0)     * to the curvature of the survival function. If, for the same date, we 
               if(moisdc[i]!=99 && andc[i]!=9999)     * estimate the model with stepm=1 month, we can keep estepm to 24 months
               agev[m][i]=agedc[i];     * to compare the new estimate of Life expectancy with the same linear 
             else {     * hypothesis. A more precise result, taking into account a more precise
               if (andc[i]!=9999){     * curvature will be obtained if estepm is as small as stepm. */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;    /* For example we decided to compute the life expectancy with the smallest unit */
               }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
             }       nhstepm is the number of hstepm from age to agelim 
           }       nstepm is the number of stepm from age to agelin. 
           else if(s[m][i] !=9){ /* Should no more exist */       Look at hpijx to understand the reason of that which relies in memory size
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);       and note for a fixed period like estepm months */
             if(mint[m][i]==99 || anint[m][i]==9999)    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
               agev[m][i]=1;       survival function given by stepm (the optimization length). Unfortunately it
             else if(agev[m][i] <agemin){       means that if the survival funtion is printed only each two years of age and if
               agemin=agev[m][i];       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/       results. So we changed our mind and took the option of the best precision.
             }    */
             else if(agev[m][i] >agemax){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
               agemax=agev[m][i];  
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    agelim=AGESUP;
             }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
             /*agev[m][i]=anint[m][i]-annais[i];*/      /* nhstepm age range expressed in number of stepm */
             /*   agev[m][i] = age[i]+2*m;*/      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
           }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           else { /* =9 */      /* if (stepm >= YEARM) hstepm=1;*/
             agev[m][i]=1;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
             s[m][i]=-1;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
         }      gp=matrix(0,nhstepm,1,nlstate*nlstate);
         else /*= 0 Unknown */      gm=matrix(0,nhstepm,1,nlstate*nlstate);
           agev[m][i]=1;  
       }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
             in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     for (i=1; i<=imx; i++)  {   
       for(m=1; (m<= maxwav); m++){  
         if (s[m][i] > (nlstate+ndeath)) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           printf("Error: Wrong value in nlstate or ndeath\n");    
           goto end;      /* Computing  Variances of health expectancies */
         }  
       }       for(theta=1; theta <=npar; theta++){
     }        for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     free_vector(severity,1,maxwav);    
     free_imatrix(outcome,1,maxwav+1,1,n);        cptj=0;
     free_vector(moisnais,1,n);        for(j=1; j<= nlstate; j++){
     free_vector(annais,1,n);          for(i=1; i<=nlstate; i++){
     /* free_matrix(mint,1,maxwav,1,n);            cptj=cptj+1;
        free_matrix(anint,1,maxwav,1,n);*/            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
     free_vector(moisdc,1,n);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     free_vector(andc,1,n);            }
           }
            }
     wav=ivector(1,imx);       
     dh=imatrix(1,lastpass-firstpass+1,1,imx);       
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        for(i=1; i<=npar; i++) 
              xp[i] = x[i] - (i==theta ?delti[theta]:0);
     /* Concatenates waves */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        
         cptj=0;
         for(j=1; j<= nlstate; j++){
       Tcode=ivector(1,100);          for(i=1;i<=nlstate;i++){
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);            cptj=cptj+1;
       ncodemax[1]=1;            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  
                    gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
    codtab=imatrix(1,100,1,10);            }
    h=0;          }
    m=pow(2,cptcoveff);        }
          for(j=1; j<= nlstate*nlstate; j++)
    for(k=1;k<=cptcoveff; k++){          for(h=0; h<=nhstepm-1; h++){
      for(i=1; i <=(m/pow(2,k));i++){            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
        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;  /* End theta */
          }  
        }       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
      }  
    }       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
    /*for(i=1; i <=m ;i++){            trgradg[h][j][theta]=gradg[h][theta][j];
      for(k=1; k <=cptcovn; k++){       
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);  
      }       for(i=1;i<=nlstate*nlstate;i++)
      printf("\n");        for(j=1;j<=nlstate*nlstate;j++)
    }          varhe[i][j][(int)age] =0.;
    scanf("%d",i);*/  
           printf("%d|",(int)age);fflush(stdout);
    /* Calculates basic frequencies. Computes observed prevalence at single age       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        and prints on file fileres'p'. */       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
              matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
              matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(i=1;i<=nlstate*nlstate;i++)
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for(j=1;j<=nlstate*nlstate;j++)
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      }
            /* Computing expectancies */
     /* For Powell, parameters are in a vector p[] starting at p[1]      for(i=1; i<=nlstate;i++)
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */        for(j=1; j<=nlstate;j++)
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     if(mle==1){            
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  /* 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]);*/
     }  
              }
     /*--------- results files --------------*/  
     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);      fprintf(ficreseij,"%3.0f",age );
        cptj=0;
       for(i=1; i<=nlstate;i++)
    jk=1;        for(j=1; j<=nlstate;j++){
    fprintf(ficres,"# Parameters\n");          cptj++;
    printf("# Parameters\n");          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
    for(i=1,jk=1; i <=nlstate; i++){        }
      for(k=1; k <=(nlstate+ndeath); k++){      fprintf(ficreseij,"\n");
        if (k != i)     
          {      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
            printf("%d%d ",i,k);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
            fprintf(ficres,"%1d%1d ",i,k);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
            for(j=1; j <=ncovmodel; j++){      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
              printf("%f ",p[jk]);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              fprintf(ficres,"%f ",p[jk]);    }
              jk++;    printf("\n");
            }    fprintf(ficlog,"\n");
            printf("\n");  
            fprintf(ficres,"\n");    free_vector(xp,1,npar);
          }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
      }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
    }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
  if(mle==1){  }
     /* Computing hessian and covariance matrix */  
     ftolhess=ftol; /* Usually correct */  /************ Variance ******************/
     hesscov(matcov, p, npar, delti, ftolhess, func);  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
  }  {
     fprintf(ficres,"# Scales\n");    /* Variance of health expectancies */
     printf("# Scales\n");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
      for(i=1,jk=1; i <=nlstate; i++){    /* double **newm;*/
       for(j=1; j <=nlstate+ndeath; j++){    double **dnewm,**doldm;
         if (j!=i) {    double **dnewmp,**doldmp;
           fprintf(ficres,"%1d%1d",i,j);    int i, j, nhstepm, hstepm, h, nstepm ;
           printf("%1d%1d",i,j);    int k, cptcode;
           for(k=1; k<=ncovmodel;k++){    double *xp;
             printf(" %.5e",delti[jk]);    double **gp, **gm;  /* for var eij */
             fprintf(ficres," %.5e",delti[jk]);    double ***gradg, ***trgradg; /*for var eij */
             jk++;    double **gradgp, **trgradgp; /* for var p point j */
           }    double *gpp, *gmp; /* for var p point j */
           printf("\n");    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
           fprintf(ficres,"\n");    double ***p3mat;
         }    double age,agelim, hf;
       }    double ***mobaverage;
      }    int theta;
        char digit[4];
     k=1;    char digitp[25];
     fprintf(ficres,"# Covariance\n");  
     printf("# Covariance\n");    char fileresprobmorprev[FILENAMELENGTH];
     for(i=1;i<=npar;i++){  
       /*  if (k>nlstate) k=1;    if(popbased==1){
       i1=(i-1)/(ncovmodel*nlstate)+1;      if(mobilav!=0)
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        strcpy(digitp,"-populbased-mobilav-");
       printf("%s%d%d",alph[k],i1,tab[i]);*/      else strcpy(digitp,"-populbased-nomobil-");
       fprintf(ficres,"%3d",i);    }
       printf("%3d",i);    else 
       for(j=1; j<=i;j++){      strcpy(digitp,"-stablbased-");
         fprintf(ficres," %.5e",matcov[i][j]);  
         printf(" %.5e",matcov[i][j]);    if (mobilav!=0) {
       }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fprintf(ficres,"\n");      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       printf("\n");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       k++;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     }      }
        }
     while((c=getc(ficpar))=='#' && c!= EOF){  
       ungetc(c,ficpar);    strcpy(fileresprobmorprev,"prmorprev"); 
       fgets(line, MAXLINE, ficpar);    sprintf(digit,"%-d",ij);
       puts(line);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       fputs(line,ficparo);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     ungetc(c,ficpar);    strcat(fileresprobmorprev,fileres);
      if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
          fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     if (fage <= 2) {    }
       bage = agemin;    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       fage = agemax;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     }    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
        fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      fprintf(ficresprobmorprev," p.%-d SE",j);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      for(i=1; i<=nlstate;i++)
          fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     while((c=getc(ficpar))=='#' && c!= EOF){    }  
     ungetc(c,ficpar);    fprintf(ficresprobmorprev,"\n");
     fgets(line, MAXLINE, ficpar);    fprintf(ficgp,"\n# Routine varevsij");
     puts(line);    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");
     fputs(line,ficparo);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   }  /*   } */
   ungetc(c,ficpar);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);    fprintf(ficresvij,"# Age");
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);    for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate;j++)
   while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     ungetc(c,ficpar);    fprintf(ficresvij,"\n");
     fgets(line, MAXLINE, ficpar);  
     puts(line);    xp=vector(1,npar);
     fputs(line,ficparo);    dnewm=matrix(1,nlstate,1,npar);
   }    doldm=matrix(1,nlstate,1,nlstate);
   ungetc(c,ficpar);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
      doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
   fscanf(ficpar,"pop_based=%d\n",&popbased);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
    fprintf(ficparo,"pop_based=%d\n",popbased);      
    fprintf(ficres,"pop_based=%d\n",popbased);      if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    else  hstepm=estepm;   
     fgets(line, MAXLINE, ficpar);    /* For example we decided to compute the life expectancy with the smallest unit */
     puts(line);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     fputs(line,ficparo);       nhstepm is the number of hstepm from age to agelim 
   }       nstepm is the number of stepm from age to agelin. 
   ungetc(c,ficpar);       Look at hpijx to understand the reason of that which relies in memory size
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);       and note for a fixed period like k years */
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);       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
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
        */
     /*------------ gnuplot -------------*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     /*chdir(pathcd);*/    agelim = AGESUP;
     strcpy(optionfilegnuplot,optionfilefiname);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     strcat(optionfilegnuplot,".plt");      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       printf("Problem with file %s",optionfilegnuplot);goto end;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
 #ifdef windows      gp=matrix(0,nhstepm,1,nlstate);
     fprintf(ficgp,"cd \"%s\" \n",pathc);      gm=matrix(0,nhstepm,1,nlstate);
 #endif  
 m=pow(2,cptcoveff);  
        for(theta=1; theta <=npar; theta++){
  /* 1eme*/        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   for (cpt=1; cpt<= nlstate ; cpt ++) {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
    for (k1=1; k1<= m ; k1 ++) {        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 #ifdef windows        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     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        if (popbased==1) {
 #ifdef unix          if(mobilav ==0){
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);            for(i=1; i<=nlstate;i++)
 #endif              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
 for (i=1; i<= nlstate ; i ++) {            for(i=1; i<=nlstate;i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              prlim[i][i]=mobaverage[(int)age][i][ij];
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }        }
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    
     for (i=1; i<= nlstate ; i ++) {        for(j=1; j<= nlstate; j++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for(h=0; h<=nhstepm; h++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
 }              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          }
      for (i=1; i<= nlstate ; i ++) {        }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        /* This for computing probability of death (h=1 means
   else fprintf(ficgp," \%%*lf (\%%*lf)");           computed over hstepm matrices product = hstepm*stepm months) 
 }             as a weighted average of prlim.
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        */
 #ifdef unix        for(j=nlstate+1;j<=nlstate+ndeath;j++){
 fprintf(ficgp,"\nset ter gif small size 400,300");          for(i=1,gpp[j]=0.; i<= nlstate; i++)
 #endif            gpp[j] += prlim[i][i]*p3mat[i][j][1];
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        }    
    }        /* end probability of death */
   }  
   /*2 eme*/        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
   for (k1=1; k1<= m ; k1 ++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       
     for (i=1; i<= nlstate+1 ; i ++) {        if (popbased==1) {
       k=2*i;          if(mobilav ==0){
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);            for(i=1; i<=nlstate;i++)
       for (j=1; j<= nlstate+1 ; j ++) {              prlim[i][i]=probs[(int)age][i][ij];
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          }else{ /* mobilav */ 
   else fprintf(ficgp," \%%*lf (\%%*lf)");            for(i=1; i<=nlstate;i++)
 }                prlim[i][i]=mobaverage[(int)age][i][ij];
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        }
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {        for(j=1; j<= nlstate; j++){
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          for(h=0; h<=nhstepm; h++){
         else fprintf(ficgp," \%%*lf (\%%*lf)");            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
 }                gm[h][j] += prlim[i][i]*p3mat[i][j][h];
       fprintf(ficgp,"\" t\"\" w l 0,");          }
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        }
       for (j=1; j<= nlstate+1 ; j ++) {        /* This for computing probability of death (h=1 means
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");           computed over hstepm matrices product = hstepm*stepm months) 
   else fprintf(ficgp," \%%*lf (\%%*lf)");           as a weighted average of prlim.
 }          */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       else fprintf(ficgp,"\" t\"\" w l 0,");          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        }    
   }        /* end probability of death */
    
   /*3eme*/        for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
   for (k1=1; k1<= m ; k1 ++) {            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     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);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       for (i=1; i< nlstate ; i ++) {          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         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);        }
       }  
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      } /* End theta */
     }  
   }      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
    
   /* CV preval stat */      for(h=0; h<=nhstepm; h++) /* veij */
   for (k1=1; k1<= m ; k1 ++) {        for(j=1; j<=nlstate;j++)
     for (cpt=1; cpt<nlstate ; cpt ++) {          for(theta=1; theta <=npar; theta++)
       k=3;            trgradg[h][j][theta]=gradg[h][theta][j];
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);  
       for (i=1; i< nlstate ; i ++)      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         fprintf(ficgp,"+$%d",k+i+1);        for(theta=1; theta <=npar; theta++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          trgradgp[j][theta]=gradgp[theta][j];
          
       l=3+(nlstate+ndeath)*cpt;  
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for (i=1; i< nlstate ; i ++) {      for(i=1;i<=nlstate;i++)
         l=3+(nlstate+ndeath)*cpt;        for(j=1;j<=nlstate;j++)
         fprintf(ficgp,"+$%d",l+i+1);          vareij[i][j][(int)age] =0.;
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        for(h=0;h<=nhstepm;h++){
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        for(k=0;k<=nhstepm;k++){
     }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   }            matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
   /* proba elementaires */            for(j=1;j<=nlstate;j++)
    for(i=1,jk=1; i <=nlstate; i++){              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     for(k=1; k <=(nlstate+ndeath); k++){        }
       if (k != i) {      }
         for(j=1; j <=ncovmodel; j++){    
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/      /* pptj */
           /*fprintf(ficgp,"%s",alph[1]);*/      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
           jk++;      for(j=nlstate+1;j<=nlstate+ndeath;j++)
           fprintf(ficgp,"\n");        for(i=nlstate+1;i<=nlstate+ndeath;i++)
         }          varppt[j][i]=doldmp[j][i];
       }      /* end ppptj */
     }      /*  x centered again */
     }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   for(jk=1; jk <=m; jk++) {   
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);      if (popbased==1) {
    i=1;        if(mobilav ==0){
    for(k2=1; k2<=nlstate; k2++) {          for(i=1; i<=nlstate;i++)
      k3=i;            prlim[i][i]=probs[(int)age][i][ij];
      for(k=1; k<=(nlstate+ndeath); k++) {        }else{ /* mobilav */ 
        if (k != k2){          for(i=1; i<=nlstate;i++)
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            prlim[i][i]=mobaverage[(int)age][i][ij];
 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]]]);      /* This for computing probability of death (h=1 means
             ij++;         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           }         as a weighted average of prlim.
           else      */
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           fprintf(ficgp,")/(1");          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
              }    
         for(k1=1; k1 <=nlstate; k1++){        /* end probability of death */
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);  
 ij=1;      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
           for(j=3; j <=ncovmodel; j++){      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        for(i=1; i<=nlstate;i++){
             ij++;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
           }        }
           else      } 
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      fprintf(ficresprobmorprev,"\n");
           }  
           fprintf(ficgp,")");      fprintf(ficresvij,"%.0f ",age );
         }      for(i=1; i<=nlstate;i++)
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        for(j=1; j<=nlstate;j++){
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         i=i+ncovmodel;        }
        }      fprintf(ficresvij,"\n");
      }      free_matrix(gp,0,nhstepm,1,nlstate);
    }      free_matrix(gm,0,nhstepm,1,nlstate);
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   }      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fclose(ficgp);    } /* End age */
   /* end gnuplot */    free_vector(gpp,nlstate+1,nlstate+ndeath);
        free_vector(gmp,nlstate+1,nlstate+ndeath);
 chdir(path);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
        free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     free_ivector(wav,1,imx);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     free_ivector(num,1,n);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     free_vector(agedc,1,n);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
     /*free_matrix(covar,1,NCOVMAX,1,n);*/  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fclose(ficparo);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fclose(ficres);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     /*  }*/    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
        fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
    /*________fin mle=1_________*/    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
        /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
    /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     /* No more information from the sample is required now */    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    free_vector(xp,1,npar);
     ungetc(c,ficpar);    free_matrix(doldm,1,nlstate,1,nlstate);
     fgets(line, MAXLINE, ficpar);    free_matrix(dnewm,1,nlstate,1,npar);
     puts(line);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     fputs(line,ficparo);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   ungetc(c,ficpar);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      fclose(ficresprobmorprev);
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    fflush(ficgp);
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);    fflush(fichtm); 
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  }  /* end varevsij */
 /*--------- index.htm --------*/  
   /************ Variance of prevlim ******************/
   strcpy(optionfilehtm,optionfile);  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)
   strcat(optionfilehtm,".htm");  {
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    /* Variance of prevalence limit */
     printf("Problem with %s \n",optionfilehtm);goto end;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   }    double **newm;
     double **dnewm,**doldm;
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">    int i, j, nhstepm, hstepm;
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    int k, cptcode;
 Total number of observations=%d <br>    double *xp;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>    double *gp, *gm;
 <hr  size=\"2\" color=\"#EC5E5E\">    double **gradg, **trgradg;
 <li>Outputs files<br><br>\n    double age,agelim;
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    int theta;
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>     
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    fprintf(ficresvpl,"# Age");
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    for(i=1; i<=nlstate;i++)
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>        fprintf(ficresvpl," %1d-%1d",i,i);
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    fprintf(ficresvpl,"\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>    xp=vector(1,npar);
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>    dnewm=matrix(1,nlstate,1,npar);
 <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);    doldm=matrix(1,nlstate,1,nlstate);
     
  fprintf(fichtm," <li>Graphs</li><p>");    hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
  m=cptcoveff;    agelim = AGESUP;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
  j1=0;      if (stepm >= YEARM) hstepm=1;
  for(k1=1; k1<=m;k1++){      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
    for(i1=1; i1<=ncodemax[k1];i1++){      gradg=matrix(1,npar,1,nlstate);
        j1++;      gp=vector(1,nlstate);
        if (cptcovn > 0) {      gm=vector(1,nlstate);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  
          for (cpt=1; cpt<=cptcoveff;cpt++)      for(theta=1; theta <=npar; theta++){
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);        for(i=1; i<=npar; i++){ /* Computes gradient */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
        }        }
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            for(i=1;i<=nlstate;i++)
        for(cpt=1; cpt<nlstate;cpt++){          gp[i] = prlim[i][i];
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        for(i=1; i<=npar; i++) /* Computes gradient */
        }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     for(cpt=1; cpt<=nlstate;cpt++) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        for(i=1;i<=nlstate;i++)
 interval) in state (%d): v%s%d%d.gif <br>          gm[i] = prlim[i][i];
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    
      }        for(i=1;i<=nlstate;i++)
      for(cpt=1; cpt<=nlstate;cpt++) {          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      } /* End theta */
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);  
      }      trgradg =matrix(1,nlstate,1,npar);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  
 health expectancies in states (1) and (2): e%s%d.gif<br>      for(j=1; j<=nlstate;j++)
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        for(theta=1; theta <=npar; theta++)
 fprintf(fichtm,"\n</body>");          trgradg[j][theta]=gradg[theta][j];
    }  
  }      for(i=1;i<=nlstate;i++)
 fclose(fichtm);        varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   /*--------------- Prevalence limit --------------*/      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
        for(i=1;i<=nlstate;i++)
   strcpy(filerespl,"pl");        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   strcat(filerespl,fileres);  
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      fprintf(ficresvpl,"%.0f ",age );
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;      for(i=1; i<=nlstate;i++)
   }        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      fprintf(ficresvpl,"\n");
   fprintf(ficrespl,"#Prevalence limit\n");      free_vector(gp,1,nlstate);
   fprintf(ficrespl,"#Age ");      free_vector(gm,1,nlstate);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      free_matrix(gradg,1,npar,1,nlstate);
   fprintf(ficrespl,"\n");      free_matrix(trgradg,1,nlstate,1,npar);
      } /* End age */
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_vector(xp,1,npar);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_matrix(doldm,1,nlstate,1,npar);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_matrix(dnewm,1,nlstate,1,nlstate);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  }
   k=0;  
   agebase=agemin;  /************ Variance of one-step probabilities  ******************/
   agelim=agemax;  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   ftolpl=1.e-10;  {
   i1=cptcoveff;    int i, j=0,  i1, k1, l1, t, tj;
   if (cptcovn < 1){i1=1;}    int k2, l2, j1,  z1;
     int k=0,l, cptcode;
   for(cptcov=1;cptcov<=i1;cptcov++){    int first=1, first1;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
         k=k+1;    double **dnewm,**doldm;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    double *xp;
         fprintf(ficrespl,"\n#******");    double *gp, *gm;
         for(j=1;j<=cptcoveff;j++)    double **gradg, **trgradg;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double **mu;
         fprintf(ficrespl,"******\n");    double age,agelim, cov[NCOVMAX];
            double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
         for (age=agebase; age<=agelim; age++){    int theta;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    char fileresprob[FILENAMELENGTH];
           fprintf(ficrespl,"%.0f",age );    char fileresprobcov[FILENAMELENGTH];
           for(i=1; i<=nlstate;i++)    char fileresprobcor[FILENAMELENGTH];
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");    double ***varpij;
         }  
       }    strcpy(fileresprob,"prob"); 
     }    strcat(fileresprob,fileres);
   fclose(ficrespl);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
   /*------------- h Pij x at various ages ------------*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
      }
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    strcpy(fileresprobcov,"probcov"); 
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    strcat(fileresprobcov,fileres);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprobcov);
   printf("Computing pij: result on file '%s' \n", filerespij);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
      }
   stepsize=(int) (stepm+YEARM-1)/YEARM;    strcpy(fileresprobcor,"probcor"); 
   /*if (stepm<=24) stepsize=2;*/    strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   agelim=AGESUP;      printf("Problem with resultfile: %s\n", fileresprobcor);
   hstepm=stepsize*YEARM; /* Every year of age */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    }
      printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   k=0;    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   for(cptcov=1;cptcov<=i1;cptcov++){    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       k=k+1;    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         fprintf(ficrespij,"\n#****** ");    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         for(j=1;j<=cptcoveff;j++)    
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
         fprintf(ficrespij,"******\n");    fprintf(ficresprob,"# Age");
            fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    fprintf(ficresprobcov,"# Age");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    fprintf(ficresprobcov,"# Age");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      for(i=1; i<=nlstate;i++)
           fprintf(ficrespij,"# Age");      for(j=1; j<=(nlstate+ndeath);j++){
           for(i=1; i<=nlstate;i++)        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
             for(j=1; j<=nlstate+ndeath;j++)        fprintf(ficresprobcov," p%1d-%1d ",i,j);
               fprintf(ficrespij," %1d-%1d",i,j);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
           fprintf(ficrespij,"\n");      }  
           for (h=0; h<=nhstepm; h++){   /* fprintf(ficresprob,"\n");
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    fprintf(ficresprobcov,"\n");
             for(i=1; i<=nlstate;i++)    fprintf(ficresprobcor,"\n");
               for(j=1; j<=nlstate+ndeath;j++)   */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);   xp=vector(1,npar);
             fprintf(ficrespij,"\n");    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           }    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    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;
     }    fprintf(ficgp,"\n# Routine varprob");
   }    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/  
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
   fclose(ficrespij);    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
   if(stepm == 1) {    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   /*---------- Forecasting ------------------*/  and drawn. It helps understanding how is the covariance between two incidences.\
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   /*printf("calage= %f", calagedate);*/  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
    would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   strcpy(fileresf,"f");  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   strcat(fileresf,fileres);  
   if((ficresf=fopen(fileresf,"w"))==NULL) {    cov[1]=1;
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;    tj=cptcoveff;
   }    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   printf("Computing forecasting: result on file '%s' \n", fileresf);    j1=0;
     for(t=1; t<=tj;t++){
   free_matrix(mint,1,maxwav,1,n);      for(i1=1; i1<=ncodemax[t];i1++){ 
   free_matrix(anint,1,maxwav,1,n);        j1++;
   free_matrix(agev,1,maxwav,1,imx);        if  (cptcovn>0) {
   /* Mobile average */          fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
   if (mobilav==1) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          fprintf(ficresprobcov, "**********\n#\n");
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)          
       for (i=1; i<=nlstate;i++)          fprintf(ficgp, "\n#********** Variable "); 
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           mobaverage[(int)agedeb][i][cptcod]=0.;          fprintf(ficgp, "**********\n#\n");
              
     for (agedeb=bage+4; agedeb<=fage; agedeb++){          
       for (i=1; i<=nlstate;i++){          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           for (cpt=0;cpt<=4;cpt++){          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          
           }          fprintf(ficresprobcor, "\n#********** Variable ");    
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         }          fprintf(ficresprobcor, "**********\n#");    
       }        }
     }          
   }        for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for (k=1; k<=cptcovn;k++) {
   if (stepm<=12) stepsize=1;            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
   agelim=AGESUP;          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   /*hstepm=stepsize*YEARM; *//* Every year of age */          for (k=1; k<=cptcovprod;k++)
   hstepm=1;            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */          
   yp1=modf(dateintmean,&yp);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   anprojmean=yp;          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   yp2=modf((yp1*12),&yp);          gp=vector(1,(nlstate)*(nlstate+ndeath));
   mprojmean=yp;          gm=vector(1,(nlstate)*(nlstate+ndeath));
   yp1=modf((yp2*30.5),&yp);      
   jprojmean=yp;          for(theta=1; theta <=npar; theta++){
   if(jprojmean==0) jprojmean=1;            for(i=1; i<=npar; i++)
   if(mprojmean==0) jprojmean=1;              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
   if (popforecast==1) {            k=0;
     if((ficpop=fopen(popfile,"r"))==NULL)    {            for(i=1; i<= (nlstate); i++){
       printf("Problem with population file : %s\n",popfile);goto end;              for(j=1; j<=(nlstate+ndeath);j++){
     }                k=k+1;
     popage=ivector(0,AGESUP);                gp[k]=pmmij[i][j];
     popeffectif=vector(0,AGESUP);              }
     popcount=vector(0,AGESUP);            }
             
     i=1;              for(i=1; i<=npar; i++)
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       {      
         i=i+1;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       }            k=0;
     imx=i;            for(i=1; i<=(nlstate); i++){
                  for(j=1; j<=(nlstate+ndeath);j++){
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];                k=k+1;
   }                gm[k]=pmmij[i][j];
               }
   for(cptcov=1;cptcov<=i1;cptcov++){            }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       
       k=k+1;            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       fprintf(ficresf,"\n#******");              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
       for(j=1;j<=cptcoveff;j++) {          }
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
       fprintf(ficresf,"******\n");            for(theta=1; theta <=npar; theta++)
       fprintf(ficresf,"# StartingAge FinalAge");              trgradg[j][theta]=gradg[theta][j];
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);          
       if (popforecast==1)  fprintf(ficresf," [Population]");          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
              matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
       for (cpt=0; cpt<4;cpt++) {          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         fprintf(ficresf,"\n");          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */  
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          pmij(pmmij,cov,ncovmodel,x,nlstate);
         nhstepm = nhstepm/hstepm;          
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/          k=0;
           for(i=1; i<=(nlstate); i++){
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(j=1; j<=(nlstate+ndeath);j++){
         oldm=oldms;savm=savms;              k=k+1;
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                mu[k][(int) age]=pmmij[i][j];
                    }
         for (h=0; h<=nhstepm; h++){          }
           if (h==(int) (calagedate+YEARM*cpt)) {          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
           }              varpij[i][j][(int)age] = doldm[i][j];
           for(j=1; j<=nlstate+ndeath;j++) {  
             kk1=0.;kk2=0;          /*printf("\n%d ",(int)age);
             for(i=1; i<=nlstate;i++) {                    for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
               if (mobilav==1)            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
               else {            }*/
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/          fprintf(ficresprob,"\n%d ",(int)age);
               }          fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];  
             }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                      fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
             if (h==(int)(calagedate+12*cpt)){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
               fprintf(ficresf," %.3f", kk1);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
                          fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);          }
             }          i=0;
           }          for (k=1; k<=(nlstate);k++){
         }            for (l=1; l<=(nlstate+ndeath);l++){ 
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              i=i++;
       }              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
       }              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     }              for (j=1; j<=i;j++){
   }                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   if (popforecast==1) {              }
     free_ivector(popage,0,AGESUP);            }
     free_vector(popeffectif,0,AGESUP);          }/* end of loop for state */
     free_vector(popcount,0,AGESUP);        } /* end of loop for age */
   }  
   free_imatrix(s,1,maxwav+1,1,n);        /* Confidence intervalle of pij  */
   free_vector(weight,1,n);        /*
   fclose(ficresf);          fprintf(ficgp,"\nset noparametric;unset label");
   }/* End forecasting */          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   else{          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     erreur=108;          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);
     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);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   }          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   /*---------- Health expectancies and variances ------------*/        */
   
   strcpy(filerest,"t");        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   strcat(filerest,fileres);        first1=1;
   if((ficrest=fopen(filerest,"w"))==NULL) {        for (k2=1; k2<=(nlstate);k2++){
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   }            if(l2==k2) continue;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);            j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   strcpy(filerese,"e");                if(l1==k1) continue;
   strcat(filerese,fileres);                i=(k1-1)*(nlstate+ndeath)+l1;
   if((ficreseij=fopen(filerese,"w"))==NULL) {                if(i<=j) continue;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                for (age=bage; age<=fage; age ++){ 
   }                  if ((int)age %5==0){
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
  strcpy(fileresv,"v");                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   strcat(fileresv,fileres);                    mu1=mu[i][(int) age]/stepm*YEARM ;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {                    mu2=mu[j][(int) age]/stepm*YEARM;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);                    c12=cv12/sqrt(v1*v2);
   }                    /* Computing eigen value of matrix of covariance */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   k=0;                    /* Eigen vectors */
   for(cptcov=1;cptcov<=i1;cptcov++){                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    /*v21=sqrt(1.-v11*v11); *//* error */
       k=k+1;                    v21=(lc1-v1)/cv12*v11;
       fprintf(ficrest,"\n#****** ");                    v12=-v21;
       for(j=1;j<=cptcoveff;j++)                    v22=v11;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    tnalp=v21/v11;
       fprintf(ficrest,"******\n");                    if(first1==1){
                       first1=0;
       fprintf(ficreseij,"\n#****** ");                      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);
       for(j=1;j<=cptcoveff;j++)                    }
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
       fprintf(ficreseij,"******\n");                    /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
       fprintf(ficresvij,"\n#****** ");                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
       for(j=1;j<=cptcoveff;j++)                    if(first==1){
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                      first=0;
       fprintf(ficresvij,"******\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);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       oldm=oldms;savm=savms;                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);     :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
       oldm=oldms;savm=savms;                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                            fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
       fprintf(ficrest,"\n");                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                              fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       hf=1;                      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",\
       if (stepm >= YEARM) hf=stepm/YEARM;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       epj=vector(1,nlstate+1);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       for(age=bage; age <=fage ;age++){                    }else{
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                      first=0;
         if (popbased==1) {                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
           for(i=1; i<=nlstate;i++)                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
             prlim[i][i]=probs[(int)age][i][k];                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
         }                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                                      mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
         fprintf(ficrest," %.0f",age);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                    }/* if first */
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                  } /* age mod 5 */
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];                } /* end loop age */
           }                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           epj[nlstate+1] +=epj[j];                first=1;
         }              } /*l12 */
         for(i=1, vepp=0.;i <=nlstate;i++)            } /* k12 */
           for(j=1;j <=nlstate;j++)          } /*l1 */
             vepp += vareij[i][j][(int)age];        }/* k1 */
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));      } /* loop covariates */
         for(j=1;j <=nlstate;j++){    }
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
         }    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
         fprintf(ficrest,"\n");    free_vector(xp,1,npar);
       }    fclose(ficresprob);
     }    fclose(ficresprobcov);
   }    fclose(ficresprobcor);
            fflush(ficgp);
            fflush(fichtmcov);
   }
   
  fclose(ficreseij);  
  fclose(ficresvij);  /******************* Printing html file ***********/
   fclose(ficrest);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   fclose(ficpar);                    int lastpass, int stepm, int weightopt, char model[],\
   free_vector(epj,1,nlstate+1);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   /*  scanf("%d ",i); */                    int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
   /*------- Variance limit prevalence------*/                      double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
 strcpy(fileresvpl,"vpl");  
   strcat(fileresvpl,fileres);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
     exit(0);     fprintf(fichtm,"\
   }   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
  k=0;   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
  for(cptcov=1;cptcov<=i1;cptcov++){             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){     fprintf(fichtm,"\
      k=k+1;   - Life expectancies by age and initial health status (estepm=%2d months): \
      fprintf(ficresvpl,"\n#****** ");     <a href=\"%s\">%s</a> <br>\n</li>",
      for(j=1;j<=cptcoveff;j++)             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
      fprintf(ficresvpl,"******\n");  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
        
      varpl=matrix(1,nlstate,(int) bage, (int) fage);   m=cptcoveff;
      oldm=oldms;savm=savms;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
    }   jj1=0;
  }   for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
   fclose(ficresvpl);       jj1++;
        if (cptcovn > 0) {
   /*---------- End : free ----------------*/         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);         for (cpt=1; cpt<=cptcoveff;cpt++) 
             fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);       }
         /* Pij */
         fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);       /* Quasi-incidences */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
    <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
   free_matrix(matcov,1,npar,1,npar);         /* Stable prevalence in each health state */
   free_vector(delti,1,npar);         for(cpt=1; cpt<nlstate;cpt++){
             fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
   if(erreur >0)       for(cpt=1; cpt<=nlstate;cpt++) {
     printf("End of Imach with error %d\n",erreur);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   else   printf("End of Imach\n");  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */       }
       } /* end i1 */
   /* 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);*/   }/* End k1 */
   /*printf("Total time was %d uSec.\n", total_usecs);*/   fprintf(fichtm,"</ul>");
   /*------ End -----------*/  
   
    fprintf(fichtm,"\
  end:  \n<br><li><h4> Result files (second order: variances)</h4>\n\
 #ifdef windows   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   /* chdir(pathcd);*/  
 #endif   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
  /*system("wgnuplot graph.plt");*/           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
  /*system("../gp37mgw/wgnuplot graph.plt");*/   fprintf(fichtm,"\
  /*system("cd ../gp37mgw");*/   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
  strcpy(plotcmd,GNUPLOTPROGRAM);  
  strcat(plotcmd," ");   fprintf(fichtm,"\
  strcat(plotcmd,optionfilegnuplot);   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
  system(plotcmd);           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
 #ifdef windows   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
   while (z[0] != 'q') {           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
     chdir(path);   fprintf(fichtm,"\
     printf("\nType e to edit output files, c to start again, and q for exiting: ");   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
     scanf("%s",z);           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
     if (z[0] == 'c') system("./imach");   fprintf(fichtm,"\
     else if (z[0] == 'e') {   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
       chdir(path);           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
       system(optionfilehtm);  
     }  /*  if(popforecast==1) fprintf(fichtm,"\n */
     else if (z[0] == 'q') exit(0);  /*  - 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 */
 #endif  /*      <br>",fileres,fileres,fileres,fileres); */
 }  /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        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 (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence 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);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),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);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE]; 
     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;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
    
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){
       j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;
         j++;
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) && (j1 != j)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     }  
     fflush(ficlog);
   
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1-i)*(j1-j)!=0){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         fprintf(ficlog,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
           fprintf(ficlog," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
         fprintf(ficlog,"\n");
       }
     }
     fflush(ficlog);
   
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
         }
         fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       numlinepar++;
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
     fflush(ficlog);
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     globpr=1; /* to print the contributions */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           printf("%d%d ",i,k);
           fprintf(ficlog,"%d%d ",i,k);
           fprintf(ficres,"%1d%1d ",i,k);
           for(j=1; j <=ncovmodel; j++){
             printf("%f ",p[jk]);
             fprintf(ficlog,"%f ",p[jk]);
             fprintf(ficres,"%f ",p[jk]);
             jk++; 
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
     if(mle!=0){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle>=1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
   
   
   /* Just to have a covariance matrix which will be more understandable
      even is we still don't want to manage dictionary of variables
   */
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               if(mle>=1)
                 printf("#%1d%1d%d",i,j,k);
               fprintf(ficlog,"#%1d%1d%d",i,j,k);
               fprintf(ficres,"#%1d%1d%d",i,j,k);
             }else{
               if(mle>=1)
                 printf("%1d%1d%d",i,j,k);
               fprintf(ficlog,"%1d%1d%d",i,j,k);
               fprintf(ficres,"%1d%1d%d",i,j,k);
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         if(mle>=1)
                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         if(mle>=1)
                           printf(" %.5e",matcov[jj][ll]); 
                         fprintf(ficlog," %.5e",matcov[jj][ll]); 
                         fprintf(ficres," %.5e",matcov[jj][ll]); 
                       }
                     }else{
                       if(itimes==1){
                         if(mle>=1)
                           printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         if(mle>=1)
                           printf(" %.5e",matcov[jj][ll]); 
                         fprintf(ficlog," %.5e",matcov[jj][ll]); 
                         fprintf(ficres," %.5e",matcov[jj][ll]); 
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             if(mle>=1)
               printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
     fflush(ficlog);
     fflush(ficres);
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     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);
     for(i=1;i<=AGESUP;i++)
       for(j=1;j<=NCOVMAX;j++)
         for(k=1;k<=NCOVMAX;k++)
           probs[i][j][k]=0.;
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     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 %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocaltime at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
     strcpy(plotcmd,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.1.22  
changed lines
  Added in v.1.97

FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>