Diff for /imach/src/imach.c between versions 1.29 and 1.99

version 1.29, 2002/03/06 19:02:50 version 1.99, 2004/06/05 08:57:40
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.99  2004/06/05 08:57:40  brouard
      *** empty log message ***
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.98  2004/05/16 15:05:56  brouard
   first survey ("cross") where individuals from different ages are    New version 0.97 . First attempt to estimate force of mortality
   interviewed on their health status or degree of disability (in the    directly from the data i.e. without the need of knowing the health
   case of a health survey which is our main interest) -2- at least a    state at each age, but using a Gompertz model: log u =a + b*age .
   second wave of interviews ("longitudinal") which measure each change    This is the basic analysis of mortality and should be done before any
   (if any) in individual health status.  Health expectancies are    other analysis, in order to test if the mortality estimated from the
   computed from the time spent in each health state according to a    cross-longitudinal survey is different from the mortality estimated
   model. More health states you consider, more time is necessary to reach the    from other sources like vital statistic data.
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    The same imach parameter file can be used but the option for mle should be -3.
   probabibility to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Agnès, who wrote this part of the code, tried to keep most of the
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    former routines in order to include the new code within the former code.
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    The output is very simple: only an estimate of the intercept and of
   where the markup *Covariates have to be included here again* invites    the slope with 95% confident intervals.
   you to do it.  More covariates you add, slower the  
   convergence.    Current limitations:
     A) Even if you enter covariates, i.e. with the
   The advantage of this computer programme, compared to a simple    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   multinomial logistic model, is clear when the delay between waves is not    B) There is no computation of Life Expectancy nor Life Table.
   identical for each individual. Also, if a individual missed an  
   intermediate interview, the information is lost, but taken into    Revision 1.97  2004/02/20 13:25:42  lievre
   account using an interpolation or extrapolation.      Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    Revision 1.96  2003/07/15 15:38:55  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   states. This elementary transition (by month or quarter trimester,    rewritten within the same printf. Workaround: many printfs.
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.95  2003/07/08 07:54:34  brouard
   and the contribution of each individual to the likelihood is simply    * imach.c (Repository):
   hPijx.    (Repository): Using imachwizard code to output a more meaningful covariance
     matrix (cov(a12,c31) instead of numbers.
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.94  2003/06/27 13:00:02  brouard
      Just cleaning
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.93  2003/06/25 16:33:55  brouard
   This software have been partly granted by Euro-REVES, a concerted action    (Module): On windows (cygwin) function asctime_r doesn't
   from the European Union.    exist so I changed back to asctime which exists.
   It is copyrighted identically to a GNU software product, ie programme and    (Module): Version 0.96b
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Revision 1.92  2003/06/25 16:30:45  brouard
   **********************************************************************/    (Module): On windows (cygwin) function asctime_r doesn't
      exist so I changed back to asctime which exists.
 #include <math.h>  
 #include <stdio.h>    Revision 1.91  2003/06/25 15:30:29  brouard
 #include <stdlib.h>    * imach.c (Repository): Duplicated warning errors corrected.
 #include <unistd.h>    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
 #define MAXLINE 256    is stamped in powell.  We created a new html file for the graphs
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    concerning matrix of covariance. It has extension -cov.htm.
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.90  2003/06/24 12:34:15  brouard
 #define windows    (Module): Some bugs corrected for windows. Also, when
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    mle=-1 a template is output in file "or"mypar.txt with the design
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    of the covariance matrix to be input.
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.89  2003/06/24 12:30:52  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 #define NINTERVMAX 8    of the covariance matrix to be input.
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.88  2003/06/23 17:54:56  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    * 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.
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.87  2003/06/18 12:26:01  brouard
 #define AGESUP 130    Version 0.96
 #define AGEBASE 40  
     Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
 int erreur; /* Error number */    routine fileappend.
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.85  2003/06/17 13:12:43  brouard
 int npar=NPARMAX;    * imach.c (Repository): Check when date of death was earlier that
 int nlstate=2; /* Number of live states */    current date of interview. It may happen when the death was just
 int ndeath=1; /* Number of dead states */    prior to the death. In this case, dh was negative and likelihood
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    was wrong (infinity). We still send an "Error" but patch by
 int popbased=0;    assuming that the date of death was just one stepm after the
     interview.
 int *wav; /* Number of waves for this individuual 0 is possible */    (Repository): Because some people have very long ID (first column)
 int maxwav; /* Maxim number of waves */    we changed int to long in num[] and we added a new lvector for
 int jmin, jmax; /* min, max spacing between 2 waves */    memory allocation. But we also truncated to 8 characters (left
 int mle, weightopt;    truncation)
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Repository): No more line truncation errors.
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Revision 1.84  2003/06/13 21:44:43  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    * imach.c (Repository): Replace "freqsummary" at a correct
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    place. It differs from routine "prevalence" which may be called
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    many times. Probs is memory consuming and must be used with
 FILE *ficgp,*ficresprob,*ficpop;    parcimony.
 FILE *ficreseij;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.83  2003/06/10 13:39:11  lievre
   char fileresv[FILENAMELENGTH];    *** empty log message ***
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    Revision 1.82  2003/06/05 15:57:20  brouard
     Add log in  imach.c and  fullversion number is now printed.
 #define NR_END 1  
 #define FREE_ARG char*  */
 #define FTOL 1.0e-10  /*
      Interpolated Markov Chain
 #define NRANSI  
 #define ITMAX 200    Short summary of the programme:
     
 #define TOL 2.0e-4    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #define CGOLD 0.3819660    first survey ("cross") where individuals from different ages are
 #define ZEPS 1.0e-10    interviewed on their health status or degree of disability (in the
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    case of a health survey which is our main interest) -2- at least a
     second wave of interviews ("longitudinal") which measure each change
 #define GOLD 1.618034    (if any) in individual health status.  Health expectancies are
 #define GLIMIT 100.0    computed from the time spent in each health state according to a
 #define TINY 1.0e-20    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
 static double maxarg1,maxarg2;    simplest model is the multinomial logistic model where pij is the
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    probability to be observed in state j at the second wave
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    conditional to be observed in state i at the first wave. Therefore
      the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    'age' is age and 'sex' is a covariate. If you want to have a more
 #define rint(a) floor(a+0.5)    complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
 static double sqrarg;    you to do it.  More covariates you add, slower the
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    convergence.
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     The advantage of this computer programme, compared to a simple
 int imx;    multinomial logistic model, is clear when the delay between waves is not
 int stepm;    identical for each individual. Also, if a individual missed an
 /* Stepm, step in month: minimum step interpolation*/    intermediate interview, the information is lost, but taken into
     account using an interpolation or extrapolation.  
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    hPijx is the probability to be observed in state i at age x+h
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    conditional to the observed state i at age x. The delay 'h' can be
 double **pmmij, ***probs, ***mobaverage;    split into an exact number (nh*stepm) of unobserved intermediate
 double dateintmean=0;    states. This elementary transition (by month, quarter,
     semester or year) is modelled as a multinomial logistic.  The hPx
 double *weight;    matrix is simply the matrix product of nh*stepm elementary matrices
 int **s; /* Status */    and the contribution of each individual to the likelihood is simply
 double *agedc, **covar, idx;    hPijx.
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Also this programme outputs the covariance matrix of the parameters but also
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    of the life expectancies. It also computes the stable prevalence. 
 double ftolhess; /* Tolerance for computing hessian */    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 /**************** split *************************/             Institut national d'études démographiques, Paris.
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    This software have been partly granted by Euro-REVES, a concerted action
 {    from the European Union.
    char *s;                             /* pointer */    It is copyrighted identically to a GNU software product, ie programme and
    int  l1, l2;                         /* length counters */    software can be distributed freely for non commercial use. Latest version
     can be accessed at http://euroreves.ined.fr/imach .
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #ifdef windows    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
    s = strrchr( path, '\\' );           /* find last / */    
 #else    **********************************************************************/
    s = strrchr( path, '/' );            /* find last / */  /*
 #endif    main
    if ( s == NULL ) {                   /* no directory, so use current */    read parameterfile
 #if     defined(__bsd__)                /* get current working directory */    read datafile
       extern char       *getwd( );    concatwav
     freqsummary
       if ( getwd( dirc ) == NULL ) {    if (mle >= 1)
 #else      mlikeli
       extern char       *getcwd( );    print results files
     if mle==1 
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {       computes hessian
 #endif    read end of parameter file: agemin, agemax, bage, fage, estepm
          return( GLOCK_ERROR_GETCWD );        begin-prev-date,...
       }    open gnuplot file
       strcpy( name, path );             /* we've got it */    open html file
    } else {                             /* strip direcotry from path */    stable prevalence
       s++;                              /* after this, the filename */     for age prevalim()
       l2 = strlen( s );                 /* length of filename */    h Pij x
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    variance of p varprob
       strcpy( name, s );                /* save file name */    forecasting if prevfcast==1 prevforecast call prevalence()
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    health expectancies
       dirc[l1-l2] = 0;                  /* add zero */    Variance-covariance of DFLE
    }    prevalence()
    l1 = strlen( dirc );                 /* length of directory */     movingaverage()
 #ifdef windows    varevsij() 
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    if popbased==1 varevsij(,popbased)
 #else    total life expectancies
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    Variance of stable prevalence
 #endif   end
    s = strrchr( name, '.' );            /* find last / */  */
    s++;  
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);  
    l2= strlen( s)+1;   
    strncpy( finame, name, l1-l2);  #include <math.h>
    finame[l1-l2]= 0;  #include <stdio.h>
    return( 0 );                         /* we're done */  #include <stdlib.h>
 }  #include <unistd.h>
   
   /* #include <sys/time.h> */
 /******************************************/  #include <time.h>
   #include "timeval.h"
 void replace(char *s, char*t)  
 {  /* #include <libintl.h> */
   int i;  /* #define _(String) gettext (String) */
   int lg=20;  
   i=0;  #define MAXLINE 256
   lg=strlen(t);  #define GNUPLOTPROGRAM "gnuplot"
   for(i=0; i<= lg; i++) {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
     (s[i] = t[i]);  #define FILENAMELENGTH 132
     if (t[i]== '\\') s[i]='/';  /*#define DEBUG*/
   }  /*#define windows*/
 }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 int nbocc(char *s, char occ)  
 {  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   int i,j=0;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   int lg=20;  
   i=0;  #define NINTERVMAX 8
   lg=strlen(s);  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   for(i=0; i<= lg; i++) {  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   if  (s[i] == occ ) j++;  #define NCOVMAX 8 /* Maximum number of covariates */
   }  #define MAXN 20000
   return j;  #define YEARM 12. /* Number of months per year */
 }  #define AGESUP 130
   #define AGEBASE 40
 void cutv(char *u,char *v, char*t, char occ)  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
 {  #ifdef unix
   int i,lg,j,p=0;  #define DIRSEPARATOR '/'
   i=0;  #define ODIRSEPARATOR '\\'
   for(j=0; j<=strlen(t)-1; j++) {  #else
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  #define DIRSEPARATOR '\\'
   }  #define ODIRSEPARATOR '/'
   #endif
   lg=strlen(t);  
   for(j=0; j<p; j++) {  /* $Id$ */
     (u[j] = t[j]);  /* $State$ */
   }  
      u[p]='\0';  char version[]="Imach version 0.97b, May 2004, INED-EUROREVES ";
   char fullversion[]="$Revision$ $Date$"; 
    for(j=0; j<= lg; j++) {  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
     if (j>=(p+1))(v[j-p-1] = t[j]);  int nvar;
   }  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 }  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
 /********************** nrerror ********************/  int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 void nrerror(char error_text[])  int popbased=0;
 {  
   fprintf(stderr,"ERREUR ...\n");  int *wav; /* Number of waves for this individuual 0 is possible */
   fprintf(stderr,"%s\n",error_text);  int maxwav; /* Maxim number of waves */
   exit(1);  int jmin, jmax; /* min, max spacing between 2 waves */
 }  int gipmx, gsw; /* Global variables on the number of contributions 
 /*********************** vector *******************/                     to the likelihood and the sum of weights (done by funcone)*/
 double *vector(int nl, int nh)  int mle, weightopt;
 {  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   double *v;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   if (!v) nrerror("allocation failure in vector");             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   return v-nl+NR_END;  double jmean; /* Mean space between 2 waves */
 }  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 /************************ free vector ******************/  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 void free_vector(double*v, int nl, int nh)  FILE *ficlog, *ficrespow;
 {  int globpr; /* Global variable for printing or not */
   free((FREE_ARG)(v+nl-NR_END));  double fretone; /* Only one call to likelihood */
 }  long ipmx; /* Number of contributions */
   double sw; /* Sum of weights */
 /************************ivector *******************************/  char filerespow[FILENAMELENGTH];
 int *ivector(long nl,long nh)  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 {  FILE *ficresilk;
   int *v;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  FILE *ficresprobmorprev;
   if (!v) nrerror("allocation failure in ivector");  FILE *fichtm, *fichtmcov; /* Html File */
   return v-nl+NR_END;  FILE *ficreseij;
 }  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
 /******************free ivector **************************/  char fileresv[FILENAMELENGTH];
 void free_ivector(int *v, long nl, long nh)  FILE  *ficresvpl;
 {  char fileresvpl[FILENAMELENGTH];
   free((FREE_ARG)(v+nl-NR_END));  char title[MAXLINE];
 }  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 /******************* imatrix *******************************/  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 int **imatrix(long nrl, long nrh, long ncl, long nch)  char command[FILENAMELENGTH];
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  int  outcmd=0;
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   int **m;  
    char filelog[FILENAMELENGTH]; /* Log file */
   /* allocate pointers to rows */  char filerest[FILENAMELENGTH];
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  char fileregp[FILENAMELENGTH];
   if (!m) nrerror("allocation failure 1 in matrix()");  char popfile[FILENAMELENGTH];
   m += NR_END;  
   m -= nrl;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
    
    struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   /* allocate rows and set pointers to them */  struct timezone tzp;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  extern int gettimeofday();
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   m[nrl] += NR_END;  long time_value;
   m[nrl] -= ncl;  extern long time();
    char strcurr[80], strfor[80];
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    #define NR_END 1
   /* return pointer to array of pointers to rows */  #define FREE_ARG char*
   return m;  #define FTOL 1.0e-10
 }  
   #define NRANSI 
 /****************** free_imatrix *************************/  #define ITMAX 200 
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  #define TOL 2.0e-4 
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */  #define CGOLD 0.3819660 
 {  #define ZEPS 1.0e-10 
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   free((FREE_ARG) (m+nrl-NR_END));  
 }  #define GOLD 1.618034 
   #define GLIMIT 100.0 
 /******************* matrix *******************************/  #define TINY 1.0e-20 
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {  static double maxarg1,maxarg2;
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   double **m;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   if (!m) nrerror("allocation failure 1 in matrix()");  #define rint(a) floor(a+0.5)
   m += NR_END;  
   m -= nrl;  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int agegomp= AGEGOMP;
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  int imx; 
   int stepm=1;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /* Stepm, step in month: minimum step interpolation*/
   return m;  
 }  int estepm;
   /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  int m,nb;
 {  long *num;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   free((FREE_ARG)(m+nrl-NR_END));  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 }  double **pmmij, ***probs;
   double *ageexmed,*agecens;
 /******************* ma3x *******************************/  double dateintmean=0;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {  double *weight;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  int **s; /* Status */
   double ***m;  double *agedc, **covar, idx;
   int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   m += NR_END;  double ftolhess; /* Tolerance for computing hessian */
   m -= nrl;  
   /**************** split *************************/
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  {
   m[nrl] += NR_END;    /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
   m[nrl] -= ncl;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     */ 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    char  *ss;                            /* pointer */
     int   l1, l2;                         /* length counters */
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    l1 = strlen(path );                   /* length of path */
   m[nrl][ncl] += NR_END;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   m[nrl][ncl] -= nll;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   for (j=ncl+1; j<=nch; j++)    if ( ss == NULL ) {                   /* no directory, so use current */
     m[nrl][j]=m[nrl][j-1]+nlay;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
          printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   for (i=nrl+1; i<=nrh; i++) {      /* get current working directory */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;      /*    extern  char* getcwd ( char *buf , int len);*/
     for (j=ncl+1; j<=nch; j++)      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       m[i][j]=m[i][j-1]+nlay;        return( GLOCK_ERROR_GETCWD );
   }      }
   return m;      strcpy( name, path );               /* we've got it */
 }    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
 /*************************free ma3x ************************/      l2 = strlen( ss );                  /* length of filename */
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 {      strcpy( name, ss );         /* save file name */
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));      dirc[l1-l2] = 0;                    /* add zero */
   free((FREE_ARG)(m+nrl-NR_END));    }
 }    l1 = strlen( dirc );                  /* length of directory */
     /*#ifdef windows
 /***************** f1dim *************************/    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 extern int ncom;  #else
 extern double *pcom,*xicom;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 extern double (*nrfunc)(double []);  #endif
      */
 double f1dim(double x)    ss = strrchr( name, '.' );            /* find last / */
 {    if (ss >0){
   int j;      ss++;
   double f;      strcpy(ext,ss);                     /* save extension */
   double *xt;      l1= strlen( name);
        l2= strlen(ss)+1;
   xt=vector(1,ncom);      strncpy( finame, name, l1-l2);
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];      finame[l1-l2]= 0;
   f=(*nrfunc)(xt);    }
   free_vector(xt,1,ncom);    return( 0 );                          /* we're done */
   return f;  }
 }  
   
 /*****************brent *************************/  /******************************************/
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {  void replace_back_to_slash(char *s, char*t)
   int iter;  {
   double a,b,d,etemp;    int i;
   double fu,fv,fw,fx;    int lg=0;
   double ftemp;    i=0;
   double p,q,r,tol1,tol2,u,v,w,x,xm;    lg=strlen(t);
   double e=0.0;    for(i=0; i<= lg; i++) {
        (s[i] = t[i]);
   a=(ax < cx ? ax : cx);      if (t[i]== '\\') s[i]='/';
   b=(ax > cx ? ax : cx);    }
   x=w=v=bx;  }
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {  int nbocc(char *s, char occ)
     xm=0.5*(a+b);  {
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    int i,j=0;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    int lg=20;
     printf(".");fflush(stdout);    i=0;
 #ifdef DEBUG    lg=strlen(s);
     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);    for(i=0; i<= lg; i++) {
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    if  (s[i] == occ ) j++;
 #endif    }
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    return j;
       *xmin=x;  }
       return fx;  
     }  void cutv(char *u,char *v, char*t, char occ)
     ftemp=fu;  {
     if (fabs(e) > tol1) {    /* cuts string t into u and v where u is ended by char occ excluding it
       r=(x-w)*(fx-fv);       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
       q=(x-v)*(fx-fw);       gives u="abcedf" and v="ghi2j" */
       p=(x-v)*q-(x-w)*r;    int i,lg,j,p=0;
       q=2.0*(q-r);    i=0;
       if (q > 0.0) p = -p;    for(j=0; j<=strlen(t)-1; j++) {
       q=fabs(q);      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
       etemp=e;    }
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    lg=strlen(t);
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    for(j=0; j<p; j++) {
       else {      (u[j] = t[j]);
         d=p/q;    }
         u=x+d;       u[p]='\0';
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);     for(j=0; j<= lg; j++) {
       }      if (j>=(p+1))(v[j-p-1] = t[j]);
     } else {    }
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  }
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  /********************** nrerror ********************/
     fu=(*f)(u);  
     if (fu <= fx) {  void nrerror(char error_text[])
       if (u >= x) a=x; else b=x;  {
       SHFT(v,w,x,u)    fprintf(stderr,"ERREUR ...\n");
         SHFT(fv,fw,fx,fu)    fprintf(stderr,"%s\n",error_text);
         } else {    exit(EXIT_FAILURE);
           if (u < x) a=u; else b=u;  }
           if (fu <= fw || w == x) {  /*********************** vector *******************/
             v=w;  double *vector(int nl, int nh)
             w=u;  {
             fv=fw;    double *v;
             fw=fu;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
           } else if (fu <= fv || v == x || v == w) {    if (!v) nrerror("allocation failure in vector");
             v=u;    return v-nl+NR_END;
             fv=fu;  }
           }  
         }  /************************ free vector ******************/
   }  void free_vector(double*v, int nl, int nh)
   nrerror("Too many iterations in brent");  {
   *xmin=x;    free((FREE_ARG)(v+nl-NR_END));
   return fx;  }
 }  
   /************************ivector *******************************/
 /****************** mnbrak ***********************/  int *ivector(long nl,long nh)
   {
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    int *v;
             double (*func)(double))    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 {    if (!v) nrerror("allocation failure in ivector");
   double ulim,u,r,q, dum;    return v-nl+NR_END;
   double fu;  }
    
   *fa=(*func)(*ax);  /******************free ivector **************************/
   *fb=(*func)(*bx);  void free_ivector(int *v, long nl, long nh)
   if (*fb > *fa) {  {
     SHFT(dum,*ax,*bx,dum)    free((FREE_ARG)(v+nl-NR_END));
       SHFT(dum,*fb,*fa,dum)  }
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);  /************************lvector *******************************/
   *fc=(*func)(*cx);  long *lvector(long nl,long nh)
   while (*fb > *fc) {  {
     r=(*bx-*ax)*(*fb-*fc);    long *v;
     q=(*bx-*cx)*(*fb-*fa);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    if (!v) nrerror("allocation failure in ivector");
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    return v-nl+NR_END;
     ulim=(*bx)+GLIMIT*(*cx-*bx);  }
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);  /******************free lvector **************************/
     } else if ((*cx-u)*(u-ulim) > 0.0) {  void free_lvector(long *v, long nl, long nh)
       fu=(*func)(u);  {
       if (fu < *fc) {    free((FREE_ARG)(v+nl-NR_END));
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  }
           SHFT(*fb,*fc,fu,(*func)(u))  
           }  /******************* imatrix *******************************/
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       u=ulim;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       fu=(*func)(u);  { 
     } else {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       u=(*cx)+GOLD*(*cx-*bx);    int **m; 
       fu=(*func)(u);    
     }    /* allocate pointers to rows */ 
     SHFT(*ax,*bx,*cx,u)    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       SHFT(*fa,*fb,*fc,fu)    if (!m) nrerror("allocation failure 1 in matrix()"); 
       }    m += NR_END; 
 }    m -= nrl; 
     
 /*************** linmin ************************/    
     /* allocate rows and set pointers to them */ 
 int ncom;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 double *pcom,*xicom;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 double (*nrfunc)(double []);    m[nrl] += NR_END; 
      m[nrl] -= ncl; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    
 {    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   double brent(double ax, double bx, double cx,    
                double (*f)(double), double tol, double *xmin);    /* return pointer to array of pointers to rows */ 
   double f1dim(double x);    return m; 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  } 
               double *fc, double (*func)(double));  
   int j;  /****************** free_imatrix *************************/
   double xx,xmin,bx,ax;  void free_imatrix(m,nrl,nrh,ncl,nch)
   double fx,fb,fa;        int **m;
          long nch,ncl,nrh,nrl; 
   ncom=n;       /* free an int matrix allocated by imatrix() */ 
   pcom=vector(1,n);  { 
   xicom=vector(1,n);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   nrfunc=func;    free((FREE_ARG) (m+nrl-NR_END)); 
   for (j=1;j<=n;j++) {  } 
     pcom[j]=p[j];  
     xicom[j]=xi[j];  /******************* matrix *******************************/
   }  double **matrix(long nrl, long nrh, long ncl, long nch)
   ax=0.0;  {
   xx=1.0;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    double **m;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    if (!m) nrerror("allocation failure 1 in matrix()");
 #endif    m += NR_END;
   for (j=1;j<=n;j++) {    m -= nrl;
     xi[j] *= xmin;  
     p[j] += xi[j];    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   free_vector(xicom,1,n);    m[nrl] += NR_END;
   free_vector(pcom,1,n);    m[nrl] -= ncl;
 }  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 /*************** powell ************************/    return m;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
             double (*func)(double []))     */
 {  }
   void linmin(double p[], double xi[], int n, double *fret,  
               double (*func)(double []));  /*************************free matrix ************************/
   int i,ibig,j;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double del,t,*pt,*ptt,*xit;  {
   double fp,fptt;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double *xits;    free((FREE_ARG)(m+nrl-NR_END));
   pt=vector(1,n);  }
   ptt=vector(1,n);  
   xit=vector(1,n);  /******************* ma3x *******************************/
   xits=vector(1,n);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   *fret=(*func)(p);  {
   for (j=1;j<=n;j++) pt[j]=p[j];    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   for (*iter=1;;++(*iter)) {    double ***m;
     fp=(*fret);  
     ibig=0;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     del=0.0;    if (!m) nrerror("allocation failure 1 in matrix()");
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    m += NR_END;
     for (i=1;i<=n;i++)    m -= nrl;
       printf(" %d %.12f",i, p[i]);  
     printf("\n");    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     for (i=1;i<=n;i++) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    m[nrl] += NR_END;
       fptt=(*fret);    m[nrl] -= ncl;
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 #endif  
       printf("%d",i);fflush(stdout);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       linmin(p,xit,n,fret,func);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       if (fabs(fptt-(*fret)) > del) {    m[nrl][ncl] += NR_END;
         del=fabs(fptt-(*fret));    m[nrl][ncl] -= nll;
         ibig=i;    for (j=ncl+1; j<=nch; j++) 
       }      m[nrl][j]=m[nrl][j-1]+nlay;
 #ifdef DEBUG    
       printf("%d %.12e",i,(*fret));    for (i=nrl+1; i<=nrh; i++) {
       for (j=1;j<=n;j++) {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      for (j=ncl+1; j<=nch; j++) 
         printf(" x(%d)=%.12e",j,xit[j]);        m[i][j]=m[i][j-1]+nlay;
       }    }
       for(j=1;j<=n;j++)    return m; 
         printf(" p=%.12e",p[j]);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       printf("\n");             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 #endif    */
     }  }
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  
 #ifdef DEBUG  /*************************free ma3x ************************/
       int k[2],l;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       k[0]=1;  {
       k[1]=-1;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       printf("Max: %.12e",(*func)(p));    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       for (j=1;j<=n;j++)    free((FREE_ARG)(m+nrl-NR_END));
         printf(" %.12e",p[j]);  }
       printf("\n");  
       for(l=0;l<=1;l++) {  /*************** function subdirf ***********/
         for (j=1;j<=n;j++) {  char *subdirf(char fileres[])
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  {
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    /* Caution optionfilefiname is hidden */
         }    strcpy(tmpout,optionfilefiname);
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    strcat(tmpout,"/"); /* Add to the right */
       }    strcat(tmpout,fileres);
 #endif    return tmpout;
   }
   
       free_vector(xit,1,n);  /*************** function subdirf2 ***********/
       free_vector(xits,1,n);  char *subdirf2(char fileres[], char *preop)
       free_vector(ptt,1,n);  {
       free_vector(pt,1,n);    
       return;    /* Caution optionfilefiname is hidden */
     }    strcpy(tmpout,optionfilefiname);
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    strcat(tmpout,"/");
     for (j=1;j<=n;j++) {    strcat(tmpout,preop);
       ptt[j]=2.0*p[j]-pt[j];    strcat(tmpout,fileres);
       xit[j]=p[j]-pt[j];    return tmpout;
       pt[j]=p[j];  }
     }  
     fptt=(*func)(ptt);  /*************** function subdirf3 ***********/
     if (fptt < fp) {  char *subdirf3(char fileres[], char *preop, char *preop2)
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  {
       if (t < 0.0) {    
         linmin(p,xit,n,fret,func);    /* Caution optionfilefiname is hidden */
         for (j=1;j<=n;j++) {    strcpy(tmpout,optionfilefiname);
           xi[j][ibig]=xi[j][n];    strcat(tmpout,"/");
           xi[j][n]=xit[j];    strcat(tmpout,preop);
         }    strcat(tmpout,preop2);
 #ifdef DEBUG    strcat(tmpout,fileres);
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    return tmpout;
         for(j=1;j<=n;j++)  }
           printf(" %.12e",xit[j]);  
         printf("\n");  /***************** f1dim *************************/
 #endif  extern int ncom; 
       }  extern double *pcom,*xicom;
     }  extern double (*nrfunc)(double []); 
   }   
 }  double f1dim(double x) 
   { 
 /**** Prevalence limit ****************/    int j; 
     double f;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    double *xt; 
 {   
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    xt=vector(1,ncom); 
      matrix by transitions matrix until convergence is reached */    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
   int i, ii,j,k;    free_vector(xt,1,ncom); 
   double min, max, maxmin, maxmax,sumnew=0.;    return f; 
   double **matprod2();  } 
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;  /*****************brent *************************/
   double agefin, delaymax=50 ; /* Max number of years to converge */  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   { 
   for (ii=1;ii<=nlstate+ndeath;ii++)    int iter; 
     for (j=1;j<=nlstate+ndeath;j++){    double a,b,d,etemp;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    double fu,fv,fw,fx;
     }    double ftemp;
     double p,q,r,tol1,tol2,u,v,w,x,xm; 
    cov[1]=1.;    double e=0.0; 
     
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    a=(ax < cx ? ax : cx); 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    b=(ax > cx ? ax : cx); 
     newm=savm;    x=w=v=bx; 
     /* Covariates have to be included here again */    fw=fv=fx=(*f)(x); 
      cov[2]=agefin;    for (iter=1;iter<=ITMAX;iter++) { 
        xm=0.5*(a+b); 
       for (k=1; k<=cptcovn;k++) {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/      printf(".");fflush(stdout);
       }      fprintf(ficlog,".");fflush(ficlog);
       for (k=1; k<=cptcovage;k++)  #ifdef DEBUG
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      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);
       for (k=1; k<=cptcovprod;k++)      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);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   #endif
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        *xmin=x; 
         return fx; 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      } 
       ftemp=fu;
     savm=oldm;      if (fabs(e) > tol1) { 
     oldm=newm;        r=(x-w)*(fx-fv); 
     maxmax=0.;        q=(x-v)*(fx-fw); 
     for(j=1;j<=nlstate;j++){        p=(x-v)*q-(x-w)*r; 
       min=1.;        q=2.0*(q-r); 
       max=0.;        if (q > 0.0) p = -p; 
       for(i=1; i<=nlstate; i++) {        q=fabs(q); 
         sumnew=0;        etemp=e; 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        e=d; 
         prlim[i][j]= newm[i][j]/(1-sumnew);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         max=FMAX(max,prlim[i][j]);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         min=FMIN(min,prlim[i][j]);        else { 
       }          d=p/q; 
       maxmin=max-min;          u=x+d; 
       maxmax=FMAX(maxmax,maxmin);          if (u-a < tol2 || b-u < tol2) 
     }            d=SIGN(tol1,xm-x); 
     if(maxmax < ftolpl){        } 
       return prlim;      } else { 
     }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   }      } 
 }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       fu=(*f)(u); 
 /*************** transition probabilities ***************/      if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        SHFT(v,w,x,u) 
 {          SHFT(fv,fw,fx,fu) 
   double s1, s2;          } else { 
   /*double t34;*/            if (u < x) a=u; else b=u; 
   int i,j,j1, nc, ii, jj;            if (fu <= fw || w == x) { 
               v=w; 
     for(i=1; i<= nlstate; i++){              w=u; 
     for(j=1; j<i;j++){              fv=fw; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){              fw=fu; 
         /*s2 += param[i][j][nc]*cov[nc];*/            } else if (fu <= fv || v == x || v == w) { 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];              v=u; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/              fv=fu; 
       }            } 
       ps[i][j]=s2;          } 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    } 
     }    nrerror("Too many iterations in brent"); 
     for(j=i+1; j<=nlstate+ndeath;j++){    *xmin=x; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    return fx; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  } 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  
       }  /****************** mnbrak ***********************/
       ps[i][j]=s2;  
     }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   }              double (*func)(double)) 
     /*ps[3][2]=1;*/  { 
     double ulim,u,r,q, dum;
   for(i=1; i<= nlstate; i++){    double fu; 
      s1=0;   
     for(j=1; j<i; j++)    *fa=(*func)(*ax); 
       s1+=exp(ps[i][j]);    *fb=(*func)(*bx); 
     for(j=i+1; j<=nlstate+ndeath; j++)    if (*fb > *fa) { 
       s1+=exp(ps[i][j]);      SHFT(dum,*ax,*bx,dum) 
     ps[i][i]=1./(s1+1.);        SHFT(dum,*fb,*fa,dum) 
     for(j=1; j<i; j++)        } 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    *cx=(*bx)+GOLD*(*bx-*ax); 
     for(j=i+1; j<=nlstate+ndeath; j++)    *fc=(*func)(*cx); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    while (*fb > *fc) { 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      r=(*bx-*ax)*(*fb-*fc); 
   } /* end i */      q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     for(jj=1; jj<= nlstate+ndeath; jj++){      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       ps[ii][jj]=0;      if ((*bx-u)*(u-*cx) > 0.0) { 
       ps[ii][ii]=1;        fu=(*func)(u); 
     }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   }        fu=(*func)(u); 
         if (fu < *fc) { 
           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){            SHFT(*fb,*fc,fu,(*func)(u)) 
     for(jj=1; jj<= nlstate+ndeath; jj++){            } 
      printf("%lf ",ps[ii][jj]);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
    }        u=ulim; 
     printf("\n ");        fu=(*func)(u); 
     }      } else { 
     printf("\n ");printf("%lf ",cov[2]);*/        u=(*cx)+GOLD*(*cx-*bx); 
 /*        fu=(*func)(u); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      } 
   goto end;*/      SHFT(*ax,*bx,*cx,u) 
     return ps;        SHFT(*fa,*fb,*fc,fu) 
 }        } 
   } 
 /**************** Product of 2 matrices ******************/  
   /*************** linmin ************************/
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  
 {  int ncom; 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  double *pcom,*xicom;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  double (*nrfunc)(double []); 
   /* in, b, out are matrice of pointers which should have been initialized   
      before: only the contents of out is modified. The function returns  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
      a pointer to pointers identical to out */  { 
   long i, j, k;    double brent(double ax, double bx, double cx, 
   for(i=nrl; i<= nrh; i++)                 double (*f)(double), double tol, double *xmin); 
     for(k=ncolol; k<=ncoloh; k++)    double f1dim(double x); 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         out[i][k] +=in[i][j]*b[j][k];                double *fc, double (*func)(double)); 
     int j; 
   return out;    double xx,xmin,bx,ax; 
 }    double fx,fb,fa;
    
     ncom=n; 
 /************* Higher Matrix Product ***************/    pcom=vector(1,n); 
     xicom=vector(1,n); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    nrfunc=func; 
 {    for (j=1;j<=n;j++) { 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      pcom[j]=p[j]; 
      duration (i.e. until      xicom[j]=xi[j]; 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    } 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    ax=0.0; 
      (typically every 2 years instead of every month which is too big).    xx=1.0; 
      Model is determined by parameters x and covariates have to be    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
      included manually here.    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   #ifdef DEBUG
      */    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   int i, j, d, h, k;  #endif
   double **out, cov[NCOVMAX];    for (j=1;j<=n;j++) { 
   double **newm;      xi[j] *= xmin; 
       p[j] += xi[j]; 
   /* Hstepm could be zero and should return the unit matrix */    } 
   for (i=1;i<=nlstate+ndeath;i++)    free_vector(xicom,1,n); 
     for (j=1;j<=nlstate+ndeath;j++){    free_vector(pcom,1,n); 
       oldm[i][j]=(i==j ? 1.0 : 0.0);  } 
       po[i][j][0]=(i==j ? 1.0 : 0.0);  
     }  char *asc_diff_time(long time_sec, char ascdiff[])
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  {
   for(h=1; h <=nhstepm; h++){    long sec_left, days, hours, minutes;
     for(d=1; d <=hstepm; d++){    days = (time_sec) / (60*60*24);
       newm=savm;    sec_left = (time_sec) % (60*60*24);
       /* Covariates have to be included here again */    hours = (sec_left) / (60*60) ;
       cov[1]=1.;    sec_left = (sec_left) %(60*60);
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    minutes = (sec_left) /60;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    sec_left = (sec_left) % (60);
       for (k=1; k<=cptcovage;k++)    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    return ascdiff;
       for (k=1; k<=cptcovprod;k++)  }
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
   /*************** powell ************************/
   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/              double (*func)(double [])) 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  { 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    void linmin(double p[], double xi[], int n, double *fret, 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));                double (*func)(double [])); 
       savm=oldm;    int i,ibig,j; 
       oldm=newm;    double del,t,*pt,*ptt,*xit;
     }    double fp,fptt;
     for(i=1; i<=nlstate+ndeath; i++)    double *xits;
       for(j=1;j<=nlstate+ndeath;j++) {    int niterf, itmp;
         po[i][j][h]=newm[i][j];  
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    pt=vector(1,n); 
          */    ptt=vector(1,n); 
       }    xit=vector(1,n); 
   } /* end h */    xits=vector(1,n); 
   return po;    *fret=(*func)(p); 
 }    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
 /*************** log-likelihood *************/      ibig=0; 
 double func( double *x)      del=0.0; 
 {      last_time=curr_time;
   int i, ii, j, k, mi, d, kk;      (void) gettimeofday(&curr_time,&tzp);
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      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);
   double **out;      /*    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);
   double sw; /* Sum of weights */      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   double lli; /* Individual log likelihood */      */
   long ipmx;     for (i=1;i<=n;i++) {
   /*extern weight */        printf(" %d %.12f",i, p[i]);
   /* We are differentiating ll according to initial status */        fprintf(ficlog," %d %.12lf",i, p[i]);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        fprintf(ficrespow," %.12lf", p[i]);
   /*for(i=1;i<imx;i++)      }
     printf(" %d\n",s[4][i]);      printf("\n");
   */      fprintf(ficlog,"\n");
   cov[1]=1.;      fprintf(ficrespow,"\n");fflush(ficrespow);
       if(*iter <=3){
   for(k=1; k<=nlstate; k++) ll[k]=0.;        tm = *localtime(&curr_time.tv_sec);
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        strcpy(strcurr,asctime(&tmf));
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  /*       asctime_r(&tm,strcurr); */
     for(mi=1; mi<= wav[i]-1; mi++){        forecast_time=curr_time;
       for (ii=1;ii<=nlstate+ndeath;ii++)        itmp = strlen(strcurr);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        if(strcurr[itmp-1]=='\n')
       for(d=0; d<dh[mi][i]; d++){          strcurr[itmp-1]='\0';
         newm=savm;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         for (kk=1; kk<=cptcovage;kk++) {        for(niterf=10;niterf<=30;niterf+=10){
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];          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); */
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,          strcpy(strfor,asctime(&tmf));
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));          itmp = strlen(strfor);
         savm=oldm;          if(strfor[itmp-1]=='\n')
         oldm=newm;          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);
                  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);
       } /* end mult */        }
            }
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      for (i=1;i<=n;i++) { 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       ipmx +=1;        fptt=(*fret); 
       sw += weight[i];  #ifdef DEBUG
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        printf("fret=%lf \n",*fret);
     } /* end of wave */        fprintf(ficlog,"fret=%lf \n",*fret);
   } /* end of individual */  #endif
         printf("%d",i);fflush(stdout);
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        fprintf(ficlog,"%d",i);fflush(ficlog);
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        linmin(p,xit,n,fret,func); 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        if (fabs(fptt-(*fret)) > del) { 
   return -l;          del=fabs(fptt-(*fret)); 
 }          ibig=i; 
         } 
   #ifdef DEBUG
 /*********** Maximum Likelihood Estimation ***************/        printf("%d %.12e",i,(*fret));
         fprintf(ficlog,"%d %.12e",i,(*fret));
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        for (j=1;j<=n;j++) {
 {          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   int i,j, iter;          printf(" x(%d)=%.12e",j,xit[j]);
   double **xi,*delti;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   double fret;        }
   xi=matrix(1,npar,1,npar);        for(j=1;j<=n;j++) {
   for (i=1;i<=npar;i++)          printf(" p=%.12e",p[j]);
     for (j=1;j<=npar;j++)          fprintf(ficlog," p=%.12e",p[j]);
       xi[i][j]=(i==j ? 1.0 : 0.0);        }
   printf("Powell\n");        printf("\n");
   powell(p,xi,npar,ftol,&iter,&fret,func);        fprintf(ficlog,"\n");
   #endif
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      } 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   #ifdef DEBUG
 }        int k[2],l;
         k[0]=1;
 /**** Computes Hessian and covariance matrix ***/        k[1]=-1;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        printf("Max: %.12e",(*func)(p));
 {        fprintf(ficlog,"Max: %.12e",(*func)(p));
   double  **a,**y,*x,pd;        for (j=1;j<=n;j++) {
   double **hess;          printf(" %.12e",p[j]);
   int i, j,jk;          fprintf(ficlog," %.12e",p[j]);
   int *indx;        }
         printf("\n");
   double hessii(double p[], double delta, int theta, double delti[]);        fprintf(ficlog,"\n");
   double hessij(double p[], double delti[], int i, int j);        for(l=0;l<=1;l++) {
   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) ;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
             printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   hess=matrix(1,npar,1,npar);            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("\nCalculation of the hessian matrix. Wait...\n");          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   for (i=1;i<=npar;i++){          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     printf("%d",i);fflush(stdout);        }
     hess[i][i]=hessii(p,ftolhess,i,delti);  #endif
     /*printf(" %f ",p[i]);*/  
     /*printf(" %lf ",hess[i][i]);*/  
   }        free_vector(xit,1,n); 
          free_vector(xits,1,n); 
   for (i=1;i<=npar;i++) {        free_vector(ptt,1,n); 
     for (j=1;j<=npar;j++)  {        free_vector(pt,1,n); 
       if (j>i) {        return; 
         printf(".%d%d",i,j);fflush(stdout);      } 
         hess[i][j]=hessij(p,delti,i,j);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
         hess[j][i]=hess[i][j];          for (j=1;j<=n;j++) { 
         /*printf(" %lf ",hess[i][j]);*/        ptt[j]=2.0*p[j]-pt[j]; 
       }        xit[j]=p[j]-pt[j]; 
     }        pt[j]=p[j]; 
   }      } 
   printf("\n");      fptt=(*func)(ptt); 
       if (fptt < fp) { 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
          if (t < 0.0) { 
   a=matrix(1,npar,1,npar);          linmin(p,xit,n,fret,func); 
   y=matrix(1,npar,1,npar);          for (j=1;j<=n;j++) { 
   x=vector(1,npar);            xi[j][ibig]=xi[j][n]; 
   indx=ivector(1,npar);            xi[j][n]=xit[j]; 
   for (i=1;i<=npar;i++)          }
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  #ifdef DEBUG
   ludcmp(a,npar,indx,&pd);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   for (j=1;j<=npar;j++) {          for(j=1;j<=n;j++){
     for (i=1;i<=npar;i++) x[i]=0;            printf(" %.12e",xit[j]);
     x[j]=1;            fprintf(ficlog," %.12e",xit[j]);
     lubksb(a,npar,indx,x);          }
     for (i=1;i<=npar;i++){          printf("\n");
       matcov[i][j]=x[i];          fprintf(ficlog,"\n");
     }  #endif
   }        }
       } 
   printf("\n#Hessian matrix#\n");    } 
   for (i=1;i<=npar;i++) {  } 
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);  /**** Prevalence limit (stable prevalence)  ****************/
     }  
     printf("\n");  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   }  {
     /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   /* Recompute Inverse */       matrix by transitions matrix until convergence is reached */
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    int i, ii,j,k;
   ludcmp(a,npar,indx,&pd);    double min, max, maxmin, maxmax,sumnew=0.;
     double **matprod2();
   /*  printf("\n#Hessian matrix recomputed#\n");    double **out, cov[NCOVMAX], **pmij();
     double **newm;
   for (j=1;j<=npar;j++) {    double agefin, delaymax=50 ; /* Max number of years to converge */
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;    for (ii=1;ii<=nlstate+ndeath;ii++)
     lubksb(a,npar,indx,x);      for (j=1;j<=nlstate+ndeath;j++){
     for (i=1;i<=npar;i++){        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       y[i][j]=x[i];      }
       printf("%.3e ",y[i][j]);  
     }     cov[1]=1.;
     printf("\n");   
   }   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   */    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       newm=savm;
   free_matrix(a,1,npar,1,npar);      /* Covariates have to be included here again */
   free_matrix(y,1,npar,1,npar);       cov[2]=agefin;
   free_vector(x,1,npar);    
   free_ivector(indx,1,npar);        for (k=1; k<=cptcovn;k++) {
   free_matrix(hess,1,npar,1,npar);          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];
         for (k=1; k<=cptcovprod;k++)
 /*************** hessian matrix ****************/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 double hessii( double x[], double delta, int theta, double delti[])  
 {        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   int i;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   int l=1, lmax=20;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   double k1,k2;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   double p2[NPARMAX+1];  
   double res;      savm=oldm;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      oldm=newm;
   double fx;      maxmax=0.;
   int k=0,kmax=10;      for(j=1;j<=nlstate;j++){
   double l1;        min=1.;
         max=0.;
   fx=func(x);        for(i=1; i<=nlstate; i++) {
   for (i=1;i<=npar;i++) p2[i]=x[i];          sumnew=0;
   for(l=0 ; l <=lmax; l++){          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     l1=pow(10,l);          prlim[i][j]= newm[i][j]/(1-sumnew);
     delts=delt;          max=FMAX(max,prlim[i][j]);
     for(k=1 ; k <kmax; k=k+1){          min=FMIN(min,prlim[i][j]);
       delt = delta*(l1*k);        }
       p2[theta]=x[theta] +delt;        maxmin=max-min;
       k1=func(p2)-fx;        maxmax=FMAX(maxmax,maxmin);
       p2[theta]=x[theta]-delt;      }
       k2=func(p2)-fx;      if(maxmax < ftolpl){
       /*res= (k1-2.0*fx+k2)/delt/delt; */        return prlim;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      }
          }
 #ifdef DEBUG  }
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  
 #endif  /*************** transition probabilities ***************/ 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         k=kmax;  {
       }    double s1, s2;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    /*double t34;*/
         k=kmax; l=lmax*10.;    int i,j,j1, nc, ii, jj;
       }  
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      for(i=1; i<= nlstate; i++){
         delts=delt;        for(j=1; j<i;j++){
       }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     }            /*s2 += param[i][j][nc]*cov[nc];*/
   }            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   delti[theta]=delts;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
   return res;          }
            ps[i][j]=s2;
 }  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
         }
 double hessij( double x[], double delti[], int thetai,int thetaj)        for(j=i+1; j<=nlstate+ndeath;j++){
 {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   int i;            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   int l=1, l1, lmax=20;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
   double k1,k2,k3,k4,res,fx;          }
   double p2[NPARMAX+1];          ps[i][j]=s2;
   int k;        }
       }
   fx=func(x);      /*ps[3][2]=1;*/
   for (k=1; k<=2; k++) {      
     for (i=1;i<=npar;i++) p2[i]=x[i];      for(i=1; i<= nlstate; i++){
     p2[thetai]=x[thetai]+delti[thetai]/k;        s1=0;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        for(j=1; j<i; j++)
     k1=func(p2)-fx;          s1+=exp(ps[i][j]);
          for(j=i+1; j<=nlstate+ndeath; j++)
     p2[thetai]=x[thetai]+delti[thetai]/k;          s1+=exp(ps[i][j]);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        ps[i][i]=1./(s1+1.);
     k2=func(p2)-fx;        for(j=1; j<i; j++)
            ps[i][j]= exp(ps[i][j])*ps[i][i];
     p2[thetai]=x[thetai]-delti[thetai]/k;        for(j=i+1; j<=nlstate+ndeath; j++)
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          ps[i][j]= exp(ps[i][j])*ps[i][i];
     k3=func(p2)-fx;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
        } /* end i */
     p2[thetai]=x[thetai]-delti[thetai]/k;      
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     k4=func(p2)-fx;        for(jj=1; jj<= nlstate+ndeath; jj++){
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          ps[ii][jj]=0;
 #ifdef DEBUG          ps[ii][ii]=1;
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        }
 #endif      }
   }      
   return res;  
 }  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
 /************** Inverse of matrix **************/  /*         printf("ddd %lf ",ps[ii][jj]); */
 void ludcmp(double **a, int n, int *indx, double *d)  /*       } */
 {  /*       printf("\n "); */
   int i,imax,j,k;  /*        } */
   double big,dum,sum,temp;  /*        printf("\n ");printf("%lf ",cov[2]); */
   double *vv;         /*
          for(i=1; i<= npar; i++) printf("%f ",x[i]);
   vv=vector(1,n);        goto end;*/
   *d=1.0;      return ps;
   for (i=1;i<=n;i++) {  }
     big=0.0;  
     for (j=1;j<=n;j++)  /**************** Product of 2 matrices ******************/
       if ((temp=fabs(a[i][j])) > big) big=temp;  
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     vv[i]=1.0/big;  {
   }    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   for (j=1;j<=n;j++) {       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     for (i=1;i<j;i++) {    /* in, b, out are matrice of pointers which should have been initialized 
       sum=a[i][j];       before: only the contents of out is modified. The function returns
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];       a pointer to pointers identical to out */
       a[i][j]=sum;    long i, j, k;
     }    for(i=nrl; i<= nrh; i++)
     big=0.0;      for(k=ncolol; k<=ncoloh; k++)
     for (i=j;i<=n;i++) {        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       sum=a[i][j];          out[i][k] +=in[i][j]*b[j][k];
       for (k=1;k<j;k++)  
         sum -= a[i][k]*a[k][j];    return out;
       a[i][j]=sum;  }
       if ( (dum=vv[i]*fabs(sum)) >= big) {  
         big=dum;  
         imax=i;  /************* 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 )
     if (j != imax) {  {
       for (k=1;k<=n;k++) {    /* Computes the transition matrix starting at age 'age' over 
         dum=a[imax][k];       'nhstepm*hstepm*stepm' months (i.e. until
         a[imax][k]=a[j][k];       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         a[j][k]=dum;       nhstepm*hstepm matrices. 
       }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       *d = -(*d);       (typically every 2 years instead of every month which is too big 
       vv[imax]=vv[j];       for the memory).
     }       Model is determined by parameters x and covariates have to be 
     indx[j]=imax;       included manually here. 
     if (a[j][j] == 0.0) a[j][j]=TINY;  
     if (j != n) {       */
       dum=1.0/(a[j][j]);  
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    int i, j, d, h, k;
     }    double **out, cov[NCOVMAX];
   }    double **newm;
   free_vector(vv,1,n);  /* Doesn't work */  
 ;    /* Hstepm could be zero and should return the unit matrix */
 }    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
 void lubksb(double **a, int n, int *indx, double b[])        oldm[i][j]=(i==j ? 1.0 : 0.0);
 {        po[i][j][0]=(i==j ? 1.0 : 0.0);
   int i,ii=0,ip,j;      }
   double sum;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
      for(h=1; h <=nhstepm; h++){
   for (i=1;i<=n;i++) {      for(d=1; d <=hstepm; d++){
     ip=indx[i];        newm=savm;
     sum=b[ip];        /* Covariates have to be included here again */
     b[ip]=b[i];        cov[1]=1.;
     if (ii)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     else if (sum) ii=i;        for (k=1; k<=cptcovage;k++)
     b[i]=sum;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   }        for (k=1; k<=cptcovprod;k++)
   for (i=n;i>=1;i--) {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     sum=b[i];  
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  
     b[i]=sum/a[i][i];        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
 }        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
 /************ Frequencies ********************/        savm=oldm;
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)        oldm=newm;
 {  /* Some frequencies */      }
        for(i=1; i<=nlstate+ndeath; i++)
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        for(j=1;j<=nlstate+ndeath;j++) {
   double ***freq; /* Frequencies */          po[i][j][h]=newm[i][j];
   double *pp;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   double pos, k2, dateintsum=0,k2cpt=0;           */
   FILE *ficresp;        }
   char fileresp[FILENAMELENGTH];    } /* end h */
      return po;
   pp=vector(1,nlstate);  }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   strcpy(fileresp,"p");  
   strcat(fileresp,fileres);  /*************** log-likelihood *************/
   if((ficresp=fopen(fileresp,"w"))==NULL) {  double func( double *x)
     printf("Problem with prevalence resultfile: %s\n", fileresp);  {
     exit(0);    int i, ii, j, k, mi, d, kk;
   }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    double **out;
   j1=0;    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
   j=cptcoveff;    int s1, s2;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    double bbh, survp;
     long ipmx;
   for(k1=1; k1<=j;k1++){    /*extern weight */
    for(i1=1; i1<=ncodemax[k1];i1++){    /* We are differentiating ll according to initial status */
        j1++;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    /*for(i=1;i<imx;i++) 
          scanf("%d", i);*/      printf(" %d\n",s[4][i]);
         for (i=-1; i<=nlstate+ndeath; i++)      */
          for (jk=-1; jk<=nlstate+ndeath; jk++)      cov[1]=1.;
            for(m=agemin; m <= agemax+3; m++)  
              freq[i][jk][m]=0;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
         dateintsum=0;    if(mle==1){
         k2cpt=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
        for (i=1; i<=imx; i++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          bool=1;        for(mi=1; mi<= wav[i]-1; mi++){
          if  (cptcovn>0) {          for (ii=1;ii<=nlstate+ndeath;ii++)
            for (z1=1; z1<=cptcoveff; z1++)            for (j=1;j<=nlstate+ndeath;j++){
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                bool=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
          }            }
          if (bool==1) {          for(d=0; d<dh[mi][i]; d++){
            for(m=firstpass; m<=lastpass; m++){            newm=savm;
              k2=anint[m][i]+(mint[m][i]/12.);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              if ((k2>=dateprev1) && (k2<=dateprev2)) {            for (kk=1; kk<=cptcovage;kk++) {
                if(agev[m][i]==0) agev[m][i]=agemax+1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                if(agev[m][i]==1) agev[m][i]=agemax+2;            }
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {            savm=oldm;
                  dateintsum=dateintsum+k2;            oldm=newm;
                  k2cpt++;          } /* end mult */
                }        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
              }          /* But now since version 0.9 we anticipate for bias and large stepm.
            }           * 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 
        }           * the nearest (and in case of equal distance, to the lowest) interval but now
                   * we keep into memory the bias bh[mi][i] and also the previous matrix product
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
         if  (cptcovn>0) {           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
          fprintf(ficresp, "\n#********** Variable ");           * -stepm/2 to stepm/2 .
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);           * For stepm=1 the results are the same as for previous versions of Imach.
        fprintf(ficresp, "**********\n#");           * For stepm > 1 the results are less biased than in previous versions. 
         }           */
        for(i=1; i<=nlstate;i++)          s1=s[mw[mi][i]][i];
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          s2=s[mw[mi+1][i]][i];
        fprintf(ficresp, "\n");          bbh=(double)bh[mi][i]/(double)stepm; 
                  /* bias is positive if real duration
   for(i=(int)agemin; i <= (int)agemax+3; i++){           * is higher than the multiple of stepm and negative otherwise.
     if(i==(int)agemax+3)           */
       printf("Total");          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     else          if( s2 > nlstate){ 
       printf("Age %d", i);            /* i.e. if s2 is a death state and if the date of death is known then the contribution
     for(jk=1; jk <=nlstate ; jk++){               to the likelihood is the probability to die between last step unit time and current 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)               step unit time, which is also the differences between probability to die before dh 
         pp[jk] += freq[jk][m][i];               and probability to die before dh-stepm . 
     }               In version up to 0.92 likelihood was computed
     for(jk=1; jk <=nlstate ; jk++){          as if date of death was unknown. Death was treated as any other
       for(m=-1, pos=0; m <=0 ; m++)          health state: the date of the interview describes the actual state
         pos += freq[jk][m][i];          and not the date of a change in health state. The former idea was
       if(pp[jk]>=1.e-10)          to consider that at each interview the state was recorded
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          (healthy, disable or death) and IMaCh was corrected; but when we
       else          introduced the exact date of death then we should have modified
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          the contribution of an exact death to the likelihood. This new
     }          contribution is smaller and very dependent of the step unit
           stepm. It is no more the probability to die between last interview
      for(jk=1; jk <=nlstate ; jk++){          and month of death but the probability to survive from last
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          interview up to one month before death multiplied by the
         pp[jk] += freq[jk][m][i];          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
     for(jk=1,pos=0; jk <=nlstate ; jk++)          which slows down the processing. The difference can be up to 10%
       pos += pp[jk];          lower mortality.
     for(jk=1; jk <=nlstate ; jk++){            */
       if(pos>=1.e-5)            lli=log(out[s1][s2] - savm[s1][s2]);
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          }else{
       else            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            /*  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( i <= (int) agemax){          } 
         if(pos>=1.e-5){          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          /*if(lli ==000.0)*/
           probs[i][jk][j1]= pp[jk]/pos;          /*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("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          ipmx +=1;
         }          sw += weight[i];
       else          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        } /* end of wave */
       }      } /* end of individual */
     }    }  else if(mle==2){
     for(jk=-1; jk <=nlstate+ndeath; jk++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(m=-1; m <=nlstate+ndeath; m++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        for(mi=1; mi<= wav[i]-1; mi++){
     if(i <= (int) agemax)          for (ii=1;ii<=nlstate+ndeath;ii++)
       fprintf(ficresp,"\n");            for (j=1;j<=nlstate+ndeath;j++){
     printf("\n");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     }            }
  }          for(d=0; d<=dh[mi][i]; d++){
   dateintmean=dateintsum/k2cpt;            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fclose(ficresp);            for (kk=1; kk<=cptcovage;kk++) {
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   free_vector(pp,1,nlstate);            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* End of Freq */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }            savm=oldm;
             oldm=newm;
 /************ Prevalence ********************/          } /* end mult */
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)        
 {  /* Some frequencies */          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          bbh=(double)bh[mi][i]/(double)stepm; 
   double ***freq; /* Frequencies */          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   double *pp;          ipmx +=1;
   double pos, k2;          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   pp=vector(1,nlstate);        } /* end of wave */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      } /* end of individual */
      }  else if(mle==3){  /* exponential inter-extrapolation */
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   j1=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
   j=cptcoveff;          for (ii=1;ii<=nlstate+ndeath;ii++)
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  for(k1=1; k1<=j;k1++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i1=1; i1<=ncodemax[k1];i1++){            }
       j1++;          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
       for (i=-1; i<=nlstate+ndeath; i++)              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for (jk=-1; jk<=nlstate+ndeath; jk++)              for (kk=1; kk<=cptcovage;kk++) {
           for(m=agemin; m <= agemax+3; m++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             freq[i][jk][m]=0;            }
                  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for (i=1; i<=imx; i++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         bool=1;            savm=oldm;
         if  (cptcovn>0) {            oldm=newm;
           for (z1=1; z1<=cptcoveff; z1++)          } /* end mult */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        
               bool=0;          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
         if (bool==1) {          bbh=(double)bh[mi][i]/(double)stepm; 
           for(m=firstpass; m<=lastpass; m++){          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 */
             k2=anint[m][i]+(mint[m][i]/12.);          ipmx +=1;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          sw += weight[i];
               if(agev[m][i]==0) agev[m][i]=agemax+1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
               if(agev[m][i]==1) agev[m][i]=agemax+2;        } /* end of wave */
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];      } /* end of individual */
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */    }else if (mle==4){  /* ml=4 no inter-extrapolation */
             }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
         for(i=(int)agemin; i <= (int)agemax+3; i++){            for (j=1;j<=nlstate+ndeath;j++){
           for(jk=1; jk <=nlstate ; jk++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
               pp[jk] += freq[jk][m][i];            }
           }          for(d=0; d<dh[mi][i]; d++){
           for(jk=1; jk <=nlstate ; jk++){            newm=savm;
             for(m=-1, pos=0; m <=0 ; m++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             pos += freq[jk][m][i];            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                    }
          for(jk=1; jk <=nlstate ; jk++){          
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
              pp[jk] += freq[jk][m][i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
          }            savm=oldm;
                      oldm=newm;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          } /* end mult */
         
          for(jk=1; jk <=nlstate ; jk++){                    s1=s[mw[mi][i]][i];
            if( i <= (int) agemax){          s2=s[mw[mi+1][i]][i];
              if(pos>=1.e-5){          if( s2 > nlstate){ 
                probs[i][jk][j1]= pp[jk]/pos;            lli=log(out[s1][s2] - savm[s1][s2]);
              }          }else{
            }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
          }          }
                    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 */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   free_vector(pp,1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 }  /* End of Freq */        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
 /************* Waves Concatenation ***************/            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 {            }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          for(d=0; d<dh[mi][i]; d++){
      Death is a valid wave (if date is known).            newm=savm;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            for (kk=1; kk<=cptcovage;kk++) {
      and mw[mi+1][i]. dh depends on stepm.              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      */            }
           
   int i, mi, m;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      double sum=0., jmean=0.;*/            savm=oldm;
             oldm=newm;
   int j, k=0,jk, ju, jl;          } /* end mult */
   double sum=0.;        
   jmin=1e+5;          s1=s[mw[mi][i]][i];
   jmax=-1;          s2=s[mw[mi+1][i]][i];
   jmean=0.;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   for(i=1; i<=imx; i++){          ipmx +=1;
     mi=0;          sw += weight[i];
     m=firstpass;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     while(s[m][i] <= nlstate){          /*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(s[m][i]>=1)        } /* end of wave */
         mw[++mi][i]=m;      } /* end of individual */
       if(m >=lastpass)    } /* End of if */
         break;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       else    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         m++;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     }/* end while */    return -l;
     if (s[m][i] > nlstate){  }
       mi++;     /* Death is another wave */  
       /* if(mi==0)  never been interviewed correctly before death */  /*************** log-likelihood *************/
          /* Only death is a correct wave */  double funcone( double *x)
       mw[mi][i]=m;  {
     }    /* Same as likeli but slower because of a lot of printf and if */
     int i, ii, j, k, mi, d, kk;
     wav[i]=mi;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     if(mi==0)    double **out;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    double lli; /* Individual log likelihood */
   }    double llt;
     int s1, s2;
   for(i=1; i<=imx; i++){    double bbh, survp;
     for(mi=1; mi<wav[i];mi++){    /*extern weight */
       if (stepm <=0)    /* We are differentiating ll according to initial status */
         dh[mi][i]=1;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       else{    /*for(i=1;i<imx;i++) 
         if (s[mw[mi+1][i]][i] > nlstate) {      printf(" %d\n",s[4][i]);
           if (agedc[i] < 2*AGESUP) {    */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    cov[1]=1.;
           if(j==0) j=1;  /* Survives at least one month after exam */  
           k=k+1;    for(k=1; k<=nlstate; k++) ll[k]=0.;
           if (j >= jmax) jmax=j;  
           if (j <= jmin) jmin=j;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           sum=sum+j;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           /* if (j<10) printf("j=%d num=%d ",j,i); */      for(mi=1; mi<= wav[i]-1; mi++){
           }        for (ii=1;ii<=nlstate+ndeath;ii++)
         }          for (j=1;j<=nlstate+ndeath;j++){
         else{            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           k=k+1;          }
           if (j >= jmax) jmax=j;        for(d=0; d<dh[mi][i]; d++){
           else if (j <= jmin)jmin=j;          newm=savm;
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           sum=sum+j;          for (kk=1; kk<=cptcovage;kk++) {
         }            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         jk= j/stepm;          }
         jl= j -jk*stepm;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         ju= j -(jk+1)*stepm;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if(jl <= -ju)          savm=oldm;
           dh[mi][i]=jk;          oldm=newm;
         else        } /* end mult */
           dh[mi][i]=jk+1;        
         if(dh[mi][i]==0)        s1=s[mw[mi][i]][i];
           dh[mi][i]=1; /* At least one step */        s2=s[mw[mi+1][i]][i];
       }        bbh=(double)bh[mi][i]/(double)stepm; 
     }        /* bias is positive if real duration
   }         * is higher than the multiple of stepm and negative otherwise.
   jmean=sum/k;         */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        if( s2 > nlstate && (mle <5) ){  /* Jackson */
  }          lli=log(out[s1][s2] - savm[s1][s2]);
 /*********** Tricode ****************************/        } else if (mle==1){
 void tricode(int *Tvar, int **nbcode, int imx)          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 {        } else if(mle==2){
   int Ndum[20],ij=1, k, j, 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 */
   int cptcode=0;        } else if(mle==3){  /* exponential inter-extrapolation */
   cptcoveff=0;          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
          } else if (mle==4){  /* mle=4 no inter-extrapolation */
   for (k=0; k<19; k++) Ndum[k]=0;          lli=log(out[s1][s2]); /* Original formula */
   for (k=1; k<=7; k++) ncodemax[k]=0;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
           lli=log(out[s1][s2]); /* Original formula */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        } /* End of if */
     for (i=1; i<=imx; i++) {        ipmx +=1;
       ij=(int)(covar[Tvar[j]][i]);        sw += weight[i];
       Ndum[ij]++;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  /*       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 (ij > cptcode) cptcode=ij;        if(globpr){
     }          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
    %10.6f %10.6f %10.6f ", \
     for (i=0; i<=cptcode; i++) {                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       if(Ndum[i]!=0) ncodemax[j]++;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     ij=1;            llt +=ll[k]*gipmx/gsw;
             fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
     for (i=1; i<=ncodemax[j]; i++) {          fprintf(ficresilk," %10.6f\n", -llt);
       for (k=0; k<=19; k++) {        }
         if (Ndum[k] != 0) {      } /* end of wave */
           nbcode[Tvar[j]][ij]=k;    } /* end of individual */
           ij++;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         if (ij > ncodemax[j]) break;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       }      if(globpr==0){ /* First time we count the contributions and weights */
     }      gipmx=ipmx;
   }        gsw=sw;
     }
  for (k=0; k<19; k++) Ndum[k]=0;    return -l;
   }
  for (i=1; i<=ncovmodel-2; i++) {  
       ij=Tvar[i];  
       Ndum[ij]++;  /*************** function likelione ***********/
     }  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   {
  ij=1;    /* This routine should help understanding what is done with 
  for (i=1; i<=10; i++) {       the selection of individuals/waves and
    if((Ndum[i]!=0) && (i<=ncov)){       to check the exact contribution to the likelihood.
      Tvaraff[ij]=i;       Plotting could be done.
      ij++;     */
    }    int k;
  }  
      if(*globpri !=0){ /* Just counts and sums, no printings */
     cptcoveff=ij-1;      strcpy(fileresilk,"ilk"); 
 }      strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
 /*********** Health Expectancies ****************/        printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)      }
 {      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");
   /* Health expectancies */      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   int i, j, nhstepm, hstepm, h;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   double age, agelim,hf;      for(k=1; k<=nlstate; k++) 
   double ***p3mat;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
        fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   fprintf(ficreseij,"# Health expectancies\n");    }
   fprintf(ficreseij,"# Age");  
   for(i=1; i<=nlstate;i++)    *fretone=(*funcone)(p);
     for(j=1; j<=nlstate;j++)    if(*globpri !=0){
       fprintf(ficreseij," %1d-%1d",i,j);      fclose(ficresilk);
   fprintf(ficreseij,"\n");      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       fflush(fichtm); 
   hstepm=1*YEARM; /*  Every j years of age (in month) */    } 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    return;
   }
   agelim=AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     /* nhstepm age range expressed in number of stepm */  /*********** Maximum Likelihood Estimation ***************/
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years = 20*12/6=40 stepm */  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     if (stepm >= YEARM) hstepm=1;  {
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */    int i,j, iter;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **xi;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    double fret;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    double fretone; /* Only one call to likelihood */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      /*  char filerespow[FILENAMELENGTH];*/
     xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
     for(i=1; i<=nlstate;i++)      for (j=1;j<=npar;j++)
       for(j=1; j<=nlstate;j++)        xi[i][j]=(i==j ? 1.0 : 0.0);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    printf("Powell\n");  fprintf(ficlog,"Powell\n");
           eij[i][j][(int)age] +=(p3mat[i][j][h]+p3mat[i][j][h+1])/2.0;    strcpy(filerespow,"pow"); 
         }    strcat(filerespow,fileres);
        if((ficrespow=fopen(filerespow,"w"))==NULL) {
     hf=1;      printf("Problem with resultfile: %s\n", filerespow);
     if (stepm >= YEARM) hf=stepm/YEARM;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
     for(i=1; i<=nlstate;i++)    fprintf(ficrespow,"# Powell\n# iter -2*LL");
       for(j=1; j<=nlstate;j++){    for (i=1;i<=nlstate;i++)
         if (j==i) eij[i][j][(int)age]= (eij[i][j][(int)age]-0.5*stepm/12./hf);      for(j=1;j<=nlstate+ndeath;j++)
         }        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     fprintf(ficrespow,"\n");
     fprintf(ficreseij,"%3.0f",age );  
     for(i=1; i<=nlstate;i++)    powell(p,xi,npar,ftol,&iter,&fret,func);
       for(j=1; j<=nlstate;j++){  
         fprintf(ficreseij," %9.4f", hf*eij[i][j][(int)age]);    fclose(ficrespow);
       }    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     fprintf(ficreseij,"\n");    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   }  
 }  }
   
 /************ Variance ******************/  /**** Computes Hessian and covariance matrix ***/
 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)  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
 {  {
   /* Variance of health expectancies */    double  **a,**y,*x,pd;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    double **hess;
   double **newm;    int i, j,jk;
   double **dnewm,**doldm;    int *indx;
   int i, j, nhstepm, hstepm, h;  
   int k, cptcode;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   double *xp;    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   double **gp, **gm;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   double ***gradg, ***trgradg;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   double ***p3mat;    double gompertz(double p[]);
   double age,agelim;    hess=matrix(1,npar,1,npar);
   int theta;  
     printf("\nCalculation of the hessian matrix. Wait...\n");
    fprintf(ficresvij,"# Covariances of life expectancies\n");    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   fprintf(ficresvij,"# 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(ficresvij," Cov(e%1d, e%1d)",i,j);     
   fprintf(ficresvij,"\n");       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       
   xp=vector(1,npar);      /*  printf(" %f ",p[i]);
   dnewm=matrix(1,nlstate,1,npar);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   doldm=matrix(1,nlstate,1,nlstate);    }
      
   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 */      for (j=1;j<=npar;j++)  {
   agelim = AGESUP;        if (j>i) { 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          printf(".%d%d",i,j);fflush(stdout);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     if (stepm >= YEARM) hstepm=1;          hess[i][j]=hessij(p,delti,i,j,func,npar);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          hess[j][i]=hess[i][j];    
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          /*printf(" %lf ",hess[i][j]);*/
     gp=matrix(0,nhstepm,1,nlstate);        }
     gm=matrix(0,nhstepm,1,nlstate);      }
     }
     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);  
       }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    
     a=matrix(1,npar,1,npar);
       if (popbased==1) {    y=matrix(1,npar,1,npar);
         for(i=1; i<=nlstate;i++)    x=vector(1,npar);
           prlim[i][i]=probs[(int)age][i][ij];    indx=ivector(1,npar);
       }    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       for(j=1; j<= nlstate; j++){    ludcmp(a,npar,indx,&pd);
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    for (j=1;j<=npar;j++) {
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      for (i=1;i<=npar;i++) x[i]=0;
         }      x[j]=1;
       }      lubksb(a,npar,indx,x);
          for (i=1;i<=npar;i++){ 
       for(i=1; i<=npar; i++) /* Computes gradient */        matcov[i][j]=x[i];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
      printf("\n#Hessian matrix#\n");
       if (popbased==1) {    fprintf(ficlog,"\n#Hessian matrix#\n");
         for(i=1; i<=nlstate;i++)    for (i=1;i<=npar;i++) { 
           prlim[i][i]=probs[(int)age][i][ij];      for (j=1;j<=npar;j++) { 
       }        printf("%.3e ",hess[i][j]);
         fprintf(ficlog,"%.3e ",hess[i][j]);
       for(j=1; j<= nlstate; j++){      }
         for(h=0; h<=nhstepm; h++){      printf("\n");
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      fprintf(ficlog,"\n");
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    }
         }  
       }    /* Recompute Inverse */
     for (i=1;i<=npar;i++)
       for(j=1; j<= nlstate; j++)      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         for(h=0; h<=nhstepm; h++){    ludcmp(a,npar,indx,&pd);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  
         }    /*  printf("\n#Hessian matrix recomputed#\n");
     } /* End theta */  
     for (j=1;j<=npar;j++) {
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
     for(h=0; h<=nhstepm; h++)      lubksb(a,npar,indx,x);
       for(j=1; j<=nlstate;j++)      for (i=1;i<=npar;i++){ 
         for(theta=1; theta <=npar; theta++)        y[i][j]=x[i];
           trgradg[h][j][theta]=gradg[h][theta][j];        printf("%.3e ",y[i][j]);
         fprintf(ficlog,"%.3e ",y[i][j]);
     for(i=1;i<=nlstate;i++)      }
       for(j=1;j<=nlstate;j++)      printf("\n");
         vareij[i][j][(int)age] =0.;      fprintf(ficlog,"\n");
     for(h=0;h<=nhstepm;h++){    }
       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]);    free_matrix(a,1,npar,1,npar);
         for(i=1;i<=nlstate;i++)    free_matrix(y,1,npar,1,npar);
           for(j=1;j<=nlstate;j++)    free_vector(x,1,npar);
             vareij[i][j][(int)age] += doldm[i][j];    free_ivector(indx,1,npar);
       }    free_matrix(hess,1,npar,1,npar);
     }  
     h=1;  
     if (stepm >= YEARM) h=stepm/YEARM;  }
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)  /*************** hessian matrix ****************/
       for(j=1; j<=nlstate;j++){  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);  {
       }    int i;
     fprintf(ficresvij,"\n");    int l=1, lmax=20;
     free_matrix(gp,0,nhstepm,1,nlstate);    double k1,k2;
     free_matrix(gm,0,nhstepm,1,nlstate);    double p2[NPARMAX+1];
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    double res;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double fx;
   } /* End age */    int k=0,kmax=10;
      double l1;
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);    fx=func(x);
   free_matrix(dnewm,1,nlstate,1,nlstate);    for (i=1;i<=npar;i++) p2[i]=x[i];
     for(l=0 ; l <=lmax; l++){
 }      l1=pow(10,l);
       delts=delt;
 /************ Variance of prevlim ******************/      for(k=1 ; k <kmax; k=k+1){
 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)        delt = delta*(l1*k);
 {        p2[theta]=x[theta] +delt;
   /* Variance of prevalence limit */        k1=func(p2)-fx;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        p2[theta]=x[theta]-delt;
   double **newm;        k2=func(p2)-fx;
   double **dnewm,**doldm;        /*res= (k1-2.0*fx+k2)/delt/delt; */
   int i, j, nhstepm, hstepm;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   int k, cptcode;        
   double *xp;  #ifdef DEBUG
   double *gp, *gm;        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   double **gradg, **trgradg;        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);
   double age,agelim;  #endif
   int theta;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
            if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          k=kmax;
   fprintf(ficresvpl,"# Age");        }
   for(i=1; i<=nlstate;i++)        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       fprintf(ficresvpl," %1d-%1d",i,i);          k=kmax; l=lmax*10.;
   fprintf(ficresvpl,"\n");        }
         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   xp=vector(1,npar);          delts=delt;
   dnewm=matrix(1,nlstate,1,npar);        }
   doldm=matrix(1,nlstate,1,nlstate);      }
      }
   hstepm=1*YEARM; /* Every year of age */    delti[theta]=delts;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    return res; 
   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;  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  {
     gradg=matrix(1,npar,1,nlstate);    int i;
     gp=vector(1,nlstate);    int l=1, l1, lmax=20;
     gm=vector(1,nlstate);    double k1,k2,k3,k4,res,fx;
     double p2[NPARMAX+1];
     for(theta=1; theta <=npar; theta++){    int k;
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    fx=func(x);
       }    for (k=1; k<=2; k++) {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      for (i=1;i<=npar;i++) p2[i]=x[i];
       for(i=1;i<=nlstate;i++)      p2[thetai]=x[thetai]+delti[thetai]/k;
         gp[i] = prlim[i][i];      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
          k1=func(p2)-fx;
       for(i=1; i<=npar; i++) /* Computes gradient */    
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      p2[thetai]=x[thetai]+delti[thetai]/k;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       for(i=1;i<=nlstate;i++)      k2=func(p2)-fx;
         gm[i] = prlim[i][i];    
       p2[thetai]=x[thetai]-delti[thetai]/k;
       for(i=1;i<=nlstate;i++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      k3=func(p2)-fx;
     } /* End theta */    
       p2[thetai]=x[thetai]-delti[thetai]/k;
     trgradg =matrix(1,nlstate,1,npar);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k4=func(p2)-fx;
     for(j=1; j<=nlstate;j++)      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       for(theta=1; theta <=npar; theta++)  #ifdef DEBUG
         trgradg[j][theta]=gradg[theta][j];      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     for(i=1;i<=nlstate;i++)  #endif
       varpl[i][(int)age] =0.;    }
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    return res;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  }
     for(i=1;i<=nlstate;i++)  
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
     fprintf(ficresvpl,"%.0f ",age );  { 
     for(i=1; i<=nlstate;i++)    int i,imax,j,k; 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    double big,dum,sum,temp; 
     fprintf(ficresvpl,"\n");    double *vv; 
     free_vector(gp,1,nlstate);   
     free_vector(gm,1,nlstate);    vv=vector(1,n); 
     free_matrix(gradg,1,npar,1,nlstate);    *d=1.0; 
     free_matrix(trgradg,1,nlstate,1,npar);    for (i=1;i<=n;i++) { 
   } /* End age */      big=0.0; 
       for (j=1;j<=n;j++) 
   free_vector(xp,1,npar);        if ((temp=fabs(a[i][j])) > big) big=temp; 
   free_matrix(doldm,1,nlstate,1,npar);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   free_matrix(dnewm,1,nlstate,1,nlstate);      vv[i]=1.0/big; 
     } 
 }    for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
 /************ Variance of one-step probabilities  ******************/        sum=a[i][j]; 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
 {        a[i][j]=sum; 
   int i, j;      } 
   int k=0, cptcode;      big=0.0; 
   double **dnewm,**doldm;      for (i=j;i<=n;i++) { 
   double *xp;        sum=a[i][j]; 
   double *gp, *gm;        for (k=1;k<j;k++) 
   double **gradg, **trgradg;          sum -= a[i][k]*a[k][j]; 
   double age,agelim, cov[NCOVMAX];        a[i][j]=sum; 
   int theta;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   char fileresprob[FILENAMELENGTH];          big=dum; 
           imax=i; 
   strcpy(fileresprob,"prob");        } 
   strcat(fileresprob,fileres);      } 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      if (j != imax) { 
     printf("Problem with resultfile: %s\n", fileresprob);        for (k=1;k<=n;k++) { 
   }          dum=a[imax][k]; 
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);          a[imax][k]=a[j][k]; 
            a[j][k]=dum; 
         } 
   xp=vector(1,npar);        *d = -(*d); 
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        vv[imax]=vv[j]; 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      } 
        indx[j]=imax; 
   cov[1]=1;      if (a[j][j] == 0.0) a[j][j]=TINY; 
   for (age=bage; age<=fage; age ++){      if (j != n) { 
     cov[2]=age;        dum=1.0/(a[j][j]); 
     gradg=matrix(1,npar,1,9);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     trgradg=matrix(1,9,1,npar);      } 
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    } 
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    free_vector(vv,1,n);  /* Doesn't work */
      ;
     for(theta=1; theta <=npar; theta++){  } 
       for(i=1; i<=npar; i++)  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  void lubksb(double **a, int n, int *indx, double b[]) 
        { 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    int i,ii=0,ip,j; 
        double sum; 
       k=0;   
       for(i=1; i<= (nlstate+ndeath); i++){    for (i=1;i<=n;i++) { 
         for(j=1; j<=(nlstate+ndeath);j++){      ip=indx[i]; 
            k=k+1;      sum=b[ip]; 
           gp[k]=pmmij[i][j];      b[ip]=b[i]; 
         }      if (ii) 
       }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else if (sum) ii=i; 
       for(i=1; i<=npar; i++)      b[i]=sum; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    } 
        for (i=n;i>=1;i--) { 
       sum=b[i]; 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       k=0;      b[i]=sum/a[i][i]; 
       for(i=1; i<=(nlstate+ndeath); i++){    } 
         for(j=1; j<=(nlstate+ndeath);j++){  } 
           k=k+1;  
           gm[k]=pmmij[i][j];  /************ Frequencies ********************/
         }  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)
       }  {  /* Some frequencies */
          
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      int first;
     }    double ***freq; /* Frequencies */
     double *pp, **prop;
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       for(theta=1; theta <=npar; theta++)    FILE *ficresp;
       trgradg[j][theta]=gradg[theta][j];    char fileresp[FILENAMELENGTH];
      
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    pp=vector(1,nlstate);
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
      pmij(pmmij,cov,ncovmodel,x,nlstate);    strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
      k=0;      printf("Problem with prevalence resultfile: %s\n", fileresp);
      for(i=1; i<=(nlstate+ndeath); i++){      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
        for(j=1; j<=(nlstate+ndeath);j++){      exit(0);
          k=k+1;    }
          gm[k]=pmmij[i][j];    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
         }    j1=0;
      }    
          j=cptcoveff;
      /*printf("\n%d ",(int)age);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  
            first=1;
   
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    for(k1=1; k1<=j;k1++){
      }*/      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
   fprintf(ficresprob,"\n%d ",(int)age);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           scanf("%d", i);*/
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        for (i=-1; i<=nlstate+ndeath; i++)  
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);            for(m=iagemin; m <= iagemax+3; m++)
   }              freq[i][jk][m]=0;
   
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      for (i=1; i<=nlstate; i++)  
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        for(m=iagemin; m <= iagemax+3; m++)
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          prop[i][m]=0;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        
 }        dateintsum=0;
  free_vector(xp,1,npar);        k2cpt=0;
 fclose(ficresprob);        for (i=1; i<=imx; i++) {
           bool=1;
 }          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
 /******************* Printing html file ***********/              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){                bool=0;
   int jj1, k1, i1, cpt;          }
   FILE *fichtm;          if (bool==1){
   /*char optionfilehtm[FILENAMELENGTH];*/            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
   strcpy(optionfilehtm,optionfile);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   strcat(optionfilehtm,".htm");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     printf("Problem with %s \n",optionfilehtm), exit(0);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   }                if (m<lastpass) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71 </font> <hr size=\"2\" color=\"#EC5E5E\">                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>                }
                 
 Total number of observations=%d <br>                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>                  dateintsum=dateintsum+k2;
 <hr  size=\"2\" color=\"#EC5E5E\">                  k2cpt++;
 <li>Outputs files<br><br>\n                }
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n                /*}*/
 - 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>          }
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>        }
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>         
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>  
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>        if  (cptcovn>0) {
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>          fprintf(ficresp, "\n#********** Variable "); 
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>          fprintf(ficresp, "**********\n#");
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);        }
          for(i=1; i<=nlstate;i++) 
 fprintf(fichtm," <li>Graphs</li><p>");          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficresp, "\n");
  m=cptcoveff;        
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        for(i=iagemin; i <= iagemax+3; i++){
           if(i==iagemax+3){
  jj1=0;            fprintf(ficlog,"Total");
  for(k1=1; k1<=m;k1++){          }else{
    for(i1=1; i1<=ncodemax[k1];i1++){            if(first==1){
        jj1++;              first=0;
        if (cptcovn > 0) {              printf("See log file for details...\n");
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");            }
          for (cpt=1; cpt<=cptcoveff;cpt++)            fprintf(ficlog,"Age %d", i);
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);          }
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          for(jk=1; jk <=nlstate ; jk++){
        }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>              pp[jk] += freq[jk][m][i]; 
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              }
        for(cpt=1; cpt<nlstate;cpt++){          for(jk=1; jk <=nlstate ; jk++){
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>            for(m=-1, pos=0; m <=0 ; m++)
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              pos += freq[jk][m][i];
        }            if(pp[jk]>=1.e-10){
     for(cpt=1; cpt<=nlstate;cpt++) {              if(first==1){
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 interval) in state (%d): v%s%d%d.gif <br>              }
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
      }            }else{
      for(cpt=1; cpt<=nlstate;cpt++) {              if(first==1)
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
      }            }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          }
 health expectancies in states (1) and (2): e%s%d.gif<br>  
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          for(jk=1; jk <=nlstate ; jk++){
 fprintf(fichtm,"\n</body>");            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
    }              pp[jk] += freq[jk][m][i];
    }          }       
 fclose(fichtm);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
 }            pos += pp[jk];
             posprop += prop[jk][i];
 /******************* Gnuplot file **************/          }
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   strcpy(optionfilegnuplot,optionfilefiname);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   strcat(optionfilegnuplot,".plt");            }else{
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {              if(first==1)
     printf("Problem with file %s",optionfilegnuplot);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
 #ifdef windows            if( i <= iagemax){
     fprintf(ficgp,"cd \"%s\" \n",pathc);              if(pos>=1.e-5){
 #endif                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
 m=pow(2,cptcoveff);                /*probs[i][jk][j1]= pp[jk]/pos;*/
                  /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
  /* 1eme*/              }
   for (cpt=1; cpt<= nlstate ; cpt ++) {              else
    for (k1=1; k1<= m ; k1 ++) {                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
 #ifdef windows          }
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);          
 #endif          for(jk=-1; jk <=nlstate+ndeath; jk++)
 #ifdef unix            for(m=-1; m <=nlstate+ndeath; m++)
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);              if(freq[jk][m][i] !=0 ) {
 #endif              if(first==1)
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
 for (i=1; i<= nlstate ; i ++) {                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              }
   else fprintf(ficgp," \%%*lf (\%%*lf)");          if(i <= iagemax)
 }            fprintf(ficresp,"\n");
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          if(first==1)
     for (i=1; i<= nlstate ; i ++) {            printf("Others in log...\n");
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(ficlog,"\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }      }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    }
      for (i=1; i<= nlstate ; i ++) {    dateintmean=dateintsum/k2cpt; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");   
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fclose(ficresp);
 }      free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    free_vector(pp,1,nlstate);
 #ifdef unix    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
 fprintf(ficgp,"\nset ter gif small size 400,300");    /* End of Freq */
 #endif  }
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
    }  /************ 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)
   /*2 eme*/  {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   for (k1=1; k1<= m ; k1 ++) {       in each health status at the date of interview (if between dateprev1 and dateprev2).
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);       We still use firstpass and lastpass as another selection.
        */
     for (i=1; i<= nlstate+1 ; i ++) {   
       k=2*i;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    double ***freq; /* Frequencies */
       for (j=1; j<= nlstate+1 ; j ++) {    double *pp, **prop;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double pos,posprop; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double  y2; /* in fractional years */
 }      int iagemin, iagemax;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");  
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    iagemin= (int) agemin;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    iagemax= (int) agemax;
       for (j=1; j<= nlstate+1 ; j ++) {    /*pp=vector(1,nlstate);*/
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    prop=matrix(1,nlstate,iagemin,iagemax+3); 
         else fprintf(ficgp," \%%*lf (\%%*lf)");    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
 }      j1=0;
       fprintf(ficgp,"\" t\"\" w l 0,");    
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    j=cptcoveff;
       for (j=1; j<= nlstate+1 ; j ++) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for(k1=1; k1<=j;k1++){
 }        for(i1=1; i1<=ncodemax[k1];i1++){
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        j1++;
       else fprintf(ficgp,"\" t\"\" w l 0,");        
     }        for (i=1; i<=nlstate; i++)  
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          for(m=iagemin; m <= iagemax+3; m++)
   }            prop[i][m]=0.0;
         
   /*3eme*/        for (i=1; i<=imx; i++) { /* Each individual */
           bool=1;
   for (k1=1; k1<= m ; k1 ++) {          if  (cptcovn>0) {
     for (cpt=1; cpt<= nlstate ; cpt ++) {            for (z1=1; z1<=cptcoveff; z1++) 
       k=2+nlstate*(cpt-1);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       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);                bool=0;
       for (i=1; i< nlstate ; i ++) {          } 
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);          if (bool==1) { 
       }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     }              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                  if(agev[m][i]==1) agev[m][i]=iagemax+2;
   /* CV preval stat */                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
     for (k1=1; k1<= m ; k1 ++) {                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     for (cpt=1; cpt<nlstate ; cpt ++) {                  /*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]]);*/
       k=3;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);                  prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
       for (i=1; i< nlstate ; i ++)              }
         fprintf(ficgp,"+$%d",k+i+1);            } /* end selection of waves */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          }
              }
       l=3+(nlstate+ndeath)*cpt;        for(i=iagemin; i <= iagemax+3; i++){  
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          
       for (i=1; i< nlstate ; i ++) {          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         l=3+(nlstate+ndeath)*cpt;            posprop += prop[jk][i]; 
         fprintf(ficgp,"+$%d",l+i+1);          } 
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            for(jk=1; jk <=nlstate ; jk++){     
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            if( i <=  iagemax){ 
     }              if(posprop>=1.e-5){ 
   }                  probs[i][jk][j1]= prop[jk][i]/posprop;
                } 
   /* proba elementaires */            } 
    for(i=1,jk=1; i <=nlstate; i++){          }/* end jk */ 
     for(k=1; k <=(nlstate+ndeath); k++){        }/* end i */ 
       if (k != i) {      } /* end i1 */
         for(j=1; j <=ncovmodel; j++){    } /* end k1 */
            
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
           jk++;    /*free_vector(pp,1,nlstate);*/
           fprintf(ficgp,"\n");    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
         }  }  /* End of prevalence */
       }  
     }  /************* Waves Concatenation ***************/
     }  
   void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
     for(jk=1; jk <=m; jk++) {  {
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
    i=1;       Death is a valid wave (if date is known).
    for(k2=1; k2<=nlstate; k2++) {       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
      k3=i;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
      for(k=1; k<=(nlstate+ndeath); k++) {       and mw[mi+1][i]. dh depends on stepm.
        if (k != k2){       */
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  
 ij=1;    int i, mi, m;
         for(j=3; j <=ncovmodel; j++) {    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {       double sum=0., jmean=0.;*/
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    int first;
             ij++;    int j, k=0,jk, ju, jl;
           }    double sum=0.;
           else    first=0;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    jmin=1e+5;
         }    jmax=-1;
           fprintf(ficgp,")/(1");    jmean=0.;
            for(i=1; i<=imx; i++){
         for(k1=1; k1 <=nlstate; k1++){        mi=0;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      m=firstpass;
 ij=1;      while(s[m][i] <= nlstate){
           for(j=3; j <=ncovmodel; j++){        if(s[m][i]>=1)
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          mw[++mi][i]=m;
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        if(m >=lastpass)
             ij++;          break;
           }        else
           else          m++;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      }/* end while */
           }      if (s[m][i] > nlstate){
           fprintf(ficgp,")");        mi++;     /* Death is another wave */
         }        /* if(mi==0)  never been interviewed correctly before death */
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);           /* Only death is a correct wave */
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        mw[mi][i]=m;
         i=i+ncovmodel;      }
        }  
      }      wav[i]=mi;
    }      if(mi==0){
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        nbwarn++;
    }        if(first==0){
              printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   fclose(ficgp);          first=1;
 }  /* end gnuplot */        }
         if(first==1){
           fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
 /*************** Moving average **************/        }
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){      } /* end mi==0 */
     } /* End individuals */
   int i, cpt, cptcod;  
     for (agedeb=agemin; agedeb<=fage; agedeb++)    for(i=1; i<=imx; i++){
       for (i=1; i<=nlstate;i++)      for(mi=1; mi<wav[i];mi++){
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        if (stepm <=0)
           mobaverage[(int)agedeb][i][cptcod]=0.;          dh[mi][i]=1;
            else{
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       for (i=1; i<=nlstate;i++){            if (agedc[i] < 2*AGESUP) {
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
           for (cpt=0;cpt<=4;cpt++){              if(j==0) j=1;  /* Survives at least one month after exam */
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];              else if(j<0){
           }                nberr++;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;                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 */
       }                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);
     }                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);
 }              }
               k=k+1;
               if (j >= jmax) jmax=j;
 /************** Forecasting ******************/              if (j <= jmin) jmin=j;
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){              sum=sum+j;
                /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   int *popage;            }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          }
   double *popeffectif,*popcount;          else{
   double ***p3mat;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   char fileresf[FILENAMELENGTH];            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             k=k+1;
  agelim=AGESUP;            if (j >= jmax) jmax=j;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;            else if (j <= jmin)jmin=j;
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
              if(j<0){
                nberr++;
   strcpy(fileresf,"f");              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]);
   strcat(fileresf,fileres);              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]);
   if((ficresf=fopen(fileresf,"w"))==NULL) {            }
     printf("Problem with forecast resultfile: %s\n", fileresf);            sum=sum+j;
   }          }
   printf("Computing forecasting: result on file '%s' \n", fileresf);          jk= j/stepm;
           jl= j -jk*stepm;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          ju= j -(jk+1)*stepm;
           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   if (mobilav==1) {            if(jl==0){
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              dh[mi][i]=jk;
     movingaverage(agedeb, fage, agemin, mobaverage);              bh[mi][i]=0;
   }            }else{ /* We want a negative bias in order to only have interpolation ie
                     * at the price of an extra matrix product in likelihood */
   stepsize=(int) (stepm+YEARM-1)/YEARM;              dh[mi][i]=jk+1;
   if (stepm<=12) stepsize=1;              bh[mi][i]=ju;
              }
   agelim=AGESUP;          }else{
              if(jl <= -ju){
   hstepm=1;              dh[mi][i]=jk;
   hstepm=hstepm/stepm;              bh[mi][i]=jl;       /* bias is positive if real duration
   yp1=modf(dateintmean,&yp);                                   * is higher than the multiple of stepm and negative otherwise.
   anprojmean=yp;                                   */
   yp2=modf((yp1*12),&yp);            }
   mprojmean=yp;            else{
   yp1=modf((yp2*30.5),&yp);              dh[mi][i]=jk+1;
   jprojmean=yp;              bh[mi][i]=ju;
   if(jprojmean==0) jprojmean=1;            }
   if(mprojmean==0) jprojmean=1;            if(dh[mi][i]==0){
                dh[mi][i]=1; /* At least one step */
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);              bh[mi][i]=ju; /* At least one step */
                /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
   for(cptcov=1;cptcov<=i2;cptcov++){            }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          } /* end if mle */
       k=k+1;        }
       fprintf(ficresf,"\n#******");      } /* end wave */
       for(j=1;j<=cptcoveff;j++) {    }
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    jmean=sum/k;
       }    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       fprintf(ficresf,"******\n");    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       fprintf(ficresf,"# StartingAge FinalAge");   }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  
        /*********** Tricode ****************************/
        void tricode(int *Tvar, int **nbcode, int imx)
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {  {
         fprintf(ficresf,"\n");    
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      int Ndum[20],ij=1, k, j, i, maxncov=19;
     int cptcode=0;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){    cptcoveff=0; 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);   
           nhstepm = nhstepm/hstepm;    for (k=0; k<maxncov; k++) Ndum[k]=0;
              for (k=1; k<=7; k++) ncodemax[k]=0;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                         modality*/ 
           for (h=0; h<=nhstepm; h++){        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
             if (h==(int) (calagedate+YEARM*cpt)) {        Ndum[ij]++; /*store the modality */
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
             }        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
             for(j=1; j<=nlstate+ndeath;j++) {                                         Tvar[j]. If V=sex and male is 0 and 
               kk1=0.;kk2=0;                                         female is 1, then  cptcode=1.*/
               for(i=1; i<=nlstate;i++) {                    }
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      for (i=0; i<=cptcode; i++) {
                 else {        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 */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      }
                 }  
                      ij=1; 
               }      for (i=1; i<=ncodemax[j]; i++) {
               if (h==(int)(calagedate+12*cpt)){        for (k=0; k<= maxncov; k++) {
                 fprintf(ficresf," %.3f", kk1);          if (Ndum[k] != 0) {
                                    nbcode[Tvar[j]][ij]=k; 
               }            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
             }            
           }            ij++;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
         }          if (ij > ncodemax[j]) break; 
       }        }  
     }      } 
   }    }  
          
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   for (k=0; k< maxncov; k++) Ndum[k]=0;
   
   fclose(ficresf);   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.*/
 /************** Forecasting ******************/     ij=Tvar[i];
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){     Ndum[ij]++;
     }
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  
   int *popage;   ij=1;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;   for (i=1; i<= maxncov; i++) {
   double *popeffectif,*popcount;     if((Ndum[i]!=0) && (i<=ncovcol)){
   double ***p3mat,***tabpop,***tabpopprev;       Tvaraff[ij]=i; /*For printing */
   char filerespop[FILENAMELENGTH];       ij++;
      }
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   }
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   
   agelim=AGESUP;   cptcoveff=ij-1; /*Number of simple covariates*/
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;  }
    
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  /*********** Health Expectancies ****************/
    
    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 )
   strcpy(filerespop,"pop");  
   strcat(filerespop,fileres);  {
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    /* Health expectancies */
     printf("Problem with forecast resultfile: %s\n", filerespop);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   }    double age, agelim, hf;
   printf("Computing forecasting: result on file '%s' \n", filerespop);    double ***p3mat,***varhe;
     double **dnewm,**doldm;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    double *xp;
     double **gp, **gm;
   if (mobilav==1) {    double ***gradg, ***trgradg;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int theta;
     movingaverage(agedeb, fage, agemin, mobaverage);  
   }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    dnewm=matrix(1,nlstate*nlstate,1,npar);
   if (stepm<=12) stepsize=1;    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
      
   agelim=AGESUP;    fprintf(ficreseij,"# Health expectancies\n");
      fprintf(ficreseij,"# Age");
   hstepm=1;    for(i=1; i<=nlstate;i++)
   hstepm=hstepm/stepm;      for(j=1; j<=nlstate;j++)
          fprintf(ficreseij," %1d-%1d (SE)",i,j);
   if (popforecast==1) {    fprintf(ficreseij,"\n");
     if((ficpop=fopen(popfile,"r"))==NULL) {  
       printf("Problem with population file : %s\n",popfile);exit(0);    if(estepm < stepm){
     }      printf ("Problem %d lower than %d\n",estepm, stepm);
     popage=ivector(0,AGESUP);    }
     popeffectif=vector(0,AGESUP);    else  hstepm=estepm;   
     popcount=vector(0,AGESUP);    /* We compute the life expectancy from trapezoids spaced every estepm months
         * This is mainly to measure the difference between two models: for example
     i=1;       * if stepm=24 months pijx are given only every 2 years and by summing them
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;     * we are calculating an estimate of the Life Expectancy assuming a linear 
         * progression in between and thus overestimating or underestimating according
     imx=i;     * to the curvature of the survival function. If, for the same date, we 
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   }     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
   for(cptcov=1;cptcov<=i2;cptcov++){     * curvature will be obtained if estepm is as small as stepm. */
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;    /* For example we decided to compute the life expectancy with the smallest unit */
       fprintf(ficrespop,"\n#******");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       for(j=1;j<=cptcoveff;j++) {       nhstepm is the number of hstepm from age to agelim 
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       nstepm is the number of stepm from age to agelin. 
       }       Look at hpijx to understand the reason of that which relies in memory size
       fprintf(ficrespop,"******\n");       and note for a fixed period like estepm months */
       fprintf(ficrespop,"# Age");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);       survival function given by stepm (the optimization length). Unfortunately it
       if (popforecast==1)  fprintf(ficrespop," [Population]");       means that if the survival funtion is printed only each two years of age and if
             you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       for (cpt=0; cpt<=0;cpt++) {       results. So we changed our mind and took the option of the best precision.
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      */
            hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    agelim=AGESUP;
           nhstepm = nhstepm/hstepm;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                /* nhstepm age range expressed in number of stepm */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
           oldm=oldms;savm=savms;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        /* if (stepm >= YEARM) hstepm=1;*/
              nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           for (h=0; h<=nhstepm; h++){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             if (h==(int) (calagedate+YEARM*cpt)) {      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
             }      gm=matrix(0,nhstepm,1,nlstate*nlstate);
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
               for(i=1; i<=nlstate;i++) {                       in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
                 if (mobilav==1)      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
                   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];      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                 }  
               }      /* Computing  Variances of health expectancies */
               if (h==(int)(calagedate+12*cpt)){  
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;       for(theta=1; theta <=npar; theta++){
                   /*fprintf(ficrespop," %.3f", kk1);        for(i=1; i<=npar; i++){ 
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/          xp[i] = x[i] + (i==theta ?delti[theta]:0);
               }        }
             }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
             for(i=1; i<=nlstate;i++){    
               kk1=0.;        cptj=0;
                 for(j=1; j<=nlstate;j++){        for(j=1; j<= nlstate; j++){
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          for(i=1; i<=nlstate; i++){
                 }            cptj=cptj+1;
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
             }              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
             if (h==(int)(calagedate+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(i=1; i<=npar; i++) 
       }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   /******/        
         cptj=0;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {        for(j=1; j<= nlstate; j++){
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            for(i=1;i<=nlstate;i++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){            cptj=cptj+1;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
           nhstepm = nhstepm/hstepm;  
                        gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           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++){        for(j=1; j<= nlstate*nlstate; j++)
             if (h==(int) (calagedate+YEARM*cpt)) {          for(h=0; h<=nhstepm-1; h++){
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
             }          }
             for(j=1; j<=nlstate+ndeath;j++) {       } 
               kk1=0.;kk2=0;     
               for(i=1; i<=nlstate;i++) {                /* End theta */
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      
               }       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  
             }       for(h=0; h<=nhstepm-1; h++)
           }        for(j=1; j<=nlstate*nlstate;j++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(theta=1; theta <=npar; theta++)
         }            trgradg[h][j][theta]=gradg[h][theta][j];
       }       
    }  
   }       for(i=1;i<=nlstate*nlstate;i++)
          for(j=1;j<=nlstate*nlstate;j++)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          varhe[i][j][(int)age] =0.;
   
   if (popforecast==1) {       printf("%d|",(int)age);fflush(stdout);
     free_ivector(popage,0,AGESUP);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     free_vector(popeffectif,0,AGESUP);       for(h=0;h<=nhstepm-1;h++){
     free_vector(popcount,0,AGESUP);        for(k=0;k<=nhstepm-1;k++){
   }          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(i=1;i<=nlstate*nlstate;i++)
   fclose(ficrespop);            for(j=1;j<=nlstate*nlstate;j++)
 }              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
 /***********************************************/      }
 /**************** Main Program *****************/      /* Computing expectancies */
 /***********************************************/      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
 int main(int argc, char *argv[])          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;
             
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;  /* 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]);*/
   double agedeb, agefin,hf;  
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;          }
   
   double fret;      fprintf(ficreseij,"%3.0f",age );
   double **xi,tmp,delta;      cptj=0;
       for(i=1; i<=nlstate;i++)
   double dum; /* Dummy variable */        for(j=1; j<=nlstate;j++){
   double ***p3mat;          cptj++;
   int *indx;          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   char line[MAXLINE], linepar[MAXLINE];        }
   char title[MAXLINE];      fprintf(ficreseij,"\n");
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];     
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
        free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   char filerest[FILENAMELENGTH];      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   char fileregp[FILENAMELENGTH];    }
   char popfile[FILENAMELENGTH];    printf("\n");
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    fprintf(ficlog,"\n");
   int firstobs=1, lastobs=10;  
   int sdeb, sfin; /* Status at beginning and end */    free_vector(xp,1,npar);
   int c,  h , cpt,l;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   int ju,jl, mi;    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  }
   int mobilav=0,popforecast=0;  
   int hstepm, nhstepm;  /************ Variance ******************/
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
   {
   double bage, fage, age, agelim, agebase;    /* Variance of health expectancies */
   double ftolpl=FTOL;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   double **prlim;    /* double **newm;*/
   double *severity;    double **dnewm,**doldm;
   double ***param; /* Matrix of parameters */    double **dnewmp,**doldmp;
   double  *p;    int i, j, nhstepm, hstepm, h, nstepm ;
   double **matcov; /* Matrix of covariance */    int k, cptcode;
   double ***delti3; /* Scale */    double *xp;
   double *delti; /* Scale */    double **gp, **gm;  /* for var eij */
   double ***eij, ***vareij;    double ***gradg, ***trgradg; /*for var eij */
   double **varpl; /* Variances of prevalence limits by age */    double **gradgp, **trgradgp; /* for var p point j */
   double *epj, vepp;    double *gpp, *gmp; /* for var p point j */
   double kk1, kk2;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    double ***p3mat;
      double age,agelim, hf;
     double ***mobaverage;
   char version[80]="Imach version 0.71, February 2002, INED-EUROREVES ";    int theta;
   char *alph[]={"a","a","b","c","d","e"}, str[4];    char digit[4];
     char digitp[25];
   
   char z[1]="c", occ;    char fileresprobmorprev[FILENAMELENGTH];
 #include <sys/time.h>  
 #include <time.h>    if(popbased==1){
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      if(mobilav!=0)
          strcpy(digitp,"-populbased-mobilav-");
   /* long total_usecs;      else strcpy(digitp,"-populbased-nomobil-");
   struct timeval start_time, end_time;    }
      else 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      strcpy(digitp,"-stablbased-");
   
     if (mobilav!=0) {
   printf("\n%s",version);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   if(argc <=1){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     printf("\nEnter the parameter file name: ");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     scanf("%s",pathtot);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   }      }
   else{    }
     strcpy(pathtot,argv[1]);  
   }    strcpy(fileresprobmorprev,"prmorprev"); 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    sprintf(digit,"%-d",ij);
   /*cygwin_split_path(pathtot,path,optionfile);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   /* cutv(path,optionfile,pathtot,'\\');*/    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   chdir(path);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   replace(pathc,path);    }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 /*-------- arguments in the command line --------*/    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);
   strcpy(fileres,"r");    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   strcat(fileres, optionfilefiname);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   strcat(fileres,".txt");    /* Other files have txt extension */      fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
   /*---------arguments file --------*/        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    fprintf(ficresprobmorprev,"\n");
     printf("Problem with optionfile %s\n",optionfile);    fprintf(ficgp,"\n# Routine varevsij");
     goto end;    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");
   }    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
   strcpy(filereso,"o");    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   strcat(filereso,fileres);  
   if((ficparo=fopen(filereso,"w"))==NULL) {    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");
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    fprintf(ficresvij,"# Age");
   }    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
   /* Reads comments: lines beginning with '#' */        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficresvij,"\n");
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    xp=vector(1,npar);
     puts(line);    dnewm=matrix(1,nlstate,1,npar);
     fputs(line,ficparo);    doldm=matrix(1,nlstate,1,nlstate);
   }    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   ungetc(c,ficpar);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
   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);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   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);    gpp=vector(nlstate+1,nlstate+ndeath);
   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);    gmp=vector(nlstate+1,nlstate+ndeath);
 while((c=getc(ficpar))=='#' && c!= EOF){    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    if(estepm < stepm){
     puts(line);      printf ("Problem %d lower than %d\n",estepm, stepm);
     fputs(line,ficparo);    }
   }    else  hstepm=estepm;   
   ungetc(c,ficpar);    /* 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 
   covar=matrix(0,NCOVMAX,1,n);       nstepm is the number of stepm from age to agelin. 
   cptcovn=0;       Look at hpijx to understand the reason of that which relies in memory size
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;       and note for a fixed period like k years */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   ncovmodel=2+cptcovn;       survival function given by stepm (the optimization length). Unfortunately it
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */       means that if the survival funtion is printed every two years of age and if
         you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   /* Read guess parameters */       results. So we changed our mind and took the option of the best precision.
   /* Reads comments: lines beginning with '#' */    */
   while((c=getc(ficpar))=='#' && c!= EOF){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     ungetc(c,ficpar);    agelim = AGESUP;
     fgets(line, MAXLINE, ficpar);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     puts(line);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     fputs(line,ficparo);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   ungetc(c,ficpar);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
        gp=matrix(0,nhstepm,1,nlstate);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      gm=matrix(0,nhstepm,1,nlstate);
     for(i=1; i <=nlstate; i++)  
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);      for(theta=1; theta <=npar; theta++){
       fprintf(ficparo,"%1d%1d",i1,j1);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       printf("%1d%1d",i,j);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       for(k=1; k<=ncovmodel;k++){        }
         fscanf(ficpar," %lf",&param[i][j][k]);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         printf(" %lf",param[i][j][k]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         fprintf(ficparo," %lf",param[i][j][k]);  
       }        if (popbased==1) {
       fscanf(ficpar,"\n");          if(mobilav ==0){
       printf("\n");            for(i=1; i<=nlstate;i++)
       fprintf(ficparo,"\n");              prlim[i][i]=probs[(int)age][i][ij];
     }          }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
   p=param[1][1];        }
      
   /* Reads comments: lines beginning with '#' */        for(j=1; j<= nlstate; j++){
   while((c=getc(ficpar))=='#' && c!= EOF){          for(h=0; h<=nhstepm; h++){
     ungetc(c,ficpar);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     puts(line);          }
     fputs(line,ficparo);        }
   }        /* This for computing probability of death (h=1 means
   ungetc(c,ficpar);           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   for(i=1; i <=nlstate; i++){          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     for(j=1; j <=nlstate+ndeath-1; j++){            gpp[j] += prlim[i][i]*p3mat[i][j][1];
       fscanf(ficpar,"%1d%1d",&i1,&j1);        }    
       printf("%1d%1d",i,j);        /* end probability of death */
       fprintf(ficparo,"%1d%1d",i1,j1);  
       for(k=1; k<=ncovmodel;k++){        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
         fscanf(ficpar,"%le",&delti3[i][j][k]);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         printf(" %le",delti3[i][j][k]);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         fprintf(ficparo," %le",delti3[i][j][k]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       }   
       fscanf(ficpar,"\n");        if (popbased==1) {
       printf("\n");          if(mobilav ==0){
       fprintf(ficparo,"\n");            for(i=1; i<=nlstate;i++)
     }              prlim[i][i]=probs[(int)age][i][ij];
   }          }else{ /* mobilav */ 
   delti=delti3[1][1];            for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
   /* Reads comments: lines beginning with '#' */          }
   while((c=getc(ficpar))=='#' && c!= EOF){        }
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);        for(j=1; j<= nlstate; j++){
     puts(line);          for(h=0; h<=nhstepm; h++){
     fputs(line,ficparo);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   }              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   ungetc(c,ficpar);          }
          }
   matcov=matrix(1,npar,1,npar);        /* This for computing probability of death (h=1 means
   for(i=1; i <=npar; i++){           computed over hstepm matrices product = hstepm*stepm months) 
     fscanf(ficpar,"%s",&str);           as a weighted average of prlim.
     printf("%s",str);        */
     fprintf(ficparo,"%s",str);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     for(j=1; j <=i; j++){          for(i=1,gmp[j]=0.; i<= nlstate; i++)
       fscanf(ficpar," %le",&matcov[i][j]);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
       printf(" %.5le",matcov[i][j]);        }    
       fprintf(ficparo," %.5le",matcov[i][j]);        /* end probability of death */
     }  
     fscanf(ficpar,"\n");        for(j=1; j<= nlstate; j++) /* vareij */
     printf("\n");          for(h=0; h<=nhstepm; h++){
     fprintf(ficparo,"\n");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   }          }
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       matcov[i][j]=matcov[j][i];          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
            }
   printf("\n");  
       } /* End theta */
   
     /*-------- Rewriting paramater file ----------*/      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
      strcpy(rfileres,"r");    /* "Rparameterfile */  
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/      for(h=0; h<=nhstepm; h++) /* veij */
      strcat(rfileres,".");    /* */        for(j=1; j<=nlstate;j++)
      strcat(rfileres,optionfilext);    /* Other files have txt extension */          for(theta=1; theta <=npar; theta++)
     if((ficres =fopen(rfileres,"w"))==NULL) {            trgradg[h][j][theta]=gradg[h][theta][j];
       printf("Problem writing new parameter file: %s\n", fileres);goto end;  
     }      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     fprintf(ficres,"#%s\n",version);        for(theta=1; theta <=npar; theta++)
              trgradgp[j][theta]=gradgp[theta][j];
     /*-------- data file ----------*/    
     if((fic=fopen(datafile,"r"))==NULL)    {  
       printf("Problem with datafile: %s\n", datafile);goto end;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     }      for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
     n= lastobs;          vareij[i][j][(int)age] =0.;
     severity = vector(1,maxwav);  
     outcome=imatrix(1,maxwav+1,1,n);      for(h=0;h<=nhstepm;h++){
     num=ivector(1,n);        for(k=0;k<=nhstepm;k++){
     moisnais=vector(1,n);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     annais=vector(1,n);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
     moisdc=vector(1,n);          for(i=1;i<=nlstate;i++)
     andc=vector(1,n);            for(j=1;j<=nlstate;j++)
     agedc=vector(1,n);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     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);      /* pptj */
     anint=matrix(1,maxwav,1,n);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
     s=imatrix(1,maxwav+1,1,n);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
     adl=imatrix(1,maxwav+1,1,n);          for(j=nlstate+1;j<=nlstate+ndeath;j++)
     tab=ivector(1,NCOVMAX);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     ncodemax=ivector(1,8);          varppt[j][i]=doldmp[j][i];
       /* end ppptj */
     i=1;      /*  x centered again */
     while (fgets(line, MAXLINE, fic) != NULL)    {      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       if ((i >= firstobs) && (i <=lastobs)) {      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
           
         for (j=maxwav;j>=1;j--){      if (popbased==1) {
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        if(mobilav ==0){
           strcpy(line,stra);          for(i=1; i<=nlstate;i++)
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            prlim[i][i]=probs[(int)age][i][ij];
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        }else{ /* mobilav */ 
         }          for(i=1; i<=nlstate;i++)
                    prlim[i][i]=mobaverage[(int)age][i][ij];
         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);      /* This for computing probability of death (h=1 means
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      */
         for (j=ncov;j>=1;j--){      for(j=nlstate+1;j<=nlstate+ndeath;j++){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
         }          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
         num[i]=atol(stra);      }    
              /* end probability of death */
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){  
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         i=i+1;        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
       }        for(i=1; i<=nlstate;i++){
     }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     /* printf("ii=%d", ij);        }
        scanf("%d",i);*/      } 
   imx=i-1; /* Number of individuals */      fprintf(ficresprobmorprev,"\n");
   
   /* for (i=1; i<=imx; i++){      fprintf(ficresvij,"%.0f ",age );
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      for(i=1; i<=nlstate;i++)
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;        for(j=1; j<=nlstate;j++){
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     }        }
       fprintf(ficresvij,"\n");
     for (i=1; i<=imx; i++)      free_matrix(gp,0,nhstepm,1,nlstate);
     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]));*/      free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   /* Calculation of the number of parameter from char model*/      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   Tvar=ivector(1,15);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   Tprod=ivector(1,15);    } /* End age */
   Tvaraff=ivector(1,15);    free_vector(gpp,nlstate+1,nlstate+ndeath);
   Tvard=imatrix(1,15,1,2);    free_vector(gmp,nlstate+1,nlstate+ndeath);
   Tage=ivector(1,15);          free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
        free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   if (strlen(model) >1){    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     j=0, j1=0, k1=1, k2=1;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     j=nbocc(model,'+');    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     j1=nbocc(model,'*');  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     cptcovn=j+1;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
     cptcovprod=j1;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
        fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
        fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     strcpy(modelsav,model);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
       printf("Error. Non available option model=%s ",model);    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);
       goto end;    /*  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); */
     for(i=(j+1); i>=1;i--){    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
       cutv(stra,strb,modelsav,'+');  
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    free_vector(xp,1,npar);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    free_matrix(doldm,1,nlstate,1,nlstate);
       /*scanf("%d",i);*/    free_matrix(dnewm,1,nlstate,1,npar);
       if (strchr(strb,'*')) {    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         cutv(strd,strc,strb,'*');    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
         if (strcmp(strc,"age")==0) {    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           cptcovprod--;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           cutv(strb,stre,strd,'V');    fclose(ficresprobmorprev);
           Tvar[i]=atoi(stre);    fflush(ficgp);
           cptcovage++;    fflush(fichtm); 
             Tage[cptcovage]=i;  }  /* end varevsij */
             /*printf("stre=%s ", stre);*/  
         }  /************ Variance of prevlim ******************/
         else if (strcmp(strd,"age")==0) {  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)
           cptcovprod--;  {
           cutv(strb,stre,strc,'V');    /* Variance of prevalence limit */
           Tvar[i]=atoi(stre);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
           cptcovage++;    double **newm;
           Tage[cptcovage]=i;    double **dnewm,**doldm;
         }    int i, j, nhstepm, hstepm;
         else {    int k, cptcode;
           cutv(strb,stre,strc,'V');    double *xp;
           Tvar[i]=ncov+k1;    double *gp, *gm;
           cutv(strb,strc,strd,'V');    double **gradg, **trgradg;
           Tprod[k1]=i;    double age,agelim;
           Tvard[k1][1]=atoi(strc);    int theta;
           Tvard[k1][2]=atoi(stre);     
           Tvar[cptcovn+k2]=Tvard[k1][1];    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    fprintf(ficresvpl,"# Age");
           for (k=1; k<=lastobs;k++)    for(i=1; i<=nlstate;i++)
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        fprintf(ficresvpl," %1d-%1d",i,i);
           k1++;    fprintf(ficresvpl,"\n");
           k2=k2+2;  
         }    xp=vector(1,npar);
       }    dnewm=matrix(1,nlstate,1,npar);
       else {    doldm=matrix(1,nlstate,1,nlstate);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    
        /*  scanf("%d",i);*/    hstepm=1*YEARM; /* Every year of age */
       cutv(strd,strc,strb,'V');    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
       Tvar[i]=atoi(strc);    agelim = AGESUP;
       }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       strcpy(modelsav,stra);        nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      if (stepm >= YEARM) hstepm=1;
         scanf("%d",i);*/      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     }      gradg=matrix(1,npar,1,nlstate);
 }      gp=vector(1,nlstate);
        gm=vector(1,nlstate);
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);  
   printf("cptcovprod=%d ", cptcovprod);      for(theta=1; theta <=npar; theta++){
   scanf("%d ",i);*/        for(i=1; i<=npar; i++){ /* Computes gradient */
     fclose(fic);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
     /*  if(mle==1){*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     if (weightopt != 1) { /* Maximisation without weights*/        for(i=1;i<=nlstate;i++)
       for(i=1;i<=n;i++) weight[i]=1.0;          gp[i] = prlim[i][i];
     }      
     /*-calculation of age at interview from date of interview and age at death -*/        for(i=1; i<=npar; i++) /* Computes gradient */
     agev=matrix(1,maxwav,1,imx);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    for (i=1; i<=imx; i++)        for(i=1;i<=nlstate;i++)
      for(m=2; (m<= maxwav); m++)          gm[i] = prlim[i][i];
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  
          anint[m][i]=9999;        for(i=1;i<=nlstate;i++)
          s[m][i]=-1;          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
        }      } /* End theta */
      
     for (i=1; i<=imx; i++)  {      trgradg =matrix(1,nlstate,1,npar);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  
       for(m=1; (m<= maxwav); m++){      for(j=1; j<=nlstate;j++)
         if(s[m][i] >0){        for(theta=1; theta <=npar; theta++)
           if (s[m][i] == nlstate+1) {          trgradg[j][theta]=gradg[theta][j];
             if(agedc[i]>0)  
               if(moisdc[i]!=99 && andc[i]!=9999)      for(i=1;i<=nlstate;i++)
               agev[m][i]=agedc[i];        varpl[i][(int)age] =0.;
             else {      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
               if (andc[i]!=9999){      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      for(i=1;i<=nlstate;i++)
               agev[m][i]=-1;        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
               }  
             }      fprintf(ficresvpl,"%.0f ",age );
           }      for(i=1; i<=nlstate;i++)
           else if(s[m][i] !=9){ /* Should no more exist */        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      fprintf(ficresvpl,"\n");
             if(mint[m][i]==99 || anint[m][i]==9999)      free_vector(gp,1,nlstate);
               agev[m][i]=1;      free_vector(gm,1,nlstate);
             else if(agev[m][i] <agemin){      free_matrix(gradg,1,npar,1,nlstate);
               agemin=agev[m][i];      free_matrix(trgradg,1,nlstate,1,npar);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    } /* End age */
             }  
             else if(agev[m][i] >agemax){    free_vector(xp,1,npar);
               agemax=agev[m][i];    free_matrix(doldm,1,nlstate,1,npar);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    free_matrix(dnewm,1,nlstate,1,nlstate);
             }  
             /*agev[m][i]=anint[m][i]-annais[i];*/  }
             /*   agev[m][i] = age[i]+2*m;*/  
           }  /************ Variance of one-step probabilities  ******************/
           else { /* =9 */  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
             agev[m][i]=1;  {
             s[m][i]=-1;    int i, j=0,  i1, k1, l1, t, tj;
           }    int k2, l2, j1,  z1;
         }    int k=0,l, cptcode;
         else /*= 0 Unknown */    int first=1, first1;
           agev[m][i]=1;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
       }    double **dnewm,**doldm;
        double *xp;
     }    double *gp, *gm;
     for (i=1; i<=imx; i++)  {    double **gradg, **trgradg;
       for(m=1; (m<= maxwav); m++){    double **mu;
         if (s[m][i] > (nlstate+ndeath)) {    double age,agelim, cov[NCOVMAX];
           printf("Error: Wrong value in nlstate or ndeath\n");      double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
           goto end;    int theta;
         }    char fileresprob[FILENAMELENGTH];
       }    char fileresprobcov[FILENAMELENGTH];
     }    char fileresprobcor[FILENAMELENGTH];
   
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    double ***varpij;
   
     free_vector(severity,1,maxwav);    strcpy(fileresprob,"prob"); 
     free_imatrix(outcome,1,maxwav+1,1,n);    strcat(fileresprob,fileres);
     free_vector(moisnais,1,n);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     free_vector(annais,1,n);      printf("Problem with resultfile: %s\n", fileresprob);
     /* free_matrix(mint,1,maxwav,1,n);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
        free_matrix(anint,1,maxwav,1,n);*/    }
     free_vector(moisdc,1,n);    strcpy(fileresprobcov,"probcov"); 
     free_vector(andc,1,n);    strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
          printf("Problem with resultfile: %s\n", fileresprobcov);
     wav=ivector(1,imx);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    }
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    strcpy(fileresprobcor,"probcor"); 
        strcat(fileresprobcor,fileres);
     /* Concatenates waves */    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
       Tcode=ivector(1,100);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       ncodemax[1]=1;    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
          printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
    codtab=imatrix(1,100,1,10);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
    h=0;    
    m=pow(2,cptcoveff);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
      fprintf(ficresprob,"# Age");
    for(k=1;k<=cptcoveff; k++){    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
      for(i=1; i <=(m/pow(2,k));i++){    fprintf(ficresprobcov,"# Age");
        for(j=1; j <= ncodemax[k]; j++){    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    fprintf(ficresprobcov,"# Age");
            h++;  
            if (h>m) h=1;codtab[h][k]=j;  
          }    for(i=1; i<=nlstate;i++)
        }      for(j=1; j<=(nlstate+ndeath);j++){
      }        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
    }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /*for(i=1; i <=m ;i++){   /* fprintf(ficresprob,"\n");
      for(k=1; k <=cptcovn; k++){    fprintf(ficresprobcov,"\n");
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);    fprintf(ficresprobcor,"\n");
      }   */
      printf("\n");   xp=vector(1,npar);
    }    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
    scanf("%d",i);*/    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
        mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
    /* Calculates basic frequencies. Computes observed prevalence at single age    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
        and prints on file fileres'p'. */    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");
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    file %s<br>\n",optionfilehtmcov);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
        and drawn. It helps understanding how is the covariance between two incidences.\
     /* For Powell, parameters are in a vector p[] starting at p[1]   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    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. \
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  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 \
     if(mle==1){  standard deviations wide on each axis. <br>\
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);   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>\
      To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
     /*--------- 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= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);    cov[1]=1;
      tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
    jk=1;    j1=0;
    fprintf(ficres,"# Parameters\n");    for(t=1; t<=tj;t++){
    printf("# Parameters\n");      for(i1=1; i1<=ncodemax[t];i1++){ 
    for(i=1,jk=1; i <=nlstate; i++){        j1++;
      for(k=1; k <=(nlstate+ndeath); k++){        if  (cptcovn>0) {
        if (k != i)          fprintf(ficresprob, "\n#********** Variable "); 
          {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            printf("%d%d ",i,k);          fprintf(ficresprob, "**********\n#\n");
            fprintf(ficres,"%1d%1d ",i,k);          fprintf(ficresprobcov, "\n#********** Variable "); 
            for(j=1; j <=ncovmodel; j++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
              printf("%f ",p[jk]);          fprintf(ficresprobcov, "**********\n#\n");
              fprintf(ficres,"%f ",p[jk]);          
              jk++;          fprintf(ficgp, "\n#********** Variable "); 
            }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            printf("\n");          fprintf(ficgp, "**********\n#\n");
            fprintf(ficres,"\n");          
          }          
      }          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
    }          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  if(mle==1){          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     /* Computing hessian and covariance matrix */          
     ftolhess=ftol; /* Usually correct */          fprintf(ficresprobcor, "\n#********** Variable ");    
     hesscov(matcov, p, npar, delti, ftolhess, func);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  }          fprintf(ficresprobcor, "**********\n#");    
     fprintf(ficres,"# Scales\n");        }
     printf("# Scales\n");        
      for(i=1,jk=1; i <=nlstate; i++){        for (age=bage; age<=fage; age ++){ 
       for(j=1; j <=nlstate+ndeath; j++){          cov[2]=age;
         if (j!=i) {          for (k=1; k<=cptcovn;k++) {
           fprintf(ficres,"%1d%1d",i,j);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           printf("%1d%1d",i,j);          }
           for(k=1; k<=ncovmodel;k++){          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
             printf(" %.5e",delti[jk]);          for (k=1; k<=cptcovprod;k++)
             fprintf(ficres," %.5e",delti[jk]);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
             jk++;          
           }          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           printf("\n");          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           fprintf(ficres,"\n");          gp=vector(1,(nlstate)*(nlstate+ndeath));
         }          gm=vector(1,(nlstate)*(nlstate+ndeath));
       }      
      }          for(theta=1; theta <=npar; theta++){
                for(i=1; i<=npar; i++)
     k=1;              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
     fprintf(ficres,"# Covariance\n");            
     printf("# Covariance\n");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     for(i=1;i<=npar;i++){            
       /*  if (k>nlstate) k=1;            k=0;
       i1=(i-1)/(ncovmodel*nlstate)+1;            for(i=1; i<= (nlstate); i++){
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);              for(j=1; j<=(nlstate+ndeath);j++){
       printf("%s%d%d",alph[k],i1,tab[i]);*/                k=k+1;
       fprintf(ficres,"%3d",i);                gp[k]=pmmij[i][j];
       printf("%3d",i);              }
       for(j=1; j<=i;j++){            }
         fprintf(ficres," %.5e",matcov[i][j]);            
         printf(" %.5e",matcov[i][j]);            for(i=1; i<=npar; i++)
       }              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       fprintf(ficres,"\n");      
       printf("\n");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       k++;            k=0;
     }            for(i=1; i<=(nlstate); i++){
                  for(j=1; j<=(nlstate+ndeath);j++){
     while((c=getc(ficpar))=='#' && c!= EOF){                k=k+1;
       ungetc(c,ficpar);                gm[k]=pmmij[i][j];
       fgets(line, MAXLINE, ficpar);              }
       puts(line);            }
       fputs(line,ficparo);       
     }            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     ungetc(c,ficpar);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
            }
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);  
              for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     if (fage <= 2) {            for(theta=1; theta <=npar; theta++)
       bage = agemin;              trgradg[j][theta]=gradg[theta][j];
       fage = agemaxpar;          
     }          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);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
            free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);          pmij(pmmij,cov,ncovmodel,x,nlstate);
     fgets(line, MAXLINE, ficpar);          
     puts(line);          k=0;
     fputs(line,ficparo);          for(i=1; i<=(nlstate); i++){
   }            for(j=1; j<=(nlstate+ndeath);j++){
   ungetc(c,ficpar);              k=k+1;
                mu[k][(int) age]=pmmij[i][j];
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);            }
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          }
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
                  for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   while((c=getc(ficpar))=='#' && c!= EOF){              varpij[i][j][(int)age] = doldm[i][j];
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);          /*printf("\n%d ",(int)age);
     puts(line);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     fputs(line,ficparo);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   }            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   ungetc(c,ficpar);            }*/
    
           fprintf(ficresprob,"\n%d ",(int)age);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          fprintf(ficresprobcov,"\n%d ",(int)age);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          fprintf(ficresprobcor,"\n%d ",(int)age);
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   fprintf(ficparo,"pop_based=%d\n",popbased);              fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   fprintf(ficres,"pop_based=%d\n",popbased);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
              fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   while((c=getc(ficpar))=='#' && c!= EOF){            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);          i=0;
     puts(line);          for (k=1; k<=(nlstate);k++){
     fputs(line,ficparo);            for (l=1; l<=(nlstate+ndeath);l++){ 
   }              i=i++;
   ungetc(c,ficpar);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);              for (j=1; j<=i;j++){
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
 while((c=getc(ficpar))=='#' && c!= EOF){          }/* end of loop for state */
     ungetc(c,ficpar);        } /* end of loop for age */
     fgets(line, MAXLINE, ficpar);  
     puts(line);        /* Confidence intervalle of pij  */
     fputs(line,ficparo);        /*
   }          fprintf(ficgp,"\nset noparametric;unset label");
   ungetc(c,ficpar);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   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(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        */
   
 /*------------ gnuplot -------------*/        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);        first1=1;
          for (k2=1; k2<=(nlstate);k2++){
 /*------------ free_vector  -------------*/          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
  chdir(path);            if(l2==k2) continue;
              j=(k2-1)*(nlstate+ndeath)+l2;
  free_ivector(wav,1,imx);            for (k1=1; k1<=(nlstate);k1++){
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                  if(l1==k1) continue;
  free_ivector(num,1,n);                i=(k1-1)*(nlstate+ndeath)+l1;
  free_vector(agedc,1,n);                if(i<=j) continue;
  /*free_matrix(covar,1,NCOVMAX,1,n);*/                for (age=bage; age<=fage; age ++){ 
  fclose(ficparo);                  if ((int)age %5==0){
  fclose(ficres);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
 /*--------- index.htm --------*/                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);                    mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                      /* Computing eigen value of matrix of covariance */
   /*--------------- Prevalence limit --------------*/                    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.;
   strcpy(filerespl,"pl");                    /* Eigen vectors */
   strcat(filerespl,fileres);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   if((ficrespl=fopen(filerespl,"w"))==NULL) {                    /*v21=sqrt(1.-v11*v11); *//* error */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;                    v21=(lc1-v1)/cv12*v11;
   }                    v12=-v21;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);                    v22=v11;
   fprintf(ficrespl,"#Prevalence limit\n");                    tnalp=v21/v11;
   fprintf(ficrespl,"#Age ");                    if(first1==1){
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);                      first1=0;
   fprintf(ficrespl,"\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);
                      }
   prlim=matrix(1,nlstate,1,nlstate);                    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);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    /*printf(fignu*/
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    if(first==1){
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                      first=0;
   k=0;                      fprintf(ficgp,"\nset parametric;unset label");
   agebase=agemin;                      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);
   agelim=agemaxpar;                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   ftolpl=1.e-10;                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   i1=cptcoveff;   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   if (cptcovn < 1){i1=1;}  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
   for(cptcov=1;cptcov<=i1;cptcov++){                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
         k=k+1;                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
         fprintf(ficrespl,"\n#******");                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
         for(j=1;j<=cptcoveff;j++)                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                      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",\
         fprintf(ficrespl,"******\n");                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                                      mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
         for (age=agebase; age<=agelim; age++){                    }else{
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                      first=0;
           fprintf(ficrespl,"%.0f",age );                      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);
           fprintf(ficrespl," %.5f", prlim[i][i]);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
           fprintf(ficrespl,"\n");                      fprintf(ficgp,"\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),\
       }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     }                    }/* if first */
   fclose(ficrespl);                  } /* age mod 5 */
                 } /* end loop age */
   /*------------- h Pij x at various ages ------------*/                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                  first=1;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);              } /*l12 */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {            } /* k12 */
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          } /*l1 */
   }        }/* k1 */
   printf("Computing pij: result on file '%s' \n", filerespij);      } /* loop covariates */
      }
   stepsize=(int) (stepm+YEARM-1)/YEARM;    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   /*if (stepm<=24) stepsize=2;*/    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
   agelim=AGESUP;    fclose(ficresprob);
   hstepm=stepsize*YEARM; /* Every year of age */    fclose(ficresprobcov);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    fclose(ficresprobcor);
      fflush(ficgp);
   k=0;    fflush(fichtmcov);
   for(cptcov=1;cptcov<=i1;cptcov++){  }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;  
         fprintf(ficrespij,"\n#****** ");  /******************* Printing html file ***********/
         for(j=1;j<=cptcoveff;j++)  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    int lastpass, int stepm, int weightopt, char model[],\
         fprintf(ficrespij,"******\n");                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                            int popforecast, int estepm ,\
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                    double jprev1, double mprev1,double anprev1, \
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                    double jprev2, double mprev2,double anprev2){
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    int jj1, k1, i1, cpt;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);     - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
           fprintf(ficrespij,"# Age");             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
           for(i=1; i<=nlstate;i++)     fprintf(fichtm,"\
             for(j=1; j<=nlstate+ndeath;j++)   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
               fprintf(ficrespij," %1d-%1d",i,j);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
           fprintf(ficrespij,"\n");     fprintf(fichtm,"\
           for (h=0; h<=nhstepm; h++){   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
             for(i=1; i<=nlstate;i++)     fprintf(fichtm,"\
               for(j=1; j<=nlstate+ndeath;j++)   - Life expectancies by age and initial health status (estepm=%2d months): \
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);     <a href=\"%s\">%s</a> <br>\n</li>",
             fprintf(ficrespij,"\n");             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
           fprintf(ficrespij,"\n");  
         }   m=cptcoveff;
     }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   }  
    jj1=0;
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/   for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
   fclose(ficrespij);       jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   /*---------- Forecasting ------------------*/         for (cpt=1; cpt<=cptcoveff;cpt++) 
   if(stepm == 1) {           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
 if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);       }
     free_matrix(mint,1,maxwav,1,n);       /* Pij */
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);       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_vector(weight,1,n);}  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
   else{       /* Quasi-incidences */
     erreur=108;       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
     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);   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); 
           /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
   /*---------- Health expectancies and variances ------------*/           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
   strcpy(filerest,"t");         }
   strcat(filerest,fileres);       for(cpt=1; cpt<=nlstate;cpt++) {
   if((ficrest=fopen(filerest,"w"))==NULL) {          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
   }       }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);     } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   strcpy(filerese,"e");  
   strcat(filerese,fileres);  
   if((ficreseij=fopen(filerese,"w"))==NULL) {   fprintf(fichtm,"\
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  \n<br><li><h4> Result files (second order: variances)</h4>\n\
   }   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
  strcpy(fileresv,"v");           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
   strcat(fileresv,fileres);   fprintf(fichtm,"\
   if((ficresvij=fopen(fileresv,"w"))==NULL) {   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   }  
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);   fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   k=0;           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
   for(cptcov=1;cptcov<=i1;cptcov++){   fprintf(fichtm,"\
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
       k=k+1;           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
       fprintf(ficrest,"\n#****** ");   fprintf(fichtm,"\
       for(j=1;j<=cptcoveff;j++)   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
       fprintf(ficrest,"******\n");   fprintf(fichtm,"\
    - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
       fprintf(ficreseij,"\n#****** ");           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  /*  if(popforecast==1) fprintf(fichtm,"\n */
       fprintf(ficreseij,"******\n");  /*  - 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 */
       fprintf(ficresvij,"\n#****** ");  /*      <br>",fileres,fileres,fileres,fileres); */
       for(j=1;j<=cptcoveff;j++)  /*  else  */
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
       fprintf(ficresvij,"******\n");   fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;   m=cptcoveff;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;   jj1=0;
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);   for(k1=1; k1<=m;k1++){
         for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
         if (cptcovn > 0) {
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);         for (cpt=1; cpt<=cptcoveff;cpt++) 
       fprintf(ficrest,"\n");           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       hf=1;       }
       if (stepm >= YEARM) hf=stepm/YEARM;       for(cpt=1; cpt<=nlstate;cpt++) {
       epj=vector(1,nlstate+1);         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
       for(age=bage; age <=fage ;age++){  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
         if (popbased==1) {       }
           for(i=1; i<=nlstate;i++)       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
             prlim[i][i]=probs[(int)age][i][k];  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 */
         fprintf(ficrest," %.0f",age);   }/* End k1 */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){   fprintf(fichtm,"</ul>");
           for(i=1, epj[j]=0.;i <=nlstate;i++) {   fflush(fichtm);
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];  }
           }  
           epj[nlstate+1] +=epj[j];  /******************* Gnuplot file **************/
         }  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
         for(i=1, vepp=0.;i <=nlstate;i++)  
           for(j=1;j <=nlstate;j++)    char dirfileres[132],optfileres[132];
             vepp += vareij[i][j][(int)age];    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    int ng;
         for(j=1;j <=nlstate;j++){  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));  /*     printf("Problem with file %s",optionfilegnuplot); */
         }  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
         fprintf(ficrest,"\n");  /*   } */
       }  
     }    /*#ifdef windows */
   }    fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   fclose(ficreseij);    m=pow(2,cptcoveff);
   fclose(ficresvij);  
   fclose(ficrest);    strcpy(dirfileres,optionfilefiname);
   fclose(ficpar);    strcpy(optfileres,"vpl");
   free_vector(epj,1,nlstate+1);   /* 1eme*/
      for (cpt=1; cpt<= nlstate ; cpt ++) {
   /*------- Variance limit prevalence------*/       for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
   strcpy(fileresvpl,"vpl");       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
   strcat(fileresvpl,fileres);       fprintf(ficgp,"set xlabel \"Age\" \n\
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  set ylabel \"Probability\" \n\
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  set ter png small\n\
     exit(0);  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);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  
        for (i=1; i<= nlstate ; i ++) {
   k=0;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   for(cptcov=1;cptcov<=i1;cptcov++){         else fprintf(ficgp," \%%*lf (\%%*lf)");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       }
       k=k+1;       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
       fprintf(ficresvpl,"\n#****** ");       for (i=1; i<= nlstate ; i ++) {
       for(j=1;j<=cptcoveff;j++)         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       fprintf(ficresvpl,"******\n");       } 
             fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
       varpl=matrix(1,nlstate,(int) bage, (int) fage);       for (i=1; i<= nlstate ; i ++) {
       oldm=oldms;savm=savms;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     }       }  
  }       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
   fclose(ficresvpl);    }
     /*2 eme*/
   /*---------- End : free ----------------*/    
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    for (k1=1; k1<= m ; k1 ++) { 
        fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      
        for (i=1; i<= nlstate+1 ; i ++) {
          k=2*i;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        for (j=1; j<= nlstate+1 ; j ++) {
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);          else fprintf(ficgp," \%%*lf (\%%*lf)");
          }   
   free_matrix(matcov,1,npar,1,npar);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   free_vector(delti,1,npar);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   free_matrix(agev,1,maxwav,1,imx);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   if(erreur >0)          else fprintf(ficgp," \%%*lf (\%%*lf)");
     printf("End of Imach with error %d\n",erreur);        }   
   else   printf("End of Imach\n");        fprintf(ficgp,"\" t\"\" w l 0,");
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
          for (j=1; j<= nlstate+1 ; j ++) {
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   /*printf("Total time was %d uSec.\n", total_usecs);*/          else fprintf(ficgp," \%%*lf (\%%*lf)");
   /*------ End -----------*/        }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
  end:      }
 #ifdef windows    }
   /* chdir(pathcd);*/    
 #endif    /*3eme*/
  /*system("wgnuplot graph.plt");*/    
  /*system("../gp37mgw/wgnuplot graph.plt");*/    for (k1=1; k1<= m ; k1 ++) { 
  /*system("cd ../gp37mgw");*/      for (cpt=1; cpt<= nlstate ; cpt ++) {
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        k=2+nlstate*(2*cpt-2);
  strcpy(plotcmd,GNUPLOTPROGRAM);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
  strcat(plotcmd," ");        fprintf(ficgp,"set ter png small\n\
  strcat(plotcmd,optionfilegnuplot);  set size 0.65,0.65\n\
  system(plotcmd);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
 #ifdef windows          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   while (z[0] != 'q') {          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     chdir(path);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     scanf("%s",z);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     if (z[0] == 'c') system("./imach");          
     else if (z[0] == 'e') {        */
       chdir(path);        for (i=1; i< nlstate ; i ++) {
       system(optionfilehtm);          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);
     }          
     else if (z[0] == 'q') exit(0);        } 
   }      }
 #endif    }
 }    
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       sump=sump+1;
       num=num+1;
     }
    
    
     /* for (i=1; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=0;i<=imx-1 ; i++)
       {
         if (cens[i]==1 & wav[i]>1)
           A=-x[1]/(x[2])*
             (exp(x[2]/YEARM*(agecens[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)));
         
         if (cens[i]==0 & wav[i]>1)
           A=-x[1]/(x[2])*
                (exp(x[2]/YEARM*(agedc[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)))
             +log(x[1]/YEARM)+x[2]/YEARM*(agedc[i]*12-agegomp*12)+log(YEARM);      
         
         if (wav[i]>1 & agecens[i]>15) {
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov){
     int i;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (j=1; j<=lastpass; j++)
           if (s[j][i]>nlstate) {
             dcwave[i]=j;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];agecens[i]=1.; 
           if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
           cens[i]=1;
           
           if (ageexmed[i]<1) cens[i]=-1;
           if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
   
       p[1]=0.1; p[2]=0.1;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow-mort"); 
     strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
     /*  for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     */
     fprintf(ficrespow,"\n");
   
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM,delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov);
     } /* Endof if mle==-3 */
   
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficrespl,"#Stable prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
   
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /*---------- Health expectancies and variances ------------*/
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total LEs with variances: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficreseij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
           }
   
    
           fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficreseij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of stable prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocaltime at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
     strcpy(plotcmd,"\"");
     strcat(plotcmd,pathimach);
     strcat(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd,"\"");
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     if((outcmd=system(plotcmd)) != 0){
       printf(" Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.29  
changed lines
  Added in v.1.99


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