Diff for /imach/src/imach.c between versions 1.5 and 1.106

version 1.5, 2001/05/02 17:42:45 version 1.106, 2006/01/19 13:24:36
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.106  2006/01/19 13:24:36  brouard
   individuals from different ages are interviewed on their health status    Some cleaning and links added in html output
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.105  2006/01/05 20:23:19  lievre
   Health expectancies are computed from the transistions observed between    *** empty log message ***
   waves and are computed for each degree of severity of disability (number  
   of life states). More degrees you consider, more time is necessary to    Revision 1.104  2005/09/30 16:11:43  lievre
   reach the Maximum Likelihood of the parameters involved in the model.    (Module): sump fixed, loop imx fixed, and simplifications.
   The simplest model is the multinomial logistic model where pij is    (Module): If the status is missing at the last wave but we know
   the probabibility to be observed in state j at the second wave conditional    that the person is alive, then we can code his/her status as -2
   to be observed in state i at the first wave. Therefore the model is:    (instead of missing=-1 in earlier versions) and his/her
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    contributions to the likelihood is 1 - Prob of dying from last
   is a covariate. If you want to have a more complex model than "constant and    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   age", you should modify the program where the markup    the healthy state at last known wave). Version is 0.98
     *Covariates have to be included here again* invites you to do it.  
   More covariates you add, less is the speed of the convergence.    Revision 1.103  2005/09/30 15:54:49  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
   The advantage that this computer programme claims, comes from that if the  
   delay between waves is not identical for each individual, or if some    Revision 1.102  2004/09/15 17:31:30  brouard
   individual missed an interview, the information is not rounded or lost, but    Add the possibility to read data file including tab characters.
   taken into account using an interpolation or extrapolation.  
   hPijx is the probability to be    Revision 1.101  2004/09/15 10:38:38  brouard
   observed in state i at age x+h conditional to the observed state i at age    Fix on curr_time
   x. The delay 'h' can be split into an exact number (nh*stepm) of  
   unobserved intermediate  states. This elementary transition (by month or    Revision 1.100  2004/07/12 18:29:06  brouard
   quarter trimester, semester or year) is model as a multinomial logistic.    Add version for Mac OS X. Just define UNIX in Makefile
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply hPijx.    Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.98  2004/05/16 15:05:56  brouard
      New version 0.97 . First attempt to estimate force of mortality
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    directly from the data i.e. without the need of knowing the health
            Institut national d'études démographiques, Paris.    state at each age, but using a Gompertz model: log u =a + b*age .
   This software have been partly granted by Euro-REVES, a concerted action    This is the basic analysis of mortality and should be done before any
   from the European Union.    other analysis, in order to test if the mortality estimated from the
   It is copyrighted identically to a GNU software product, ie programme and    cross-longitudinal survey is different from the mortality estimated
   software can be distributed freely for non commercial use. Latest version    from other sources like vital statistic data.
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    The same imach parameter file can be used but the option for mle should be -3.
    
 #include <math.h>    Agnès, who wrote this part of the code, tried to keep most of the
 #include <stdio.h>    former routines in order to include the new code within the former code.
 #include <stdlib.h>  
 #include <unistd.h>    The output is very simple: only an estimate of the intercept and of
     the slope with 95% confident intervals.
 #define MAXLINE 256  
 #define FILENAMELENGTH 80    Current limitations:
 /*#define DEBUG*/    A) Even if you enter covariates, i.e. with the
 #define windows    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    B) There is no computation of Life Expectancy nor Life Table.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.96  2003/07/15 15:38:55  brouard
     * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #define NINTERVMAX 8    rewritten within the same printf. Workaround: many printfs.
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.95  2003/07/08 07:54:34  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    * imach.c (Repository):
 #define MAXN 20000    (Repository): Using imachwizard code to output a more meaningful covariance
 #define YEARM 12. /* Number of months per year */    matrix (cov(a12,c31) instead of numbers.
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
   
 int nvar;    Revision 1.93  2003/06/25 16:33:55  brouard
 static int cptcov;    (Module): On windows (cygwin) function asctime_r doesn't
 int cptcovn;    exist so I changed back to asctime which exists.
 int npar=NPARMAX;    (Module): Version 0.96b
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.92  2003/06/25 16:30:45  brouard
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.91  2003/06/25 15:30:29  brouard
 int mle, weightopt;    * imach.c (Repository): Duplicated warning errors corrected.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Repository): Elapsed time after each iteration is now output. It
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    helps to forecast when convergence will be reached. Elapsed time
 double **oldm, **newm, **savm; /* Working pointers to matrices */    is stamped in powell.  We created a new html file for the graphs
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    concerning matrix of covariance. It has extension -cov.htm.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;  
 FILE *ficgp, *fichtm;    Revision 1.90  2003/06/24 12:34:15  brouard
 FILE *ficreseij;    (Module): Some bugs corrected for windows. Also, when
   char filerese[FILENAMELENGTH];    mle=-1 a template is output in file "or"mypar.txt with the design
  FILE  *ficresvij;    of the covariance matrix to be input.
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.89  2003/06/24 12:30:52  brouard
   char fileresvpl[FILENAMELENGTH];    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
   
     Revision 1.88  2003/06/23 17:54:56  brouard
 #define NR_END 1    * 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 FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
 #define NRANSI  
 #define ITMAX 200    Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
 #define TOL 2.0e-4    routine fileappend.
   
 #define CGOLD 0.3819660    Revision 1.85  2003/06/17 13:12:43  brouard
 #define ZEPS 1.0e-10    * imach.c (Repository): Check when date of death was earlier that
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
 #define GOLD 1.618034    was wrong (infinity). We still send an "Error" but patch by
 #define GLIMIT 100.0    assuming that the date of death was just one stepm after the
 #define TINY 1.0e-20    interview.
     (Repository): Because some people have very long ID (first column)
 static double maxarg1,maxarg2;    we changed int to long in num[] and we added a new lvector for
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    memory allocation. But we also truncated to 8 characters (left
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    truncation)
      (Repository): No more line truncation errors.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
 static double sqrarg;    place. It differs from routine "prevalence" which may be called
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    many times. Probs is memory consuming and must be used with
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 int imx;  
 int stepm;    Revision 1.83  2003/06/10 13:39:11  lievre
 /* Stepm, step in month: minimum step interpolation*/    *** empty log message ***
   
 int m,nb;    Revision 1.82  2003/06/05 15:57:20  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax;    Add log in  imach.c and  fullversion number is now printed.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij;  */
   /*
 double *weight;     Interpolated Markov Chain
 int **s; /* Status */  
 double *agedc, **covar, idx;    Short summary of the programme:
 int **nbcode, *Tcode, *Tvar, **codtab;    
     This program computes Healthy Life Expectancies from
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 double ftolhess; /* Tolerance for computing hessian */    first survey ("cross") where individuals from different ages are
     interviewed on their health status or degree of disability (in the
     case of a health survey which is our main interest) -2- at least a
 static  int split( char *path, char *dirc, char *name )    second wave of interviews ("longitudinal") which measure each change
 {    (if any) in individual health status.  Health expectancies are
    char *s;                             /* pointer */    computed from the time spent in each health state according to a
    int  l1, l2;                         /* length counters */    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
    l1 = strlen( path );                 /* length of path */    simplest model is the multinomial logistic model where pij is the
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    probability to be observed in state j at the second wave
    s = strrchr( path, '\\' );           /* find last / */    conditional to be observed in state i at the first wave. Therefore
    if ( s == NULL ) {                   /* no directory, so use current */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #if     defined(__bsd__)                /* get current working directory */    'age' is age and 'sex' is a covariate. If you want to have a more
       extern char       *getwd( );    complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
       if ( getwd( dirc ) == NULL ) {    you to do it.  More covariates you add, slower the
 #else    convergence.
       extern char       *getcwd( );  
     The advantage of this computer programme, compared to a simple
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    multinomial logistic model, is clear when the delay between waves is not
 #endif    identical for each individual. Also, if a individual missed an
          return( GLOCK_ERROR_GETCWD );    intermediate interview, the information is lost, but taken into
       }    account using an interpolation or extrapolation.  
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    hPijx is the probability to be observed in state i at age x+h
       s++;                              /* after this, the filename */    conditional to the observed state i at age x. The delay 'h' can be
       l2 = strlen( s );                 /* length of filename */    split into an exact number (nh*stepm) of unobserved intermediate
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    states. This elementary transition (by month, quarter,
       strcpy( name, s );                /* save file name */    semester or year) is modelled as a multinomial logistic.  The hPx
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    matrix is simply the matrix product of nh*stepm elementary matrices
       dirc[l1-l2] = 0;                  /* add zero */    and the contribution of each individual to the likelihood is simply
    }    hPijx.
    l1 = strlen( dirc );                 /* length of directory */  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Also this programme outputs the covariance matrix of the parameters but also
    return( 0 );                         /* we're done */    of the life expectancies. It also computes the stable prevalence. 
 }    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
 /******************************************/    This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
 void replace(char *s, char*t)    It is copyrighted identically to a GNU software product, ie programme and
 {    software can be distributed freely for non commercial use. Latest version
   int i;    can be accessed at http://euroreves.ined.fr/imach .
   int lg=20;  
   i=0;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   lg=strlen(t);    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   for(i=0; i<= lg; i++) {    
     (s[i] = t[i]);    **********************************************************************/
     if (t[i]== '\\') s[i]='/';  /*
   }    main
 }    read parameterfile
     read datafile
 int nbocc(char *s, char occ)    concatwav
 {    freqsummary
   int i,j=0;    if (mle >= 1)
   int lg=20;      mlikeli
   i=0;    print results files
   lg=strlen(s);    if mle==1 
   for(i=0; i<= lg; i++) {       computes hessian
   if  (s[i] == occ ) j++;    read end of parameter file: agemin, agemax, bage, fage, estepm
   }        begin-prev-date,...
   return j;    open gnuplot file
 }    open html file
     stable prevalence
 void cutv(char *u,char *v, char*t, char occ)     for age prevalim()
 {    h Pij x
   int i,lg,j,p;    variance of p varprob
   i=0;    forecasting if prevfcast==1 prevforecast call prevalence()
   for(j=0; j<=strlen(t)-1; j++) {    health expectancies
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Variance-covariance of DFLE
   }    prevalence()
      movingaverage()
   lg=strlen(t);    varevsij() 
   for(j=0; j<p; j++) {    if popbased==1 varevsij(,popbased)
     (u[j] = t[j]);    total life expectancies
     u[p]='\0';    Variance of stable prevalence
   }   end
   */
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }  
 }   
   #include <math.h>
 /********************** nrerror ********************/  #include <stdio.h>
   #include <stdlib.h>
 void nrerror(char error_text[])  #include <string.h>
 {  #include <unistd.h>
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  /* #include <sys/time.h> */
   exit(1);  #include <time.h>
 }  #include "timeval.h"
 /*********************** vector *******************/  
 double *vector(int nl, int nh)  /* #include <libintl.h> */
 {  /* #define _(String) gettext (String) */
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #define MAXLINE 256
   if (!v) nrerror("allocation failure in vector");  #define GNUPLOTPROGRAM "gnuplot"
   return v-nl+NR_END;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 }  #define FILENAMELENGTH 132
   /*#define DEBUG*/
 /************************ free vector ******************/  /*#define windows*/
 void free_vector(double*v, int nl, int nh)  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 {  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   free((FREE_ARG)(v+nl-NR_END));  
 }  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  #define NINTERVMAX 8
 {  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   int *v;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #define NCOVMAX 8 /* Maximum number of covariates */
   if (!v) nrerror("allocation failure in ivector");  #define MAXN 20000
   return v-nl+NR_END;  #define YEARM 12. /* Number of months per year */
 }  #define AGESUP 130
   #define AGEBASE 40
 /******************free ivector **************************/  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
 void free_ivector(int *v, long nl, long nh)  #ifdef UNIX
 {  #define DIRSEPARATOR '/'
   free((FREE_ARG)(v+nl-NR_END));  #define ODIRSEPARATOR '\\'
 }  #else
   #define DIRSEPARATOR '\\'
 /******************* imatrix *******************************/  #define ODIRSEPARATOR '/'
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #endif
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {  /* $Id$ */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  /* $State$ */
   int **m;  
    char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";
   /* allocate pointers to rows */  char fullversion[]="$Revision$ $Date$"; 
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   if (!m) nrerror("allocation failure 1 in matrix()");  int nvar;
   m += NR_END;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   m -= nrl;  int npar=NPARMAX;
    int nlstate=2; /* Number of live states */
    int ndeath=1; /* Number of dead states */
   /* allocate rows and set pointers to them */  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  int popbased=0;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  int *wav; /* Number of waves for this individuual 0 is possible */
   m[nrl] -= ncl;  int maxwav; /* Maxim number of waves */
    int jmin, jmax; /* min, max spacing between 2 waves */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  int gipmx, gsw; /* Global variables on the number of contributions 
                       to the likelihood and the sum of weights (done by funcone)*/
   /* return pointer to array of pointers to rows */  int mle, weightopt;
   return m;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 }  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 /****************** free_imatrix *************************/             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 void free_imatrix(m,nrl,nrh,ncl,nch)  double jmean; /* Mean space between 2 waves */
       int **m;  double **oldm, **newm, **savm; /* Working pointers to matrices */
       long nch,ncl,nrh,nrl;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
      /* free an int matrix allocated by imatrix() */  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 {  FILE *ficlog, *ficrespow;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  int globpr; /* Global variable for printing or not */
   free((FREE_ARG) (m+nrl-NR_END));  double fretone; /* Only one call to likelihood */
 }  long ipmx; /* Number of contributions */
   double sw; /* Sum of weights */
 /******************* matrix *******************************/  char filerespow[FILENAMELENGTH];
 double **matrix(long nrl, long nrh, long ncl, long nch)  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 {  FILE *ficresilk;
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   double **m;  FILE *ficresprobmorprev;
   FILE *fichtm, *fichtmcov; /* Html File */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  FILE *ficreseij;
   if (!m) nrerror("allocation failure 1 in matrix()");  char filerese[FILENAMELENGTH];
   m += NR_END;  FILE  *ficresvij;
   m -= nrl;  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  char fileresvpl[FILENAMELENGTH];
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  char title[MAXLINE];
   m[nrl] += NR_END;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   m[nrl] -= ncl;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  char command[FILENAMELENGTH];
   return m;  int  outcmd=0;
 }  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  char filelog[FILENAMELENGTH]; /* Log file */
 {  char filerest[FILENAMELENGTH];
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  char fileregp[FILENAMELENGTH];
   free((FREE_ARG)(m+nrl-NR_END));  char popfile[FILENAMELENGTH];
 }  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 {  struct timezone tzp;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  extern int gettimeofday();
   double ***m;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   long time_value;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  extern long time();
   if (!m) nrerror("allocation failure 1 in matrix()");  char strcurr[80], strfor[80];
   m += NR_END;  
   m -= nrl;  #define NR_END 1
   #define FREE_ARG char*
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define FTOL 1.0e-10
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  #define NRANSI 
   m[nrl] -= ncl;  #define ITMAX 200 
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define TOL 2.0e-4 
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #define CGOLD 0.3819660 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  #define ZEPS 1.0e-10 
   m[nrl][ncl] += NR_END;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)  #define GOLD 1.618034 
     m[nrl][j]=m[nrl][j-1]+nlay;  #define GLIMIT 100.0 
    #define TINY 1.0e-20 
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  static double maxarg1,maxarg2;
     for (j=ncl+1; j<=nch; j++)  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       m[i][j]=m[i][j-1]+nlay;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   }    
   return m;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 }  #define rint(a) floor(a+0.5)
   
 /*************************free ma3x ************************/  static double sqrarg;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 {  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  int agegomp= AGEGOMP;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  int imx; 
 }  int stepm=1;
   /* Stepm, step in month: minimum step interpolation*/
 /***************** f1dim *************************/  
 extern int ncom;  int estepm;
 extern double *pcom,*xicom;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 extern double (*nrfunc)(double []);  
    int m,nb;
 double f1dim(double x)  long *num;
 {  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   int j;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double f;  double **pmmij, ***probs;
   double *xt;  double *ageexmed,*agecens;
    double dateintmean=0;
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  double *weight;
   f=(*nrfunc)(xt);  int **s; /* Status */
   free_vector(xt,1,ncom);  double *agedc, **covar, idx;
   return f;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 }  double *lsurv, *lpop, *tpop;
   
 /*****************brent *************************/  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  double ftolhess; /* Tolerance for computing hessian */
 {  
   int iter;  /**************** split *************************/
   double a,b,d,etemp;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   double fu,fv,fw,fx;  {
   double ftemp;    /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
   double p,q,r,tol1,tol2,u,v,w,x,xm;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   double e=0.0;    */ 
      char  *ss;                            /* pointer */
   a=(ax < cx ? ax : cx);    int   l1, l2;                         /* length counters */
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    l1 = strlen(path );                   /* length of path */
   fw=fv=fx=(*f)(x);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   for (iter=1;iter<=ITMAX;iter++) {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     xm=0.5*(a+b);    if ( ss == NULL ) {                   /* no directory, so use current */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     printf(".");fflush(stdout);      /* get current working directory */
 #ifdef DEBUG      /*    extern  char* getcwd ( char *buf , int len);*/
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */        return( GLOCK_ERROR_GETCWD );
 #endif      }
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){      strcpy( name, path );               /* we've got it */
       *xmin=x;    } else {                              /* strip direcotry from path */
       return fx;      ss++;                               /* after this, the filename */
     }      l2 = strlen( ss );                  /* length of filename */
     ftemp=fu;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     if (fabs(e) > tol1) {      strcpy( name, ss );         /* save file name */
       r=(x-w)*(fx-fv);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       q=(x-v)*(fx-fw);      dirc[l1-l2] = 0;                    /* add zero */
       p=(x-v)*q-(x-w)*r;    }
       q=2.0*(q-r);    l1 = strlen( dirc );                  /* length of directory */
       if (q > 0.0) p = -p;    /*#ifdef windows
       q=fabs(q);    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
       etemp=e;  #else
       e=d;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  #endif
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    */
       else {    ss = strrchr( name, '.' );            /* find last / */
         d=p/q;    if (ss >0){
         u=x+d;      ss++;
         if (u-a < tol2 || b-u < tol2)      strcpy(ext,ss);                     /* save extension */
           d=SIGN(tol1,xm-x);      l1= strlen( name);
       }      l2= strlen(ss)+1;
     } else {      strncpy( finame, name, l1-l2);
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      finame[l1-l2]= 0;
     }    }
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    return( 0 );                          /* we're done */
     fu=(*f)(u);  }
     if (fu <= fx) {  
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)  /******************************************/
         SHFT(fv,fw,fx,fu)  
         } else {  void replace_back_to_slash(char *s, char*t)
           if (u < x) a=u; else b=u;  {
           if (fu <= fw || w == x) {    int i;
             v=w;    int lg=0;
             w=u;    i=0;
             fv=fw;    lg=strlen(t);
             fw=fu;    for(i=0; i<= lg; i++) {
           } else if (fu <= fv || v == x || v == w) {      (s[i] = t[i]);
             v=u;      if (t[i]== '\\') s[i]='/';
             fv=fu;    }
           }  }
         }  
   }  int nbocc(char *s, char occ)
   nrerror("Too many iterations in brent");  {
   *xmin=x;    int i,j=0;
   return fx;    int lg=20;
 }    i=0;
     lg=strlen(s);
 /****************** mnbrak ***********************/    for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    }
             double (*func)(double))    return j;
 {  }
   double ulim,u,r,q, dum;  
   double fu;  void cutv(char *u,char *v, char*t, char occ)
    {
   *fa=(*func)(*ax);    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
   *fb=(*func)(*bx);       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
   if (*fb > *fa) {       gives u="abcedf" and v="ghi2j" */
     SHFT(dum,*ax,*bx,dum)    int i,lg,j,p=0;
       SHFT(dum,*fb,*fa,dum)    i=0;
       }    for(j=0; j<=strlen(t)-1; j++) {
   *cx=(*bx)+GOLD*(*bx-*ax);      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   *fc=(*func)(*cx);    }
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);    lg=strlen(t);
     q=(*bx-*cx)*(*fb-*fa);    for(j=0; j<p; j++) {
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      (u[j] = t[j]);
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    }
     ulim=(*bx)+GLIMIT*(*cx-*bx);       u[p]='\0';
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);     for(j=0; j<= lg; j++) {
     } else if ((*cx-u)*(u-ulim) > 0.0) {      if (j>=(p+1))(v[j-p-1] = t[j]);
       fu=(*func)(u);    }
       if (fu < *fc) {  }
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  /********************** nrerror ********************/
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  void nrerror(char error_text[])
       u=ulim;  {
       fu=(*func)(u);    fprintf(stderr,"ERREUR ...\n");
     } else {    fprintf(stderr,"%s\n",error_text);
       u=(*cx)+GOLD*(*cx-*bx);    exit(EXIT_FAILURE);
       fu=(*func)(u);  }
     }  /*********************** vector *******************/
     SHFT(*ax,*bx,*cx,u)  double *vector(int nl, int nh)
       SHFT(*fa,*fb,*fc,fu)  {
       }    double *v;
 }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
 /*************** linmin ************************/    return v-nl+NR_END;
   }
 int ncom;  
 double *pcom,*xicom;  /************************ free vector ******************/
 double (*nrfunc)(double []);  void free_vector(double*v, int nl, int nh)
    {
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    free((FREE_ARG)(v+nl-NR_END));
 {  }
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);  /************************ivector *******************************/
   double f1dim(double x);  int *ivector(long nl,long nh)
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  {
               double *fc, double (*func)(double));    int *v;
   int j;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   double xx,xmin,bx,ax;    if (!v) nrerror("allocation failure in ivector");
   double fx,fb,fa;    return v-nl+NR_END;
    }
   ncom=n;  
   pcom=vector(1,n);  /******************free ivector **************************/
   xicom=vector(1,n);  void free_ivector(int *v, long nl, long nh)
   nrfunc=func;  {
   for (j=1;j<=n;j++) {    free((FREE_ARG)(v+nl-NR_END));
     pcom[j]=p[j];  }
     xicom[j]=xi[j];  
   }  /************************lvector *******************************/
   ax=0.0;  long *lvector(long nl,long nh)
   xx=1.0;  {
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    long *v;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 #ifdef DEBUG    if (!v) nrerror("allocation failure in ivector");
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    return v-nl+NR_END;
 #endif  }
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;  /******************free lvector **************************/
     p[j] += xi[j];  void free_lvector(long *v, long nl, long nh)
   }  {
   free_vector(xicom,1,n);    free((FREE_ARG)(v+nl-NR_END));
   free_vector(pcom,1,n);  }
 }  
   /******************* imatrix *******************************/
 /*************** powell ************************/  int **imatrix(long nrl, long nrh, long ncl, long nch) 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
             double (*func)(double []))  { 
 {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   void linmin(double p[], double xi[], int n, double *fret,    int **m; 
               double (*func)(double []));    
   int i,ibig,j;    /* allocate pointers to rows */ 
   double del,t,*pt,*ptt,*xit;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   double fp,fptt;    if (!m) nrerror("allocation failure 1 in matrix()"); 
   double *xits;    m += NR_END; 
   pt=vector(1,n);    m -= nrl; 
   ptt=vector(1,n);    
   xit=vector(1,n);    
   xits=vector(1,n);    /* allocate rows and set pointers to them */ 
   *fret=(*func)(p);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   for (j=1;j<=n;j++) pt[j]=p[j];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   for (*iter=1;;++(*iter)) {    m[nrl] += NR_END; 
     fp=(*fret);    m[nrl] -= ncl; 
     ibig=0;    
     del=0.0;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    
     for (i=1;i<=n;i++)    /* return pointer to array of pointers to rows */ 
       printf(" %d %.12f",i, p[i]);    return m; 
     printf("\n");  } 
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  /****************** free_imatrix *************************/
       fptt=(*fret);  void free_imatrix(m,nrl,nrh,ncl,nch)
 #ifdef DEBUG        int **m;
       printf("fret=%lf \n",*fret);        long nch,ncl,nrh,nrl; 
 #endif       /* free an int matrix allocated by imatrix() */ 
       printf("%d",i);fflush(stdout);  { 
       linmin(p,xit,n,fret,func);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       if (fabs(fptt-(*fret)) > del) {    free((FREE_ARG) (m+nrl-NR_END)); 
         del=fabs(fptt-(*fret));  } 
         ibig=i;  
       }  /******************* matrix *******************************/
 #ifdef DEBUG  double **matrix(long nrl, long nrh, long ncl, long nch)
       printf("%d %.12e",i,(*fret));  {
       for (j=1;j<=n;j++) {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    double **m;
         printf(" x(%d)=%.12e",j,xit[j]);  
       }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       for(j=1;j<=n;j++)    if (!m) nrerror("allocation failure 1 in matrix()");
         printf(" p=%.12e",p[j]);    m += NR_END;
       printf("\n");    m -= nrl;
 #endif  
     }    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 #ifdef DEBUG    m[nrl] += NR_END;
       int k[2],l;    m[nrl] -= ncl;
       k[0]=1;  
       k[1]=-1;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       printf("Max: %.12e",(*func)(p));    return m;
       for (j=1;j<=n;j++)    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
         printf(" %.12e",p[j]);     */
       printf("\n");  }
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {  /*************************free matrix ************************/
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  {
         }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    free((FREE_ARG)(m+nrl-NR_END));
       }  }
 #endif  
   /******************* ma3x *******************************/
   double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       free_vector(xit,1,n);  {
       free_vector(xits,1,n);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       free_vector(ptt,1,n);    double ***m;
       free_vector(pt,1,n);  
       return;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     }    if (!m) nrerror("allocation failure 1 in matrix()");
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    m += NR_END;
     for (j=1;j<=n;j++) {    m -= nrl;
       ptt[j]=2.0*p[j]-pt[j];  
       xit[j]=p[j]-pt[j];    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       pt[j]=p[j];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     }    m[nrl] += NR_END;
     fptt=(*func)(ptt);    m[nrl] -= ncl;
     if (fptt < fp) {  
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         for (j=1;j<=n;j++) {    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
           xi[j][ibig]=xi[j][n];    m[nrl][ncl] += NR_END;
           xi[j][n]=xit[j];    m[nrl][ncl] -= nll;
         }    for (j=ncl+1; j<=nch; j++) 
 #ifdef DEBUG      m[nrl][j]=m[nrl][j-1]+nlay;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    
         for(j=1;j<=n;j++)    for (i=nrl+1; i<=nrh; i++) {
           printf(" %.12e",xit[j]);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         printf("\n");      for (j=ncl+1; j<=nch; j++) 
 #endif        m[i][j]=m[i][j-1]+nlay;
       }    }
     }    return m; 
   }    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 }             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     */
 /**** Prevalence limit ****************/  }
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  /*************************free ma3x ************************/
 {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  {
      matrix by transitions matrix until convergence is reached */    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
   int i, ii,j,k;    free((FREE_ARG)(m+nrl-NR_END));
   double min, max, maxmin, maxmax,sumnew=0.;  }
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();  /*************** function subdirf ***********/
   double **newm;  char *subdirf(char fileres[])
   double agefin, delaymax=50 ; /* Max number of years to converge */  {
     /* Caution optionfilefiname is hidden */
   for (ii=1;ii<=nlstate+ndeath;ii++)    strcpy(tmpout,optionfilefiname);
     for (j=1;j<=nlstate+ndeath;j++){    strcat(tmpout,"/"); /* Add to the right */
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    strcat(tmpout,fileres);
     }    return tmpout;
   /* 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;  /*************** function subdirf2 ***********/
     /* Covariates have to be included here again */  char *subdirf2(char fileres[], char *preop)
     cov[1]=1.;  {
     cov[2]=agefin;    
     if (cptcovn>0){    /* Caution optionfilefiname is hidden */
       for (k=1; k<=cptcovn;k++) {cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];/*printf("Tcode[ij]=%d nbcode=%d\n",Tcode[ij],nbcode[k][Tcode[ij]]);*/}    strcpy(tmpout,optionfilefiname);
     }    strcat(tmpout,"/");
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    strcat(tmpout,preop);
     strcat(tmpout,fileres);
     savm=oldm;    return tmpout;
     oldm=newm;  }
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){  /*************** function subdirf3 ***********/
       min=1.;  char *subdirf3(char fileres[], char *preop, char *preop2)
       max=0.;  {
       for(i=1; i<=nlstate; i++) {    
         sumnew=0;    /* Caution optionfilefiname is hidden */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    strcpy(tmpout,optionfilefiname);
         prlim[i][j]= newm[i][j]/(1-sumnew);    strcat(tmpout,"/");
         max=FMAX(max,prlim[i][j]);    strcat(tmpout,preop);
         min=FMIN(min,prlim[i][j]);    strcat(tmpout,preop2);
       }    strcat(tmpout,fileres);
       maxmin=max-min;    return tmpout;
       maxmax=FMAX(maxmax,maxmin);  }
     }  
     if(maxmax < ftolpl){  /***************** f1dim *************************/
       return prlim;  extern int ncom; 
     }  extern double *pcom,*xicom;
   }  extern double (*nrfunc)(double []); 
 }   
   double f1dim(double x) 
 /*************** transition probabilities **********/  { 
     int j; 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    double f;
 {    double *xt; 
   double s1, s2;   
   /*double t34;*/    xt=vector(1,ncom); 
   int i,j,j1, nc, ii, jj;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
     for(i=1; i<= nlstate; i++){    free_vector(xt,1,ncom); 
     for(j=1; j<i;j++){    return f; 
       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];  /*****************brent *************************/
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       }  { 
       ps[i][j]=s2;    int iter; 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    double a,b,d,etemp;
     }    double fu,fv,fw,fx;
     for(j=i+1; j<=nlstate+ndeath;j++){    double ftemp;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    double p,q,r,tol1,tol2,u,v,w,x,xm; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    double e=0.0; 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/   
       }    a=(ax < cx ? ax : cx); 
       ps[i][j]=s2;    b=(ax > cx ? ax : cx); 
     }    x=w=v=bx; 
   }    fw=fv=fx=(*f)(x); 
   for(i=1; i<= nlstate; i++){    for (iter=1;iter<=ITMAX;iter++) { 
      s1=0;      xm=0.5*(a+b); 
     for(j=1; j<i; j++)      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       s1+=exp(ps[i][j]);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     for(j=i+1; j<=nlstate+ndeath; j++)      printf(".");fflush(stdout);
       s1+=exp(ps[i][j]);      fprintf(ficlog,".");fflush(ficlog);
     ps[i][i]=1./(s1+1.);  #ifdef DEBUG
     for(j=1; j<i; j++)      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       ps[i][j]= exp(ps[i][j])*ps[i][i];      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     for(j=i+1; j<=nlstate+ndeath; j++)      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  #endif
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   } /* end i */        *xmin=x; 
         return fx; 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      } 
     for(jj=1; jj<= nlstate+ndeath; jj++){      ftemp=fu;
       ps[ii][jj]=0;      if (fabs(e) > tol1) { 
       ps[ii][ii]=1;        r=(x-w)*(fx-fv); 
     }        q=(x-v)*(fx-fw); 
   }        p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        if (q > 0.0) p = -p; 
     for(jj=1; jj<= nlstate+ndeath; jj++){        q=fabs(q); 
      printf("%lf ",ps[ii][jj]);        etemp=e; 
    }        e=d; 
     printf("\n ");        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     }          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     printf("\n ");printf("%lf ",cov[2]);*/        else { 
 /*          d=p/q; 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          u=x+d; 
   goto end;*/          if (u-a < tol2 || b-u < tol2) 
     return ps;            d=SIGN(tol1,xm-x); 
 }        } 
       } else { 
 /**************** Product of 2 matrices ******************/        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 {      fu=(*f)(u); 
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      if (fu <= fx) { 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        if (u >= x) a=x; else b=x; 
   /* in, b, out are matrice of pointers which should have been initialized        SHFT(v,w,x,u) 
      before: only the contents of out is modified. The function returns          SHFT(fv,fw,fx,fu) 
      a pointer to pointers identical to out */          } else { 
   long i, j, k;            if (u < x) a=u; else b=u; 
   for(i=nrl; i<= nrh; i++)            if (fu <= fw || w == x) { 
     for(k=ncolol; k<=ncoloh; k++)              v=w; 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)              w=u; 
         out[i][k] +=in[i][j]*b[j][k];              fv=fw; 
               fw=fu; 
   return out;            } else if (fu <= fv || v == x || v == w) { 
 }              v=u; 
               fv=fu; 
             } 
 /************* 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 )    nrerror("Too many iterations in brent"); 
 {    *xmin=x; 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    return fx; 
      duration (i.e. until  } 
      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  /****************** mnbrak ***********************/
      (typically every 2 years instead of every month which is too big).  
      Model is determined by parameters x and covariates have to be  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
      included manually here.              double (*func)(double)) 
   { 
      */    double ulim,u,r,q, dum;
     double fu; 
   int i, j, d, h, k;   
   double **out, cov[NCOVMAX];    *fa=(*func)(*ax); 
   double **newm;    *fb=(*func)(*bx); 
     if (*fb > *fa) { 
   /* Hstepm could be zero and should return the unit matrix */      SHFT(dum,*ax,*bx,dum) 
   for (i=1;i<=nlstate+ndeath;i++)        SHFT(dum,*fb,*fa,dum) 
     for (j=1;j<=nlstate+ndeath;j++){        } 
       oldm[i][j]=(i==j ? 1.0 : 0.0);    *cx=(*bx)+GOLD*(*bx-*ax); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);    *fc=(*func)(*cx); 
     }    while (*fb > *fc) { 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      r=(*bx-*ax)*(*fb-*fc); 
   for(h=1; h <=nhstepm; h++){      q=(*bx-*cx)*(*fb-*fa); 
     for(d=1; d <=hstepm; d++){      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       newm=savm;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       /* Covariates have to be included here again */      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       cov[1]=1.;      if ((*bx-u)*(u-*cx) > 0.0) { 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        fu=(*func)(u); 
       if (cptcovn>0){      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];        fu=(*func)(u); 
     }        if (fu < *fc) { 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/            SHFT(*fb,*fc,fu,(*func)(u)) 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,            } 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       savm=oldm;        u=ulim; 
       oldm=newm;        fu=(*func)(u); 
     }      } else { 
     for(i=1; i<=nlstate+ndeath; i++)        u=(*cx)+GOLD*(*cx-*bx); 
       for(j=1;j<=nlstate+ndeath;j++) {        fu=(*func)(u); 
         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]);      SHFT(*ax,*bx,*cx,u) 
          */        SHFT(*fa,*fb,*fc,fu) 
       }        } 
   } /* end h */  } 
   return po;  
 }  /*************** linmin ************************/
   
   int ncom; 
 /*************** log-likelihood *************/  double *pcom,*xicom;
 double func( double *x)  double (*nrfunc)(double []); 
 {   
   int i, ii, j, k, mi, d;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  { 
   double **out;    double brent(double ax, double bx, double cx, 
   double sw; /* Sum of weights */                 double (*f)(double), double tol, double *xmin); 
   double lli; /* Individual log likelihood */    double f1dim(double x); 
   long ipmx;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   /*extern weight */                double *fc, double (*func)(double)); 
   /* We are differentiating ll according to initial status */    int j; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    double xx,xmin,bx,ax; 
   /*for(i=1;i<imx;i++)    double fx,fb,fa;
 printf(" %d\n",s[4][i]);   
   */    ncom=n; 
     pcom=vector(1,n); 
   for(k=1; k<=nlstate; k++) ll[k]=0.;    xicom=vector(1,n); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    nrfunc=func; 
        for(mi=1; mi<= wav[i]-1; mi++){    for (j=1;j<=n;j++) { 
       for (ii=1;ii<=nlstate+ndeath;ii++)      pcom[j]=p[j]; 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      xicom[j]=xi[j]; 
             for(d=0; d<dh[mi][i]; d++){    } 
         newm=savm;    ax=0.0; 
           cov[1]=1.;    xx=1.0; 
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
           if (cptcovn>0){    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
             for (k=1; k<=cptcovn;k++) cov[2+k]=covar[1+k-1][i];  #ifdef DEBUG
             }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  #endif
           savm=oldm;    for (j=1;j<=n;j++) { 
           oldm=newm;      xi[j] *= xmin; 
       p[j] += xi[j]; 
     } 
       } /* end mult */    free_vector(xicom,1,n); 
        free_vector(pcom,1,n); 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  } 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  
       ipmx +=1;  char *asc_diff_time(long time_sec, char ascdiff[])
       sw += weight[i];  {
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    long sec_left, days, hours, minutes;
     } /* end of wave */    days = (time_sec) / (60*60*24);
   } /* end of individual */    sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    sec_left = (sec_left) %(60*60);
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    minutes = (sec_left) /60;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    sec_left = (sec_left) % (60);
   return -l;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
 }    return ascdiff;
   }
   
 /*********** Maximum Likelihood Estimation ***************/  /*************** powell ************************/
   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))              double (*func)(double [])) 
 {  { 
   int i,j, iter;    void linmin(double p[], double xi[], int n, double *fret, 
   double **xi,*delti;                double (*func)(double [])); 
   double fret;    int i,ibig,j; 
   xi=matrix(1,npar,1,npar);    double del,t,*pt,*ptt,*xit;
   for (i=1;i<=npar;i++)    double fp,fptt;
     for (j=1;j<=npar;j++)    double *xits;
       xi[i][j]=(i==j ? 1.0 : 0.0);    int niterf, itmp;
   printf("Powell\n");  
   powell(p,xi,npar,ftol,&iter,&fret,func);    pt=vector(1,n); 
     ptt=vector(1,n); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    xit=vector(1,n); 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));    xits=vector(1,n); 
     *fret=(*func)(p); 
 }    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
 /**** Computes Hessian and covariance matrix ***/      fp=(*fret); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      ibig=0; 
 {      del=0.0; 
   double  **a,**y,*x,pd;      last_time=curr_time;
   double **hess;      (void) gettimeofday(&curr_time,&tzp);
   int i, j,jk;      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);
   int *indx;      /*    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
       fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   double hessii(double p[], double delta, int theta, double delti[]);      */
   double hessij(double p[], double delti[], int i, int j);     for (i=1;i<=n;i++) {
   void lubksb(double **a, int npar, int *indx, double b[]) ;        printf(" %d %.12f",i, p[i]);
   void ludcmp(double **a, int npar, int *indx, double *d) ;        fprintf(ficlog," %d %.12lf",i, p[i]);
         fprintf(ficrespow," %.12lf", p[i]);
       }
   hess=matrix(1,npar,1,npar);      printf("\n");
       fprintf(ficlog,"\n");
   printf("\nCalculation of the hessian matrix. Wait...\n");      fprintf(ficrespow,"\n");fflush(ficrespow);
   for (i=1;i<=npar;i++){      if(*iter <=3){
     printf("%d",i);fflush(stdout);        tm = *localtime(&curr_time.tv_sec);
     hess[i][i]=hessii(p,ftolhess,i,delti);        strcpy(strcurr,asctime(&tm));
     /*printf(" %f ",p[i]);*/  /*       asctime_r(&tm,strcurr); */
   }        forecast_time=curr_time; 
         itmp = strlen(strcurr);
   for (i=1;i<=npar;i++) {        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     for (j=1;j<=npar;j++)  {          strcurr[itmp-1]='\0';
       if (j>i) {        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         printf(".%d%d",i,j);fflush(stdout);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         hess[i][j]=hessij(p,delti,i,j);        for(niterf=10;niterf<=30;niterf+=10){
         hess[j][i]=hess[i][j];          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); */
   }          strcpy(strfor,asctime(&tmf));
   printf("\n");          itmp = strlen(strfor);
           if(strfor[itmp-1]=='\n')
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          strfor[itmp-1]='\0';
            printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
   a=matrix(1,npar,1,npar);          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
   y=matrix(1,npar,1,npar);        }
   x=vector(1,npar);      }
   indx=ivector(1,npar);      for (i=1;i<=n;i++) { 
   for (i=1;i<=npar;i++)        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        fptt=(*fret); 
   ludcmp(a,npar,indx,&pd);  #ifdef DEBUG
         printf("fret=%lf \n",*fret);
   for (j=1;j<=npar;j++) {        fprintf(ficlog,"fret=%lf \n",*fret);
     for (i=1;i<=npar;i++) x[i]=0;  #endif
     x[j]=1;        printf("%d",i);fflush(stdout);
     lubksb(a,npar,indx,x);        fprintf(ficlog,"%d",i);fflush(ficlog);
     for (i=1;i<=npar;i++){        linmin(p,xit,n,fret,func); 
       matcov[i][j]=x[i];        if (fabs(fptt-(*fret)) > del) { 
     }          del=fabs(fptt-(*fret)); 
   }          ibig=i; 
         } 
   printf("\n#Hessian matrix#\n");  #ifdef DEBUG
   for (i=1;i<=npar;i++) {        printf("%d %.12e",i,(*fret));
     for (j=1;j<=npar;j++) {        fprintf(ficlog,"%d %.12e",i,(*fret));
       printf("%.3e ",hess[i][j]);        for (j=1;j<=n;j++) {
     }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     printf("\n");          printf(" x(%d)=%.12e",j,xit[j]);
   }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         }
   /* Recompute Inverse */        for(j=1;j<=n;j++) {
   for (i=1;i<=npar;i++)          printf(" p=%.12e",p[j]);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          fprintf(ficlog," p=%.12e",p[j]);
   ludcmp(a,npar,indx,&pd);        }
         printf("\n");
   /*  printf("\n#Hessian matrix recomputed#\n");        fprintf(ficlog,"\n");
   #endif
   for (j=1;j<=npar;j++) {      } 
     for (i=1;i<=npar;i++) x[i]=0;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     x[j]=1;  #ifdef DEBUG
     lubksb(a,npar,indx,x);        int k[2],l;
     for (i=1;i<=npar;i++){        k[0]=1;
       y[i][j]=x[i];        k[1]=-1;
       printf("%.3e ",y[i][j]);        printf("Max: %.12e",(*func)(p));
     }        fprintf(ficlog,"Max: %.12e",(*func)(p));
     printf("\n");        for (j=1;j<=n;j++) {
   }          printf(" %.12e",p[j]);
   */          fprintf(ficlog," %.12e",p[j]);
         }
   free_matrix(a,1,npar,1,npar);        printf("\n");
   free_matrix(y,1,npar,1,npar);        fprintf(ficlog,"\n");
   free_vector(x,1,npar);        for(l=0;l<=1;l++) {
   free_ivector(indx,1,npar);          for (j=1;j<=n;j++) {
   free_matrix(hess,1,npar,1,npar);            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]);
             fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 }          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 /*************** hessian matrix ****************/          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 double hessii( double x[], double delta, int theta, double delti[])        }
 {  #endif
   int i;  
   int l=1, lmax=20;  
   double k1,k2;        free_vector(xit,1,n); 
   double p2[NPARMAX+1];        free_vector(xits,1,n); 
   double res;        free_vector(ptt,1,n); 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        free_vector(pt,1,n); 
   double fx;        return; 
   int k=0,kmax=10;      } 
   double l1;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
   fx=func(x);        ptt[j]=2.0*p[j]-pt[j]; 
   for (i=1;i<=npar;i++) p2[i]=x[i];        xit[j]=p[j]-pt[j]; 
   for(l=0 ; l <=lmax; l++){        pt[j]=p[j]; 
     l1=pow(10,l);      } 
     delts=delt;      fptt=(*func)(ptt); 
     for(k=1 ; k <kmax; k=k+1){      if (fptt < fp) { 
       delt = delta*(l1*k);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       p2[theta]=x[theta] +delt;        if (t < 0.0) { 
       k1=func(p2)-fx;          linmin(p,xit,n,fret,func); 
       p2[theta]=x[theta]-delt;          for (j=1;j<=n;j++) { 
       k2=func(p2)-fx;            xi[j][ibig]=xi[j][n]; 
       /*res= (k1-2.0*fx+k2)/delt/delt; */            xi[j][n]=xit[j]; 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          }
        #ifdef DEBUG
 #ifdef DEBUG          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 #endif          for(j=1;j<=n;j++){
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */            printf(" %.12e",xit[j]);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){            fprintf(ficlog," %.12e",xit[j]);
         k=kmax;          }
       }          printf("\n");
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          fprintf(ficlog,"\n");
         k=kmax; l=lmax*10.;  #endif
       }        }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      } 
         delts=delt;    } 
       }  } 
     }  
   }  /**** Prevalence limit (stable prevalence)  ****************/
   delti[theta]=delts;  
   return res;  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
        matrix by transitions matrix until convergence is reached */
 double hessij( double x[], double delti[], int thetai,int thetaj)  
 {    int i, ii,j,k;
   int i;    double min, max, maxmin, maxmax,sumnew=0.;
   int l=1, l1, lmax=20;    double **matprod2();
   double k1,k2,k3,k4,res,fx;    double **out, cov[NCOVMAX], **pmij();
   double p2[NPARMAX+1];    double **newm;
   int k;    double agefin, delaymax=50 ; /* Max number of years to converge */
   
   fx=func(x);    for (ii=1;ii<=nlstate+ndeath;ii++)
   for (k=1; k<=2; k++) {      for (j=1;j<=nlstate+ndeath;j++){
     for (i=1;i<=npar;i++) p2[i]=x[i];        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetai]=x[thetai]+delti[thetai]/k;      }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k1=func(p2)-fx;     cov[1]=1.;
     
     p2[thetai]=x[thetai]+delti[thetai]/k;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     k2=func(p2)-fx;      newm=savm;
        /* Covariates have to be included here again */
     p2[thetai]=x[thetai]-delti[thetai]/k;       cov[2]=agefin;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    
     k3=func(p2)-fx;        for (k=1; k<=cptcovn;k++) {
            cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     p2[thetai]=x[thetai]-delti[thetai]/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]]);*/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        }
     k4=func(p2)-fx;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        for (k=1; k<=cptcovprod;k++)
 #ifdef DEBUG          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     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        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   }        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   return res;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
 }      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
 /************** Inverse of matrix **************/      savm=oldm;
 void ludcmp(double **a, int n, int *indx, double *d)      oldm=newm;
 {      maxmax=0.;
   int i,imax,j,k;      for(j=1;j<=nlstate;j++){
   double big,dum,sum,temp;        min=1.;
   double *vv;        max=0.;
          for(i=1; i<=nlstate; i++) {
   vv=vector(1,n);          sumnew=0;
   *d=1.0;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   for (i=1;i<=n;i++) {          prlim[i][j]= newm[i][j]/(1-sumnew);
     big=0.0;          max=FMAX(max,prlim[i][j]);
     for (j=1;j<=n;j++)          min=FMIN(min,prlim[i][j]);
       if ((temp=fabs(a[i][j])) > big) big=temp;        }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        maxmin=max-min;
     vv[i]=1.0/big;        maxmax=FMAX(maxmax,maxmin);
   }      }
   for (j=1;j<=n;j++) {      if(maxmax < ftolpl){
     for (i=1;i<j;i++) {        return prlim;
       sum=a[i][j];      }
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    }
       a[i][j]=sum;  }
     }  
     big=0.0;  /*************** transition probabilities ***************/ 
     for (i=j;i<=n;i++) {  
       sum=a[i][j];  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       for (k=1;k<j;k++)  {
         sum -= a[i][k]*a[k][j];    double s1, s2;
       a[i][j]=sum;    /*double t34;*/
       if ( (dum=vv[i]*fabs(sum)) >= big) {    int i,j,j1, nc, ii, jj;
         big=dum;  
         imax=i;      for(i=1; i<= nlstate; i++){
       }        for(j=1; j<i;j++){
     }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     if (j != imax) {            /*s2 += param[i][j][nc]*cov[nc];*/
       for (k=1;k<=n;k++) {            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         dum=a[imax][k];  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
         a[imax][k]=a[j][k];          }
         a[j][k]=dum;          ps[i][j]=s2;
       }  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
       *d = -(*d);        }
       vv[imax]=vv[j];        for(j=i+1; j<=nlstate+ndeath;j++){
     }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     indx[j]=imax;            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     if (a[j][j] == 0.0) a[j][j]=TINY;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     if (j != n) {          }
       dum=1.0/(a[j][j]);          ps[i][j]=s2;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        }
     }      }
   }      /*ps[3][2]=1;*/
   free_vector(vv,1,n);  /* Doesn't work */      
 ;      for(i=1; i<= nlstate; i++){
 }        s1=0;
         for(j=1; j<i; j++)
 void lubksb(double **a, int n, int *indx, double b[])          s1+=exp(ps[i][j]);
 {        for(j=i+1; j<=nlstate+ndeath; j++)
   int i,ii=0,ip,j;          s1+=exp(ps[i][j]);
   double sum;        ps[i][i]=1./(s1+1.);
          for(j=1; j<i; j++)
   for (i=1;i<=n;i++) {          ps[i][j]= exp(ps[i][j])*ps[i][i];
     ip=indx[i];        for(j=i+1; j<=nlstate+ndeath; j++)
     sum=b[ip];          ps[i][j]= exp(ps[i][j])*ps[i][i];
     b[ip]=b[i];        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     if (ii)      } /* end i */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      
     else if (sum) ii=i;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     b[i]=sum;        for(jj=1; jj<= nlstate+ndeath; jj++){
   }          ps[ii][jj]=0;
   for (i=n;i>=1;i--) {          ps[ii][ii]=1;
     sum=b[i];        }
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      }
     b[i]=sum/a[i][i];      
   }  
 }  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
 /************ Frequencies ********************/  /*         printf("ddd %lf ",ps[ii][jj]); */
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)  /*       } */
 {  /* Some frequencies */  /*       printf("\n "); */
    /*        } */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  /*        printf("\n ");printf("%lf ",cov[2]); */
   double ***freq; /* Frequencies */         /*
   double *pp;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   double pos;        goto end;*/
   FILE *ficresp;      return ps;
   char fileresp[FILENAMELENGTH];  }
   
   pp=vector(1,nlstate);  /**************** Product of 2 matrices ******************/
   
   strcpy(fileresp,"p");  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   strcat(fileresp,fileres);  {
   if((ficresp=fopen(fileresp,"w"))==NULL) {    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     printf("Problem with prevalence resultfile: %s\n", fileresp);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     exit(0);    /* in, b, out are matrice of pointers which should have been initialized 
   }       before: only the contents of out is modified. The function returns
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);       a pointer to pointers identical to out */
   j1=0;    long i, j, k;
     for(i=nrl; i<= nrh; i++)
   j=cptcovn;      for(k=ncolol; k<=ncoloh; k++)
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        for(j=ncl,out[i][k]=0.; j<=nch; j++)
           out[i][k] +=in[i][j]*b[j][k];
   for(k1=1; k1<=j;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){    return out;
        j1++;  }
   
         for (i=-1; i<=nlstate+ndeath; i++)    
          for (jk=-1; jk<=nlstate+ndeath; jk++)    /************* Higher Matrix Product ***************/
            for(m=agemin; m <= agemax+3; m++)  
              freq[i][jk][m]=0;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
          {
        for (i=1; i<=imx; i++) {    /* Computes the transition matrix starting at age 'age' over 
          bool=1;       'nhstepm*hstepm*stepm' months (i.e. until
          if  (cptcovn>0) {       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
            for (z1=1; z1<=cptcovn; z1++)       nhstepm*hstepm matrices. 
              if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
          }       (typically every 2 years instead of every month which is too big 
           if (bool==1) {       for the memory).
            for(m=firstpass; m<=lastpass-1; m++){       Model is determined by parameters x and covariates have to be 
              if(agev[m][i]==0) agev[m][i]=agemax+1;       included manually here. 
              if(agev[m][i]==1) agev[m][i]=agemax+2;  
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];       */
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  
            }    int i, j, d, h, k;
          }    double **out, cov[NCOVMAX];
        }    double **newm;
         if  (cptcovn>0) {  
          fprintf(ficresp, "\n#Variable");    /* Hstepm could be zero and should return the unit matrix */
          for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);    for (i=1;i<=nlstate+ndeath;i++)
        }      for (j=1;j<=nlstate+ndeath;j++){
        fprintf(ficresp, "\n#");        oldm[i][j]=(i==j ? 1.0 : 0.0);
        for(i=1; i<=nlstate;i++)        po[i][j][0]=(i==j ? 1.0 : 0.0);
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      }
        fprintf(ficresp, "\n");    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
            for(h=1; h <=nhstepm; h++){
   for(i=(int)agemin; i <= (int)agemax+3; i++){      for(d=1; d <=hstepm; d++){
     if(i==(int)agemax+3)        newm=savm;
       printf("Total");        /* Covariates have to be included here again */
     else        cov[1]=1.;
       printf("Age %d", i);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     for(jk=1; jk <=nlstate ; jk++){        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        for (k=1; k<=cptcovage;k++)
         pp[jk] += freq[jk][m][i];          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     }        for (k=1; k<=cptcovprod;k++)
     for(jk=1; jk <=nlstate ; jk++){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       for(m=-1, pos=0; m <=0 ; m++)  
         pos += freq[jk][m][i];  
       if(pp[jk]>=1.e-10)        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       else        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     }        savm=oldm;
     for(jk=1; jk <=nlstate ; jk++){        oldm=newm;
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)      }
         pp[jk] += freq[jk][m][i];      for(i=1; i<=nlstate+ndeath; i++)
     }        for(j=1;j<=nlstate+ndeath;j++) {
     for(jk=1,pos=0; jk <=nlstate ; jk++)          po[i][j][h]=newm[i][j];
       pos += pp[jk];          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     for(jk=1; jk <=nlstate ; jk++){           */
       if(pos>=1.e-5)        }
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    } /* end h */
       else    return po;
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  }
       if( i <= (int) agemax){  
         if(pos>=1.e-5)  
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  /*************** log-likelihood *************/
       else  double func( double *x)
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  {
       }    int i, ii, j, k, mi, d, kk;
     }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     for(jk=-1; jk <=nlstate+ndeath; jk++)    double **out;
       for(m=-1; m <=nlstate+ndeath; m++)    double sw; /* Sum of weights */
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    double lli; /* Individual log likelihood */
     if(i <= (int) agemax)    int s1, s2;
       fprintf(ficresp,"\n");    double bbh, survp;
     printf("\n");    long ipmx;
     }    /*extern weight */
     }    /* We are differentiating ll according to initial status */
  }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      /*for(i=1;i<imx;i++) 
   fclose(ficresp);      printf(" %d\n",s[4][i]);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    */
   free_vector(pp,1,nlstate);    cov[1]=1.;
   
 }  /* End of Freq */    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
 /************* Waves Concatenation ***************/    if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 {        for(mi=1; mi<= wav[i]-1; mi++){
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          for (ii=1;ii<=nlstate+ndeath;ii++)
      Death is a valid wave (if date is known).            for (j=1;j<=nlstate+ndeath;j++){
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]              savm[ii][j]=(ii==j ? 1.0 : 0.0);
      and mw[mi+1][i]. dh depends on stepm.            }
      */          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   int i, mi, m;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;            for (kk=1; kk<=cptcovage;kk++) {
 float sum=0.;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
   for(i=1; i<=imx; i++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     mi=0;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     m=firstpass;            savm=oldm;
     while(s[m][i] <= nlstate){            oldm=newm;
       if(s[m][i]>=1)          } /* end mult */
         mw[++mi][i]=m;        
       if(m >=lastpass)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         break;          /* But now since version 0.9 we anticipate for bias at large stepm.
       else           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         m++;           * (in months) between two waves is not a multiple of stepm, we rounded to 
     }/* end while */           * the nearest (and in case of equal distance, to the lowest) interval but now
     if (s[m][i] > nlstate){           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       mi++;     /* Death is another wave */           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
       /* if(mi==0)  never been interviewed correctly before death */           * probability in order to take into account the bias as a fraction of the way
          /* Only death is a correct wave */           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
       mw[mi][i]=m;           * -stepm/2 to stepm/2 .
     }           * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
     wav[i]=mi;           */
     if(mi==0)          s1=s[mw[mi][i]][i];
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          s2=s[mw[mi+1][i]][i];
   }          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias bh is positive if real duration
   for(i=1; i<=imx; i++){           * is higher than the multiple of stepm and negative otherwise.
     for(mi=1; mi<wav[i];mi++){           */
       if (stepm <=0)          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         dh[mi][i]=1;          if( s2 > nlstate){ 
       else{            /* i.e. if s2 is a death state and if the date of death is known 
         if (s[mw[mi+1][i]][i] > nlstate) {               then the contribution to the likelihood is the probability to 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);               die between last step unit time and current  step unit time, 
           if(j=0) j=1;  /* Survives at least one month after exam */               which is also equal to probability to die before dh 
         }               minus probability to die before dh-stepm . 
         else{               In version up to 0.92 likelihood was computed
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          as if date of death was unknown. Death was treated as any other
           k=k+1;          health state: the date of the interview describes the actual state
           if (j >= jmax) jmax=j;          and not the date of a change in health state. The former idea was
           else if (j <= jmin)jmin=j;          to consider that at each interview the state was recorded
           sum=sum+j;          (healthy, disable or death) and IMaCh was corrected; but when we
         }          introduced the exact date of death then we should have modified
         jk= j/stepm;          the contribution of an exact death to the likelihood. This new
         jl= j -jk*stepm;          contribution is smaller and very dependent of the step unit
         ju= j -(jk+1)*stepm;          stepm. It is no more the probability to die between last interview
         if(jl <= -ju)          and month of death but the probability to survive from last
           dh[mi][i]=jk;          interview up to one month before death multiplied by the
         else          probability to die within a month. Thanks to Chris
           dh[mi][i]=jk+1;          Jackson for correcting this bug.  Former versions increased
         if(dh[mi][i]==0)          mortality artificially. The bad side is that we add another loop
           dh[mi][i]=1; /* At least one step */          which slows down the processing. The difference can be up to 10%
       }          lower mortality.
     }            */
   }            lli=log(out[s1][s2] - savm[s1][s2]);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);  
 }  
 /*********** Tricode ****************************/          } else if  (s2==-2) {
 void tricode(int *Tvar, int **nbcode, int imx)            for (j=1,survp=0. ; j<=nlstate; j++) 
 {              survp += out[s1][j];
   int Ndum[80],ij, k, j, i;            lli= survp;
   int cptcode=0;          }
   for (k=0; k<79; k++) Ndum[k]=0;          
   for (k=1; k<=7; k++) ncodemax[k]=0;          else if  (s2==-4) {
              for (j=3,survp=0. ; j<=nlstate; j++) 
   for (j=1; j<=cptcovn; j++) {              survp += out[s1][j];
     for (i=1; i<=imx; i++) {            lli= survp;
       ij=(int)(covar[Tvar[j]][i]);          }
       Ndum[ij]++;          
       if (ij > cptcode) cptcode=ij;          else if  (s2==-5) {
     }            for (j=1,survp=0. ; j<=2; j++) 
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/              survp += out[s1][j];
     for (i=0; i<=cptcode; i++) {            lli= survp;
       if(Ndum[i]!=0) ncodemax[j]++;          }
     }  
    
     ij=1;          else{
     for (i=1; i<=ncodemax[j]; i++) {            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       for (k=0; k<=79; k++) {            /*  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 (Ndum[k] != 0) {          } 
           nbcode[Tvar[j]][ij]=k;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           ij++;          /*if(lli ==000.0)*/
         }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
         if (ij > ncodemax[j]) break;          ipmx +=1;
       }            sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }          } /* end of wave */
       } /* end of individual */
   }    }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 /*********** Health Expectancies ****************/        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          for (ii=1;ii<=nlstate+ndeath;ii++)
 {            for (j=1;j<=nlstate+ndeath;j++){
   /* Health expectancies */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, j, nhstepm, hstepm, h;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double age, agelim,hf;            }
   double ***p3mat;          for(d=0; d<=dh[mi][i]; d++){
              newm=savm;
   fprintf(ficreseij,"# Health expectancies\n");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficreseij,"# Age");            for (kk=1; kk<=cptcovage;kk++) {
   for(i=1; i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(j=1; j<=nlstate;j++)            }
       fprintf(ficreseij," %1d-%1d",i,j);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   fprintf(ficreseij,"\n");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   hstepm=1*YEARM; /*  Every j years of age (in month) */            oldm=newm;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          } /* end mult */
         
   agelim=AGESUP;          s1=s[mw[mi][i]][i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          s2=s[mw[mi+1][i]][i];
     /* nhstepm age range expressed in number of stepm */          bbh=(double)bh[mi][i]/(double)stepm; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);          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 */
     /* Typically if 20 years = 20*12/6=40 stepm */          ipmx +=1;
     if (stepm >= YEARM) hstepm=1;          sw += weight[i];
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        } /* end of wave */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      } /* end of individual */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    }  else if(mle==3){  /* exponential inter-extrapolation */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        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(i=1; i<=nlstate;i++)          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(j=1; j<=nlstate;j++)            for (j=1;j<=nlstate+ndeath;j++){
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           eij[i][j][(int)age] +=p3mat[i][j][h];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            }
              for(d=0; d<dh[mi][i]; d++){
     hf=1;            newm=savm;
     if (stepm >= YEARM) hf=stepm/YEARM;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     fprintf(ficreseij,"%.0f",age );            for (kk=1; kk<=cptcovage;kk++) {
     for(i=1; i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(j=1; j<=nlstate;j++){            }
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     fprintf(ficreseij,"\n");            savm=oldm;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            oldm=newm;
   }          } /* end mult */
 }        
           s1=s[mw[mi][i]][i];
 /************ Variance ******************/          s2=s[mw[mi+1][i]][i];
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)          bbh=(double)bh[mi][i]/(double)stepm; 
 {          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   /* Variance of health expectancies */          ipmx +=1;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          sw += weight[i];
   double **newm;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double **dnewm,**doldm;        } /* end of wave */
   int i, j, nhstepm, hstepm, h;      } /* end of individual */
   int k, cptcode;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
    double *xp;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double **gp, **gm;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double ***gradg, ***trgradg;        for(mi=1; mi<= wav[i]-1; mi++){
   double ***p3mat;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double age,agelim;            for (j=1;j<=nlstate+ndeath;j++){
   int theta;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
    fprintf(ficresvij,"# Covariances of life expectancies\n");            }
   fprintf(ficresvij,"# Age");          for(d=0; d<dh[mi][i]; d++){
   for(i=1; i<=nlstate;i++)            newm=savm;
     for(j=1; j<=nlstate;j++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            for (kk=1; kk<=cptcovage;kk++) {
   fprintf(ficresvij,"\n");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
   xp=vector(1,npar);          
   dnewm=matrix(1,nlstate,1,npar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   doldm=matrix(1,nlstate,1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
   hstepm=1*YEARM; /* Every year of age */            oldm=newm;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          } /* end mult */
   agelim = AGESUP;        
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          s1=s[mw[mi][i]][i];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          s2=s[mw[mi+1][i]][i];
     if (stepm >= YEARM) hstepm=1;          if( s2 > nlstate){ 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            lli=log(out[s1][s2] - savm[s1][s2]);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }else{
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     gp=matrix(0,nhstepm,1,nlstate);          }
     gm=matrix(0,nhstepm,1,nlstate);          ipmx +=1;
           sw += weight[i];
     for(theta=1; theta <=npar; theta++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(i=1; i<=npar; i++){ /* Computes gradient */  /*      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]); */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        } /* end of wave */
       }      } /* end of individual */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(j=1; j<= nlstate; j++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(h=0; h<=nhstepm; h++){        for(mi=1; mi<= wav[i]-1; mi++){
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          for (ii=1;ii<=nlstate+ndeath;ii++)
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            for (j=1;j<=nlstate+ndeath;j++){
         }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                }
       for(i=1; i<=npar; i++) /* Computes gradient */          for(d=0; d<dh[mi][i]; d++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            newm=savm;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            for (kk=1; kk<=cptcovage;kk++) {
       for(j=1; j<= nlstate; j++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for(h=0; h<=nhstepm; h++){            }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
       for(j=1; j<= nlstate; j++)            oldm=newm;
         for(h=0; h<=nhstepm; h++){          } /* end mult */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        
         }          s1=s[mw[mi][i]][i];
     } /* End theta */          s2=s[mw[mi+1][i]][i];
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          ipmx +=1;
           sw += weight[i];
     for(h=0; h<=nhstepm; h++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(j=1; j<=nlstate;j++)          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         for(theta=1; theta <=npar; theta++)        } /* end of wave */
           trgradg[h][j][theta]=gradg[h][theta][j];      } /* end of individual */
     } /* End of if */
     for(i=1;i<=nlstate;i++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       for(j=1;j<=nlstate;j++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         vareij[i][j][(int)age] =0.;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     for(h=0;h<=nhstepm;h++){    return -l;
       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]);  /*************** log-likelihood *************/
         for(i=1;i<=nlstate;i++)  double funcone( double *x)
           for(j=1;j<=nlstate;j++)  {
             vareij[i][j][(int)age] += doldm[i][j];    /* Same as likeli but slower because of a lot of printf and if */
       }    int i, ii, j, k, mi, d, kk;
     }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     h=1;    double **out;
     if (stepm >= YEARM) h=stepm/YEARM;    double lli; /* Individual log likelihood */
     fprintf(ficresvij,"%.0f ",age );    double llt;
     for(i=1; i<=nlstate;i++)    int s1, s2;
       for(j=1; j<=nlstate;j++){    double bbh, survp;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    /*extern weight */
       }    /* We are differentiating ll according to initial status */
     fprintf(ficresvij,"\n");    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     free_matrix(gp,0,nhstepm,1,nlstate);    /*for(i=1;i<imx;i++) 
     free_matrix(gm,0,nhstepm,1,nlstate);      printf(" %d\n",s[4][i]);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    cov[1]=1.;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   } /* End age */    for(k=1; k<=nlstate; k++) ll[k]=0.;
    
   free_vector(xp,1,npar);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   free_matrix(doldm,1,nlstate,1,npar);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   free_matrix(dnewm,1,nlstate,1,nlstate);      for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)
 }          for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 /************ Variance of prevlim ******************/            savm[ii][j]=(ii==j ? 1.0 : 0.0);
 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)          }
 {        for(d=0; d<dh[mi][i]; d++){
   /* Variance of prevalence limit */          newm=savm;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double **newm;          for (kk=1; kk<=cptcovage;kk++) {
   double **dnewm,**doldm;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int i, j, nhstepm, hstepm;          }
   int k, cptcode;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double *xp;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double *gp, *gm;          savm=oldm;
   double **gradg, **trgradg;          oldm=newm;
   double age,agelim;        } /* end mult */
   int theta;        
            s1=s[mw[mi][i]][i];
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");        s2=s[mw[mi+1][i]][i];
   fprintf(ficresvpl,"# Age");        bbh=(double)bh[mi][i]/(double)stepm; 
   for(i=1; i<=nlstate;i++)        /* bias is positive if real duration
       fprintf(ficresvpl," %1d-%1d",i,i);         * is higher than the multiple of stepm and negative otherwise.
   fprintf(ficresvpl,"\n");         */
         if( s2 > nlstate && (mle <5) ){  /* Jackson */
   xp=vector(1,npar);          lli=log(out[s1][s2] - savm[s1][s2]);
   dnewm=matrix(1,nlstate,1,npar);        } else if (mle==1){
   doldm=matrix(1,nlstate,1,nlstate);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
          } else if(mle==2){
   hstepm=1*YEARM; /* Every year of age */          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 */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        } else if(mle==3){  /* exponential inter-extrapolation */
   agelim = AGESUP;          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 */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          lli=log(out[s1][s2]); /* Original formula */
     if (stepm >= YEARM) hstepm=1;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          lli=log(out[s1][s2]); /* Original formula */
     gradg=matrix(1,npar,1,nlstate);        } /* End of if */
     gp=vector(1,nlstate);        ipmx +=1;
     gm=vector(1,nlstate);        sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(theta=1; theta <=npar; theta++){  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       for(i=1; i<=npar; i++){ /* Computes gradient */        if(globpr){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
       }   %10.6f %10.6f %10.6f ", \
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       for(i=1;i<=nlstate;i++)                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         gp[i] = prlim[i][i];          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
                llt +=ll[k]*gipmx/gsw;
       for(i=1; i<=npar; i++) /* Computes gradient */            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          fprintf(ficresilk," %10.6f\n", -llt);
       for(i=1;i<=nlstate;i++)        }
         gm[i] = prlim[i][i];      } /* end of wave */
     } /* end of individual */
       for(i=1;i<=nlstate;i++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     } /* End theta */    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 */
     trgradg =matrix(1,nlstate,1,npar);      gipmx=ipmx;
       gsw=sw;
     for(j=1; j<=nlstate;j++)    }
       for(theta=1; theta <=npar; theta++)    return -l;
         trgradg[j][theta]=gradg[theta][j];  }
   
     for(i=1;i<=nlstate;i++)  
       varpl[i][(int)age] =0.;  /*************** function likelione ***********/
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  {
     for(i=1;i<=nlstate;i++)    /* This routine should help understanding what is done with 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */       the selection of individuals/waves and
        to check the exact contribution to the likelihood.
     fprintf(ficresvpl,"%.0f ",age );       Plotting could be done.
     for(i=1; i<=nlstate;i++)     */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    int k;
     fprintf(ficresvpl,"\n");  
     free_vector(gp,1,nlstate);    if(*globpri !=0){ /* Just counts and sums, no printings */
     free_vector(gm,1,nlstate);      strcpy(fileresilk,"ilk"); 
     free_matrix(gradg,1,npar,1,nlstate);      strcat(fileresilk,fileres);
     free_matrix(trgradg,1,nlstate,1,npar);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   } /* End age */        printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   free_vector(xp,1,npar);      }
   free_matrix(doldm,1,nlstate,1,npar);      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");
   free_matrix(dnewm,1,nlstate,1,nlstate);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
 }      for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
 /***********************************************/  
 /**************** Main Program *****************/    *fretone=(*funcone)(p);
 /***********************************************/    if(*globpri !=0){
       fclose(ficresilk);
 /*int main(int argc, char *argv[])*/      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
 int main()      fflush(fichtm); 
 {    } 
     return;
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;  }
   double agedeb, agefin,hf;  
   double agemin=1.e20, agemax=-1.e20;  
   /*********** Maximum Likelihood Estimation ***************/
   double fret;  
   double **xi,tmp,delta;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
   double dum; /* Dummy variable */    int i,j, iter;
   double ***p3mat;    double **xi;
   int *indx;    double fret;
   char line[MAXLINE], linepar[MAXLINE];    double fretone; /* Only one call to likelihood */
   char title[MAXLINE];    /*  char filerespow[FILENAMELENGTH];*/
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    xi=matrix(1,npar,1,npar);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];    for (i=1;i<=npar;i++)
   char filerest[FILENAMELENGTH];      for (j=1;j<=npar;j++)
   char fileregp[FILENAMELENGTH];        xi[i][j]=(i==j ? 1.0 : 0.0);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   int firstobs=1, lastobs=10;    strcpy(filerespow,"pow"); 
   int sdeb, sfin; /* Status at beginning and end */    strcat(filerespow,fileres);
   int c,  h , cpt,l;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   int ju,jl, mi;      printf("Problem with resultfile: %s\n", filerespow);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    }
      fprintf(ficrespow,"# Powell\n# iter -2*LL");
   int hstepm, nhstepm;    for (i=1;i<=nlstate;i++)
   double bage, fage, age, agelim, agebase;      for(j=1;j<=nlstate+ndeath;j++)
   double ftolpl=FTOL;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   double **prlim;    fprintf(ficrespow,"\n");
   double *severity;  
   double ***param; /* Matrix of parameters */    powell(p,xi,npar,ftol,&iter,&fret,func);
   double  *p;  
   double **matcov; /* Matrix of covariance */    fclose(ficrespow);
   double ***delti3; /* Scale */    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   double *delti; /* Scale */    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double ***eij, ***vareij;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double **varpl; /* Variances of prevalence limits by age */  
   double *epj, vepp;  }
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";  
   char *alph[]={"a","a","b","c","d","e"}, str[4];  /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   char z[1]="c", occ;  {
 #include <sys/time.h>    double  **a,**y,*x,pd;
 #include <time.h>    double **hess;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    int i, j,jk;
   /* long total_usecs;    int *indx;
   struct timeval start_time, end_time;  
      double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
   printf("\nIMACH, Version 0.64a");    double gompertz(double p[]);
   printf("\nEnter the parameter file name: ");    hess=matrix(1,npar,1,npar);
   
 #ifdef windows    printf("\nCalculation of the hessian matrix. Wait...\n");
   scanf("%s",pathtot);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   getcwd(pathcd, size);    for (i=1;i<=npar;i++){
   /*cygwin_split_path(pathtot,path,optionfile);      printf("%d",i);fflush(stdout);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      fprintf(ficlog,"%d",i);fflush(ficlog);
   /* cutv(path,optionfile,pathtot,'\\');*/     
        hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
 split(pathtot, path,optionfile);      
   chdir(path);      /*  printf(" %f ",p[i]);
   replace(pathc,path);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
 #endif    }
 #ifdef unix    
   scanf("%s",optionfile);    for (i=1;i<=npar;i++) {
 #endif      for (j=1;j<=npar;j++)  {
         if (j>i) { 
 /*-------- arguments in the command line --------*/          printf(".%d%d",i,j);fflush(stdout);
           fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   strcpy(fileres,"r");          hess[i][j]=hessij(p,delti,i,j,func,npar);
   strcat(fileres, optionfile);          
           hess[j][i]=hess[i][j];    
   /*---------arguments file --------*/          /*printf(" %lf ",hess[i][j]);*/
         }
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      }
     printf("Problem with optionfile %s\n",optionfile);    }
     goto end;    printf("\n");
   }    fprintf(ficlog,"\n");
   
   strcpy(filereso,"o");    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   strcat(filereso,fileres);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   if((ficparo=fopen(filereso,"w"))==NULL) {    
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    a=matrix(1,npar,1,npar);
   }    y=matrix(1,npar,1,npar);
     x=vector(1,npar);
   /* Reads comments: lines beginning with '#' */    indx=ivector(1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){    for (i=1;i<=npar;i++)
     ungetc(c,ficpar);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     fgets(line, MAXLINE, ficpar);    ludcmp(a,npar,indx,&pd);
     puts(line);  
     fputs(line,ficparo);    for (j=1;j<=npar;j++) {
   }      for (i=1;i<=npar;i++) x[i]=0;
   ungetc(c,ficpar);      x[j]=1;
       lubksb(a,npar,indx,x);
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);      for (i=1;i<=npar;i++){ 
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);        matcov[i][j]=x[i];
   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);      }
     }
   covar=matrix(1,NCOVMAX,1,n);      
   if (strlen(model)<=1) cptcovn=0;    printf("\n#Hessian matrix#\n");
   else {    fprintf(ficlog,"\n#Hessian matrix#\n");
     j=0;    for (i=1;i<=npar;i++) { 
     j=nbocc(model,'+');      for (j=1;j<=npar;j++) { 
     cptcovn=j+1;        printf("%.3e ",hess[i][j]);
   }        fprintf(ficlog,"%.3e ",hess[i][j]);
       }
   ncovmodel=2+cptcovn;      printf("\n");
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      fprintf(ficlog,"\n");
      }
   /* Read guess parameters */  
   /* Reads comments: lines beginning with '#' */    /* Recompute Inverse */
   while((c=getc(ficpar))=='#' && c!= EOF){    for (i=1;i<=npar;i++)
     ungetc(c,ficpar);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     fgets(line, MAXLINE, ficpar);    ludcmp(a,npar,indx,&pd);
     puts(line);  
     fputs(line,ficparo);    /*  printf("\n#Hessian matrix recomputed#\n");
   }  
   ungetc(c,ficpar);    for (j=1;j<=npar;j++) {
        for (i=1;i<=npar;i++) x[i]=0;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      x[j]=1;
     for(i=1; i <=nlstate; i++)      lubksb(a,npar,indx,x);
     for(j=1; j <=nlstate+ndeath-1; j++){      for (i=1;i<=npar;i++){ 
       fscanf(ficpar,"%1d%1d",&i1,&j1);        y[i][j]=x[i];
       fprintf(ficparo,"%1d%1d",i1,j1);        printf("%.3e ",y[i][j]);
       printf("%1d%1d",i,j);        fprintf(ficlog,"%.3e ",y[i][j]);
       for(k=1; k<=ncovmodel;k++){      }
         fscanf(ficpar," %lf",&param[i][j][k]);      printf("\n");
         printf(" %lf",param[i][j][k]);      fprintf(ficlog,"\n");
         fprintf(ficparo," %lf",param[i][j][k]);    }
       }    */
       fscanf(ficpar,"\n");  
       printf("\n");    free_matrix(a,1,npar,1,npar);
       fprintf(ficparo,"\n");    free_matrix(y,1,npar,1,npar);
     }    free_vector(x,1,npar);
      free_ivector(indx,1,npar);
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    free_matrix(hess,1,npar,1,npar);
   p=param[1][1];  
    
   /* Reads comments: lines beginning with '#' */  }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  /*************** hessian matrix ****************/
     fgets(line, MAXLINE, ficpar);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     puts(line);  {
     fputs(line,ficparo);    int i;
   }    int l=1, lmax=20;
   ungetc(c,ficpar);    double k1,k2;
     double p2[NPARMAX+1];
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    double res;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   for(i=1; i <=nlstate; i++){    double fx;
     for(j=1; j <=nlstate+ndeath-1; j++){    int k=0,kmax=10;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    double l1;
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);    fx=func(x);
       for(k=1; k<=ncovmodel;k++){    for (i=1;i<=npar;i++) p2[i]=x[i];
         fscanf(ficpar,"%le",&delti3[i][j][k]);    for(l=0 ; l <=lmax; l++){
         printf(" %le",delti3[i][j][k]);      l1=pow(10,l);
         fprintf(ficparo," %le",delti3[i][j][k]);      delts=delt;
       }      for(k=1 ; k <kmax; k=k+1){
       fscanf(ficpar,"\n");        delt = delta*(l1*k);
       printf("\n");        p2[theta]=x[theta] +delt;
       fprintf(ficparo,"\n");        k1=func(p2)-fx;
     }        p2[theta]=x[theta]-delt;
   }        k2=func(p2)-fx;
   delti=delti3[1][1];        /*res= (k1-2.0*fx+k2)/delt/delt; */
          res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   /* Reads comments: lines beginning with '#' */        
   while((c=getc(ficpar))=='#' && c!= EOF){  #ifdef DEBUG
     ungetc(c,ficpar);        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);
     fgets(line, MAXLINE, ficpar);        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);
     puts(line);  #endif
     fputs(line,ficparo);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   ungetc(c,ficpar);          k=kmax;
          }
   matcov=matrix(1,npar,1,npar);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   for(i=1; i <=npar; i++){          k=kmax; l=lmax*10.;
     fscanf(ficpar,"%s",&str);        }
     printf("%s",str);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     fprintf(ficparo,"%s",str);          delts=delt;
     for(j=1; j <=i; j++){        }
       fscanf(ficpar," %le",&matcov[i][j]);      }
       printf(" %.5le",matcov[i][j]);    }
       fprintf(ficparo," %.5le",matcov[i][j]);    delti[theta]=delts;
     }    return res; 
     fscanf(ficpar,"\n");    
     printf("\n");  }
     fprintf(ficparo,"\n");  
   }  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   for(i=1; i <=npar; i++)  {
     for(j=i+1;j<=npar;j++)    int i;
       matcov[i][j]=matcov[j][i];    int l=1, l1, lmax=20;
        double k1,k2,k3,k4,res,fx;
   printf("\n");    double p2[NPARMAX+1];
     int k;
   
    if(mle==1){    fx=func(x);
     /*-------- data file ----------*/    for (k=1; k<=2; k++) {
     if((ficres =fopen(fileres,"w"))==NULL) {      for (i=1;i<=npar;i++) p2[i]=x[i];
       printf("Problem with resultfile: %s\n", fileres);goto end;      p2[thetai]=x[thetai]+delti[thetai]/k;
     }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     fprintf(ficres,"#%s\n",version);      k1=func(p2)-fx;
        
     if((fic=fopen(datafile,"r"))==NULL)    {      p2[thetai]=x[thetai]+delti[thetai]/k;
       printf("Problem with datafile: %s\n", datafile);goto end;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     }      k2=func(p2)-fx;
     
     n= lastobs;      p2[thetai]=x[thetai]-delti[thetai]/k;
     severity = vector(1,maxwav);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     outcome=imatrix(1,maxwav+1,1,n);      k3=func(p2)-fx;
     num=ivector(1,n);    
     moisnais=vector(1,n);      p2[thetai]=x[thetai]-delti[thetai]/k;
     annais=vector(1,n);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     moisdc=vector(1,n);      k4=func(p2)-fx;
     andc=vector(1,n);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     agedc=vector(1,n);  #ifdef DEBUG
     cod=ivector(1,n);      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);
     weight=vector(1,n);      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<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */  #endif
     mint=matrix(1,maxwav,1,n);    }
     anint=matrix(1,maxwav,1,n);    return res;
     s=imatrix(1,maxwav+1,1,n);  }
     adl=imatrix(1,maxwav+1,1,n);      
     tab=ivector(1,NCOVMAX);  /************** Inverse of matrix **************/
     ncodemax=ivector(1,8);  void ludcmp(double **a, int n, int *indx, double *d) 
   { 
     i=1;    int i,imax,j,k; 
     while (fgets(line, MAXLINE, fic) != NULL)    {    double big,dum,sum,temp; 
       if ((i >= firstobs) && (i <=lastobs)) {    double *vv; 
           
         for (j=maxwav;j>=1;j--){    vv=vector(1,n); 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    *d=1.0; 
           strcpy(line,stra);    for (i=1;i<=n;i++) { 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      big=0.0; 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      for (j=1;j<=n;j++) 
         }        if ((temp=fabs(a[i][j])) > big) big=temp; 
              if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      vv[i]=1.0/big; 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    } 
     for (j=1;j<=n;j++) { 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      for (i=1;i<j;i++) { 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        a[i][j]=sum; 
         for (j=ncov;j>=1;j--){      } 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      big=0.0; 
         }      for (i=j;i<=n;i++) { 
         num[i]=atol(stra);        sum=a[i][j]; 
         for (k=1;k<j;k++) 
         /*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]));*/          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
         i=i+1;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       }          big=dum; 
     }          imax=i; 
         } 
     /*scanf("%d",i);*/      } 
   imx=i-1; /* Number of individuals */      if (j != imax) { 
         for (k=1;k<=n;k++) { 
   /* Calculation of the number of parameter from char model*/          dum=a[imax][k]; 
   Tvar=ivector(1,8);              a[imax][k]=a[j][k]; 
              a[j][k]=dum; 
   if (strlen(model) >1){        } 
     j=0;        *d = -(*d); 
     j=nbocc(model,'+');        vv[imax]=vv[j]; 
     cptcovn=j+1;      } 
          indx[j]=imax; 
     strcpy(modelsav,model);      if (a[j][j] == 0.0) a[j][j]=TINY; 
     if (j==0) {      if (j != n) { 
       cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb);        dum=1.0/(a[j][j]); 
     }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     else {      } 
       for(i=j; i>=1;i--){    } 
         cutv(stra,strb,modelsav,'+');    free_vector(vv,1,n);  /* Doesn't work */
         if (strchr(strb,'*')) {  ;
           cutv(strd,strc,strb,'*');  } 
           cutv(strb,stre,strc,'V');Tvar[i+1]=ncov+1;  
           cutv(strb,strc,strd,'V');  void lubksb(double **a, int n, int *indx, double b[]) 
           for (k=1; k<=lastobs;k++)  { 
             covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    int i,ii=0,ip,j; 
         }    double sum; 
         else {cutv(strd,strc,strb,'V');   
         Tvar[i+1]=atoi(strc);    for (i=1;i<=n;i++) { 
         }      ip=indx[i]; 
         strcpy(modelsav,stra);        sum=b[ip]; 
       }      b[ip]=b[i]; 
       cutv(strd,strc,stra,'V');      if (ii) 
       Tvar[1]=atoi(strc);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     }      else if (sum) ii=i; 
   }      b[i]=sum; 
   /*printf("tvar=%d ",Tvar[1]);    } 
   scanf("%d ",i);*/    for (i=n;i>=1;i--) { 
     fclose(fic);      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     if (weightopt != 1) { /* Maximisation without weights*/      b[i]=sum/a[i][i]; 
       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);  /************ 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, char strstart[])
     for (i=1; i<=imx; i++)  {  {  /* Some frequencies */
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    
       for(m=1; (m<= maxwav); m++){    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
         if(s[m][i] >0){    int first;
           if (s[m][i] == nlstate+1) {    double ***freq; /* Frequencies */
             if(agedc[i]>0)    double *pp, **prop;
               if(moisdc[i]!=99 && andc[i]!=9999)    double pos,posprop, k2, dateintsum=0,k2cpt=0;
               agev[m][i]=agedc[i];    FILE *ficresp;
             else{    char fileresp[FILENAMELENGTH];
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    
               agev[m][i]=-1;    pp=vector(1,nlstate);
             }    prop=matrix(1,nlstate,iagemin,iagemax+3);
           }    strcpy(fileresp,"p");
           else if(s[m][i] !=9){ /* Should no more exist */    strcat(fileresp,fileres);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    if((ficresp=fopen(fileresp,"w"))==NULL) {
             if(mint[m][i]==99 || anint[m][i]==9999)      printf("Problem with prevalence resultfile: %s\n", fileresp);
               agev[m][i]=1;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
             else if(agev[m][i] <agemin){      exit(0);
               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);*/    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
             }    j1=0;
             else if(agev[m][i] >agemax){    
               agemax=agev[m][i];    j=cptcoveff;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    if (cptcovn<1) {j=1;ncodemax[1]=1;}
             }  
             /*agev[m][i]=anint[m][i]-annais[i];*/    first=1;
             /*   agev[m][i] = age[i]+2*m;*/  
           }    for(k1=1; k1<=j;k1++){
           else { /* =9 */      for(i1=1; i1<=ncodemax[k1];i1++){
             agev[m][i]=1;        j1++;
             s[m][i]=-1;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           }          scanf("%d", i);*/
         }        for (i=-5; i<=nlstate+ndeath; i++)  
         else /*= 0 Unknown */          for (jk=-5; jk<=nlstate+ndeath; jk++)  
           agev[m][i]=1;            for(m=iagemin; m <= iagemax+3; m++)
       }              freq[i][jk][m]=0;
      
     }      for (i=1; i<=nlstate; i++)  
     for (i=1; i<=imx; i++)  {        for(m=iagemin; m <= iagemax+3; m++)
       for(m=1; (m<= maxwav); m++){          prop[i][m]=0;
         if (s[m][i] > (nlstate+ndeath)) {        
           printf("Error: Wrong value in nlstate or ndeath\n");          dateintsum=0;
           goto end;        k2cpt=0;
         }        for (i=1; i<=imx; i++) {
       }          bool=1;
     }          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
     free_vector(severity,1,maxwav);          }
     free_imatrix(outcome,1,maxwav+1,1,n);          if (bool==1){
     free_vector(moisnais,1,n);            for(m=firstpass; m<=lastpass; m++){
     free_vector(annais,1,n);              k2=anint[m][i]+(mint[m][i]/12.);
     free_matrix(mint,1,maxwav,1,n);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     free_matrix(anint,1,maxwav,1,n);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     free_vector(moisdc,1,n);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     free_vector(andc,1,n);                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];
     wav=ivector(1,imx);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     dh=imatrix(1,lastpass-firstpass+1,1,imx);                }
     mw=imatrix(1,lastpass-firstpass+1,1,imx);                
                    if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     /* Concatenates waves */                  dateintsum=dateintsum+k2;
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);                  k2cpt++;
                 }
                 /*}*/
 Tcode=ivector(1,100);            }
    nbcode=imatrix(1,nvar,1,8);            }
    ncodemax[1]=1;        }
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);         
          /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
    codtab=imatrix(1,100,1,10);  fprintf(ficresp, "#Local time at start: %s", strstart);
    h=0;        if  (cptcovn>0) {
    m=pow(2,cptcovn);          fprintf(ficresp, "\n#********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    for(k=1;k<=cptcovn; k++){          fprintf(ficresp, "**********\n#");
      for(i=1; i <=(m/pow(2,k));i++){        }
        for(j=1; j <= ncodemax[k]; j++){        for(i=1; i<=nlstate;i++) 
          for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
            h++;        fprintf(ficresp, "\n");
            if (h>m) h=1;codtab[h][k]=j;        
          }        for(i=iagemin; i <= iagemax+3; i++){
        }          if(i==iagemax+3){
      }            fprintf(ficlog,"Total");
    }          }else{
             if(first==1){
    /*for(i=1; i <=m ;i++){              first=0;
      for(k=1; k <=cptcovn; k++){              printf("See log file for details...\n");
        printf("i=%d k=%d %d ",i,k,codtab[i][k]);            }
      }            fprintf(ficlog,"Age %d", i);
      printf("\n");          }
    }*/          for(jk=1; jk <=nlstate ; jk++){
    /*scanf("%d",i);*/            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                  pp[jk] += freq[jk][m][i]; 
    /* Calculates basic frequencies. Computes observed prevalence at single age          }
        and prints on file fileres'p'. */          for(jk=1; jk <=nlstate ; jk++){
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);            for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            if(pp[jk]>=1.e-10){
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              if(first==1){
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              }
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                }else{
     /* For Powell, parameters are in a vector p[] starting at p[1]              if(first==1)
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          }
   
              for(jk=1; jk <=nlstate ; jk++){
     /*--------- results files --------------*/            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     fprintf(ficres,"\ntitle=%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);              pp[jk] += freq[jk][m][i];
              }       
    jk=1;          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
    fprintf(ficres,"# Parameters\n");            pos += pp[jk];
    printf("# Parameters\n");            posprop += prop[jk][i];
    for(i=1,jk=1; i <=nlstate; i++){          }
      for(k=1; k <=(nlstate+ndeath); k++){          for(jk=1; jk <=nlstate ; jk++){
        if (k != i)            if(pos>=1.e-5){
          {              if(first==1)
            printf("%d%d ",i,k);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
            fprintf(ficres,"%1d%1d ",i,k);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
            for(j=1; j <=ncovmodel; j++){            }else{
              printf("%f ",p[jk]);              if(first==1)
              fprintf(ficres,"%f ",p[jk]);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
              jk++;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
            }            }
            printf("\n");            if( i <= iagemax){
            fprintf(ficres,"\n");              if(pos>=1.e-5){
          }                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
      }                /*probs[i][jk][j1]= pp[jk]/pos;*/
    }                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
               }
     /* Computing hessian and covariance matrix */              else
     ftolhess=ftol; /* Usually correct */                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     hesscov(matcov, p, npar, delti, ftolhess, func);            }
     fprintf(ficres,"# Scales\n");          }
     printf("# Scales\n");          
      for(i=1,jk=1; i <=nlstate; i++){          for(jk=-1; jk <=nlstate+ndeath; jk++)
       for(j=1; j <=nlstate+ndeath; j++){            for(m=-1; m <=nlstate+ndeath; m++)
         if (j!=i) {              if(freq[jk][m][i] !=0 ) {
           fprintf(ficres,"%1d%1d",i,j);              if(first==1)
           printf("%1d%1d",i,j);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
           for(k=1; k<=ncovmodel;k++){                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
             printf(" %.5e",delti[jk]);              }
             fprintf(ficres," %.5e",delti[jk]);          if(i <= iagemax)
             jk++;            fprintf(ficresp,"\n");
           }          if(first==1)
           printf("\n");            printf("Others in log...\n");
           fprintf(ficres,"\n");          fprintf(ficlog,"\n");
         }        }
       }      }
       }    }
        dateintmean=dateintsum/k2cpt; 
     k=1;   
     fprintf(ficres,"# Covariance\n");    fclose(ficresp);
     printf("# Covariance\n");    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     for(i=1;i<=npar;i++){    free_vector(pp,1,nlstate);
       /*  if (k>nlstate) k=1;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       i1=(i-1)/(ncovmodel*nlstate)+1;    /* End of Freq */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);  }
       printf("%s%d%d",alph[k],i1,tab[i]);*/  
       fprintf(ficres,"%3d",i);  /************ Prevalence ********************/
       printf("%3d",i);  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
       for(j=1; j<=i;j++){  {  
         fprintf(ficres," %.5e",matcov[i][j]);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         printf(" %.5e",matcov[i][j]);       in each health status at the date of interview (if between dateprev1 and dateprev2).
       }       We still use firstpass and lastpass as another selection.
       fprintf(ficres,"\n");    */
       printf("\n");   
       k++;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     }    double ***freq; /* Frequencies */
        double *pp, **prop;
     while((c=getc(ficpar))=='#' && c!= EOF){    double pos,posprop; 
       ungetc(c,ficpar);    double  y2; /* in fractional years */
       fgets(line, MAXLINE, ficpar);    int iagemin, iagemax;
       puts(line);  
       fputs(line,ficparo);    iagemin= (int) agemin;
     }    iagemax= (int) agemax;
     ungetc(c,ficpar);    /*pp=vector(1,nlstate);*/
      prop=matrix(1,nlstate,iagemin,iagemax+3); 
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
        j1=0;
     if (fage <= 2) {    
       bage = agemin;    j=cptcoveff;
       fage = agemax;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     }    
     for(k1=1; k1<=j;k1++){
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      for(i1=1; i1<=ncodemax[k1];i1++){
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        j1++;
 /*------------ gnuplot -------------*/        
 chdir(pathcd);        for (i=1; i<=nlstate; i++)  
   if((ficgp=fopen("graph.plt","w"))==NULL) {          for(m=iagemin; m <= iagemax+3; m++)
     printf("Problem with file graph.gp");goto end;            prop[i][m]=0.0;
   }       
 #ifdef windows        for (i=1; i<=imx; i++) { /* Each individual */
   fprintf(ficgp,"cd \"%s\" \n",pathc);          bool=1;
 #endif          if  (cptcovn>0) {
 m=pow(2,cptcovn);            for (z1=1; z1<=cptcoveff; z1++) 
                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
  /* 1eme*/                bool=0;
   for (cpt=1; cpt<= nlstate ; cpt ++) {          } 
    for (k1=1; k1<= m ; k1 ++) {          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
 #ifdef windows              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     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);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
 #endif                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 #ifdef unix                if(agev[m][i]==1) agev[m][i]=iagemax+2;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);                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); 
 #endif                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
 for (i=1; i<= nlstate ; i ++) {                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                  prop[s[m][i]][iagemax+3] += weight[i]; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");                } 
 }              }
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);            } /* end selection of waves */
     for (i=1; i<= nlstate ; i ++) {          }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(i=iagemin; i <= iagemax+3; i++){  
 }          
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
      for (i=1; i<= nlstate ; i ++) {            posprop += prop[jk][i]; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }            for(jk=1; jk <=nlstate ; jk++){     
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));            if( i <=  iagemax){ 
 #ifdef unix              if(posprop>=1.e-5){ 
 fprintf(ficgp,"\nset ter gif small size 400,300");                probs[i][jk][j1]= prop[jk][i]/posprop;
 #endif              } 
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            } 
    }          }/* end jk */ 
   }        }/* end i */ 
   /*2 eme*/      } /* end i1 */
     } /* end k1 */
   for (k1=1; k1<= m ; k1 ++) {    
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
        /*free_vector(pp,1,nlstate);*/
     for (i=1; i<= nlstate+1 ; i ++) {    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       k=2*i;  }  /* End of prevalence */
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {  /************* Waves Concatenation ***************/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  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)
 }    {
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);       Death is a valid wave (if date is known).
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       for (j=1; j<= nlstate+1 ; j ++) {       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");       and mw[mi+1][i]. dh depends on stepm.
         else fprintf(ficgp," \%%*lf (\%%*lf)");       */
 }    
       fprintf(ficgp,"\" t\"\" w l 0,");    int i, mi, m;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       for (j=1; j<= nlstate+1 ; j ++) {       double sum=0., jmean=0.;*/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    int first;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    int j, k=0,jk, ju, jl;
 }      double sum=0.;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    first=0;
       else fprintf(ficgp,"\" t\"\" w l 0,");    jmin=1e+5;
     }    jmax=-1;
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    jmean=0.;
   }    for(i=1; i<=imx; i++){
        mi=0;
   /*3eme*/      m=firstpass;
       while(s[m][i] <= nlstate){
   for (k1=1; k1<= m ; k1 ++) {        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
     for (cpt=1; cpt<= nlstate ; cpt ++) {          mw[++mi][i]=m;
       k=2+nlstate*(cpt-1);        if(m >=lastpass)
       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);          break;
       for (i=1; i< nlstate ; i ++) {        else
         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);          m++;
       }      }/* end while */
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      if (s[m][i] > nlstate){
     }        mi++;     /* Death is another wave */
   }        /* if(mi==0)  never been interviewed correctly before death */
             /* Only death is a correct wave */
   /* CV preval stat */        mw[mi][i]=m;
   for (k1=1; k1<= m ; k1 ++) {      }
     for (cpt=1; cpt<nlstate ; cpt ++) {  
       k=3;      wav[i]=mi;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);      if(mi==0){
       for (i=1; i< nlstate ; i ++)        nbwarn++;
         fprintf(ficgp,"+$%d",k+i+1);        if(first==0){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
                first=1;
       l=3+(nlstate+ndeath)*cpt;        }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        if(first==1){
       for (i=1; i< nlstate ; i ++) {          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
         l=3+(nlstate+ndeath)*cpt;        }
         fprintf(ficgp,"+$%d",l+i+1);      } /* end mi==0 */
       }    } /* End individuals */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    for(i=1; i<=imx; i++){
     }      for(mi=1; mi<wav[i];mi++){
   }        if (stepm <=0)
           dh[mi][i]=1;
   /* proba elementaires */        else{
    for(i=1,jk=1; i <=nlstate; i++){          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     for(k=1; k <=(nlstate+ndeath); k++){            if (agedc[i] < 2*AGESUP) {
       if (k != i) {              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
         for(j=1; j <=ncovmodel; j++){              if(j==0) j=1;  /* Survives at least one month after exam */
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/              else if(j<0){
           /*fprintf(ficgp,"%s",alph[1]);*/                nberr++;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);                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]);
           jk++;                j=1; /* Temporary Dangerous patch */
           fprintf(ficgp,"\n");                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. 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. You MUST fix the contradiction between dates.\n",stepm);
     }              }
     }              k=k+1;
               if (j >= jmax) jmax=j;
   for(jk=1; jk <=m; jk++) {              if (j <= jmin) jmin=j;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);              sum=sum+j;
    i=1;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
    for(k2=1; k2<=nlstate; k2++) {              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
      k3=i;            }
      for(k=1; k<=(nlstate+ndeath); k++) {          }
        if (k != k2){          else{
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
         for(j=3; j <=ncovmodel; j++)  
           fprintf(ficgp,"+p%d*%d",k2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            k=k+1;
         fprintf(ficgp,")/(1");            if (j >= jmax) jmax=j;
             else if (j <= jmin)jmin=j;
         for(k1=1; k1 <=nlstate+1; k1=k1+2){              /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             fprintf(ficgp,"+exp(p%d+p%d*x",k1+k3-1,k1+k3);            /*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){
             for(j=3; j <=ncovmodel; j++)              nberr++;
               fprintf(ficgp,"+p%d*%d",k2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             fprintf(ficgp,")");              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]);
         }            }
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);            sum=sum+j;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          }
     i=i+ncovmodel;          jk= j/stepm;
        }          jl= j -jk*stepm;
      }          ju= j -(jk+1)*stepm;
    }          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);            if(jl==0){
    }              dh[mi][i]=jk;
                  bh[mi][i]=0;
   fclose(ficgp);            }else{ /* We want a negative bias in order to only have interpolation ie
                        * at the price of an extra matrix product in likelihood */
 chdir(path);              dh[mi][i]=jk+1;
     free_matrix(agev,1,maxwav,1,imx);              bh[mi][i]=ju;
     free_ivector(wav,1,imx);            }
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          }else{
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            if(jl <= -ju){
                  dh[mi][i]=jk;
     free_imatrix(s,1,maxwav+1,1,n);              bh[mi][i]=jl;       /* bias is positive if real duration
                                       * is higher than the multiple of stepm and negative otherwise.
                                       */
     free_ivector(num,1,n);            }
     free_vector(agedc,1,n);            else{
     free_vector(weight,1,n);              dh[mi][i]=jk+1;
     /*free_matrix(covar,1,NCOVMAX,1,n);*/              bh[mi][i]=ju;
     fclose(ficparo);            }
     fclose(ficres);            if(dh[mi][i]==0){
    }              dh[mi][i]=1; /* At least one step */
                  bh[mi][i]=ju; /* At least one step */
    /*________fin mle=1_________*/              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
                }
           } /* end if mle */
          }
     /* No more information from the sample is required now */      } /* end wave */
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){    jmean=sum/k;
     ungetc(c,ficpar);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     fgets(line, MAXLINE, ficpar);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     puts(line);   }
     fputs(line,ficparo);  
   }  /*********** Tricode ****************************/
   ungetc(c,ficpar);  void tricode(int *Tvar, int **nbcode, int imx)
    {
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);    int Ndum[20],ij=1, k, j, i, maxncov=19;
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    int cptcode=0;
 /*--------- index.htm --------*/    cptcoveff=0; 
    
   if((fichtm=fopen("index.htm","w"))==NULL)    {    for (k=0; k<maxncov; k++) Ndum[k]=0;
     printf("Problem with index.htm \n");goto end;    for (k=1; k<=7; k++) ncodemax[k]=0;
   }  
     for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
  fprintf(fichtm,"<body><ul> Imach, Version 0.64a<hr> <li>Outputs files<br><br>\n      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n                                 modality*/ 
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>        Ndum[ij]++; /*store the modality */
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>                                         Tvar[j]. If V=sex and male is 0 and 
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>                                         female is 1, then  cptcode=1.*/
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>      }
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);  
       for (i=0; i<=cptcode; i++) {
  fprintf(fichtm," <li>Graphs</li>\n<p>");        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 */
       }
  m=cptcovn;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      ij=1; 
       for (i=1; i<=ncodemax[j]; i++) {
  j1=0;        for (k=0; k<= maxncov; k++) {
  for(k1=1; k1<=m;k1++){          if (Ndum[k] != 0) {
    for(i1=1; i1<=ncodemax[k1];i1++){            nbcode[Tvar[j]][ij]=k; 
        j1++;            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
        if (cptcovn > 0) {            
          fprintf(fichtm,"<hr>************ Results for covariates");            ij++;
          for (cpt=1; cpt<=cptcovn;cpt++)          }
            fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);          if (ij > ncodemax[j]) break; 
          fprintf(fichtm," ************\n<hr>");        }  
        }      } 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    }  
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);      
        for(cpt=1; cpt<nlstate;cpt++){   for (k=0; k< maxncov; k++) Ndum[k]=0;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>  
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);   for (i=1; i<=ncovmodel-2; i++) { 
        }     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     for(cpt=1; cpt<=nlstate;cpt++) {     ij=Tvar[i];
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident     Ndum[ij]++;
 interval) in state (%d): v%s%d%d.gif <br>   }
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    
      }   ij=1;
      for(cpt=1; cpt<=nlstate;cpt++) {   for (i=1; i<= maxncov; i++) {
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>     if((Ndum[i]!=0) && (i<=ncovcol)){
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);       Tvaraff[ij]=i; /*For printing */
      }       ij++;
      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, "."),j1,strtok(optionfile, "."),j1);   
 fprintf(fichtm,"\n</body>");   cptcoveff=ij-1; /*Number of simple covariates*/
    }  }
  }  
 fclose(fichtm);  /*********** Health Expectancies ****************/
   
   /*--------------- Prevalence limit --------------*/  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,char strstart[] )
    
   strcpy(filerespl,"pl");  {
   strcat(filerespl,fileres);    /* Health expectancies */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    double age, agelim, hf;
   }    double ***p3mat,***varhe;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    double **dnewm,**doldm;
   fprintf(ficrespl,"#Prevalence limit\n");    double *xp;
   fprintf(ficrespl,"#Age ");    double **gp, **gm;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    double ***gradg, ***trgradg;
   fprintf(ficrespl,"\n");    int theta;
    
   prlim=matrix(1,nlstate,1,nlstate);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    xp=vector(1,npar);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    dnewm=matrix(1,nlstate*nlstate,1,npar);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fprintf(ficreseij,"# Local time at start: %s", strstart);
   k=0;    fprintf(ficreseij,"# Health expectancies\n");
   agebase=agemin;    fprintf(ficreseij,"# Age");
   agelim=agemax;    for(i=1; i<=nlstate;i++)
   ftolpl=1.e-10;      for(j=1; j<=nlstate;j++)
   i1=cptcovn;        fprintf(ficreseij," %1d-%1d (SE)",i,j);
   if (cptcovn < 1){i1=1;}    fprintf(ficreseij,"\n");
   
   for(cptcov=1;cptcov<=i1;cptcov++){    if(estepm < stepm){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      printf ("Problem %d lower than %d\n",estepm, stepm);
         k=k+1;    }
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    else  hstepm=estepm;   
         fprintf(ficrespl,"\n#****** ");    /* We compute the life expectancy from trapezoids spaced every estepm months
         for(j=1;j<=cptcovn;j++)     * This is mainly to measure the difference between two models: for example
           fprintf(ficrespl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);     * if stepm=24 months pijx are given only every 2 years and by summing them
         fprintf(ficrespl,"******\n");     * we are calculating an estimate of the Life Expectancy assuming a linear 
             * progression in between and thus overestimating or underestimating according
         for (age=agebase; age<=agelim; age++){     * to the curvature of the survival function. If, for the same date, we 
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           fprintf(ficrespl,"%.0f",age );     * to compare the new estimate of Life expectancy with the same linear 
           for(i=1; i<=nlstate;i++)     * hypothesis. A more precise result, taking into account a more precise
           fprintf(ficrespl," %.5f", prlim[i][i]);     * curvature will be obtained if estepm is as small as stepm. */
           fprintf(ficrespl,"\n");  
         }    /* 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 
   fclose(ficrespl);       nstepm is the number of stepm from age to agelin. 
   /*------------- h Pij x at various ages ------------*/       Look at hpijx to understand the reason of that which relies in memory size
         and note for a fixed period like estepm months */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   if((ficrespij=fopen(filerespij,"w"))==NULL) {       survival function given by stepm (the optimization length). Unfortunately it
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;       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 
   printf("Computing pij: result on file '%s' \n", filerespij);       results. So we changed our mind and took the option of the best precision.
      */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   if (stepm<=24) stepsize=2;  
     agelim=AGESUP;
   agelim=AGESUP;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   hstepm=stepsize*YEARM; /* Every year of age */      /* nhstepm age range expressed in number of stepm */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
        /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   k=0;      /* if (stepm >= YEARM) hstepm=1;*/
   for(cptcov=1;cptcov<=i1;cptcov++){      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       k=k+1;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
         fprintf(ficrespij,"\n#****** ");      gp=matrix(0,nhstepm,1,nlstate*nlstate);
         for(j=1;j<=cptcovn;j++)      gm=matrix(0,nhstepm,1,nlstate*nlstate);
           fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);  
         fprintf(ficrespij,"******\n");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
                 in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */   
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        /* Computing  Variances of health expectancies */
           fprintf(ficrespij,"# Age");  
           for(i=1; i<=nlstate;i++)       for(theta=1; theta <=npar; theta++){
             for(j=1; j<=nlstate+ndeath;j++)        for(i=1; i<=npar; i++){ 
               fprintf(ficrespij," %1d-%1d",i,j);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           fprintf(ficrespij,"\n");        }
           for (h=0; h<=nhstepm; h++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    
             for(i=1; i<=nlstate;i++)        cptj=0;
               for(j=1; j<=nlstate+ndeath;j++)        for(j=1; j<= nlstate; j++){
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);          for(i=1; i<=nlstate; i++){
             fprintf(ficrespij,"\n");            cptj=cptj+1;
           }            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           fprintf(ficrespij,"\n");            }
         }          }
     }        }
   }       
        
   fclose(ficrespij);        for(i=1; i<=npar; i++) 
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
   /*---------- Health expectancies and variances ------------*/        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         
   strcpy(filerest,"t");        cptj=0;
   strcat(filerest,fileres);        for(j=1; j<= nlstate; j++){
   if((ficrest=fopen(filerest,"w"))==NULL) {          for(i=1;i<=nlstate;i++){
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;            cptj=cptj+1;
   }            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  
               gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
   strcpy(filerese,"e");          }
   strcat(filerese,fileres);        }
   if((ficreseij=fopen(filerese,"w"))==NULL) {        for(j=1; j<= nlstate*nlstate; j++)
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          for(h=0; h<=nhstepm-1; h++){
   }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);          }
        } 
  strcpy(fileresv,"v");     
   strcat(fileresv,fileres);  /* End theta */
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   }  
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
   k=0;          for(theta=1; theta <=npar; theta++)
   for(cptcov=1;cptcov<=i1;cptcov++){            trgradg[h][j][theta]=gradg[h][theta][j];
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       
       k=k+1;  
       fprintf(ficrest,"\n#****** ");       for(i=1;i<=nlstate*nlstate;i++)
       for(j=1;j<=cptcovn;j++)        for(j=1;j<=nlstate*nlstate;j++)
         fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);          varhe[i][j][(int)age] =0.;
       fprintf(ficrest,"******\n");  
        printf("%d|",(int)age);fflush(stdout);
       fprintf(ficreseij,"\n#****** ");       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       for(j=1;j<=cptcovn;j++)       for(h=0;h<=nhstepm-1;h++){
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);        for(k=0;k<=nhstepm-1;k++){
       fprintf(ficreseij,"******\n");          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       fprintf(ficresvij,"\n#****** ");          for(i=1;i<=nlstate*nlstate;i++)
       for(j=1;j<=cptcovn;j++)            for(j=1;j<=nlstate*nlstate;j++)
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       fprintf(ficresvij,"******\n");        }
       }
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      /* Computing expectancies */
       oldm=oldms;savm=savms;      for(i=1; i<=nlstate;i++)
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);          for(j=1; j<=nlstate;j++)
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       oldm=oldms;savm=savms;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            
        /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          }
       fprintf(ficrest,"\n");  
              fprintf(ficreseij,"%3.0f",age );
       hf=1;      cptj=0;
       if (stepm >= YEARM) hf=stepm/YEARM;      for(i=1; i<=nlstate;i++)
       epj=vector(1,nlstate+1);        for(j=1; j<=nlstate;j++){
       for(age=bage; age <=fage ;age++){          cptj++;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
         fprintf(ficrest," %.0f",age);        }
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      fprintf(ficreseij,"\n");
           for(i=1, epj[j]=0.;i <=nlstate;i++) {     
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
           }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
           epj[nlstate+1] +=epj[j];      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
         }      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
         for(i=1, vepp=0.;i <=nlstate;i++)      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           for(j=1;j <=nlstate;j++)    }
             vepp += vareij[i][j][(int)age];    printf("\n");
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    fprintf(ficlog,"\n");
         for(j=1;j <=nlstate;j++){  
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    free_vector(xp,1,npar);
         }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
         fprintf(ficrest,"\n");    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     }  }
   }  
          /************ Variance ******************/
  fclose(ficreseij);  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, char strstart[])
  fclose(ficresvij);  {
   fclose(ficrest);    /* Variance of health expectancies */
   fclose(ficpar);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   free_vector(epj,1,nlstate+1);    /* double **newm;*/
   /*  scanf("%d ",i); */    double **dnewm,**doldm;
     double **dnewmp,**doldmp;
   /*------- Variance limit prevalence------*/      int i, j, nhstepm, hstepm, h, nstepm ;
     int k, cptcode;
 strcpy(fileresvpl,"vpl");    double *xp;
   strcat(fileresvpl,fileres);    double **gp, **gm;  /* for var eij */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    double ***gradg, ***trgradg; /*for var eij */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    double **gradgp, **trgradgp; /* for var p point j */
     exit(0);    double *gpp, *gmp; /* for var p point j */
   }    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    double ***p3mat;
     double age,agelim, hf;
  k=0;    double ***mobaverage;
  for(cptcov=1;cptcov<=i1;cptcov++){    int theta;
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    char digit[4];
      k=k+1;    char digitp[25];
      fprintf(ficresvpl,"\n#****** ");  
      for(j=1;j<=cptcovn;j++)    char fileresprobmorprev[FILENAMELENGTH];
        fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);  
      fprintf(ficresvpl,"******\n");    if(popbased==1){
            if(mobilav!=0)
      varpl=matrix(1,nlstate,(int) bage, (int) fage);        strcpy(digitp,"-populbased-mobilav-");
      oldm=oldms;savm=savms;      else strcpy(digitp,"-populbased-nomobil-");
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    }
    }    else 
  }      strcpy(digitp,"-stablbased-");
   
   fclose(ficresvpl);    if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   /*---------- End : free ----------------*/      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
          printf(" Error in movingaverage mobilav=%d\n",mobilav);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      }
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    }
    
      strcpy(fileresprobmorprev,"prmorprev"); 
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    sprintf(digit,"%-d",ij);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
      strcat(fileresprobmorprev,fileres);
   free_matrix(matcov,1,npar,1,npar);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   free_vector(delti,1,npar);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   printf("End of Imach\n");   
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
   /* 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);*/    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
   /*printf("Total time was %d uSec.\n", total_usecs);*/    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   /*------ End -----------*/    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
  end:      for(i=1; i<=nlstate;i++)
 #ifdef windows        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
  chdir(pathcd);    }  
 #endif    fprintf(ficresprobmorprev,"\n");
  system("wgnuplot graph.plt");    fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
 #ifdef windows    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");
   while (z[0] != 'q') {    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     chdir(pathcd);  /*   } */
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     scanf("%s",z);   fprintf(ficresvij, "#Local time at start: %s", strstart);
     if (z[0] == 'c') system("./imach");    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");
     else if (z[0] == 'e') {    fprintf(ficresvij,"# Age");
       chdir(path);    for(i=1; i<=nlstate;i++)
       system("index.htm");      for(j=1; j<=nlstate;j++)
     }        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     else if (z[0] == 'q') exit(0);    fprintf(ficresvij,"\n");
   }  
 #endif    xp=vector(1,npar);
 }    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       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]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         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]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     int k, cptcode;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     fprintf(ficresvpl, "#Local time at start: %s", strstart); 
     fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     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;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     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);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficresprob, "#Local time at start: %s", strstart);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     fprintf(ficresprobcov, "#Local time at start: %s", strstart);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor, "#Local time at start: %s", strstart);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# Age");
   
   
     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);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
    xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     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.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    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");
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\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]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           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);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     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.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     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);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a> href="#firstorder">Result files (first order: no variance)</a>\n \
      <li><a> href="#secondorder">Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name="firstorder">Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - Life expectancies by age and initial health status (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %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++){
            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);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name="secondorder">Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\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 */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* 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=0; 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=1;i<=imx ; i++)
       {
         if (cens[i]==1 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i]==0 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+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,double agemortsup){
     int i,k;
   
     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>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     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;
     int agemortsup;
     float  sumlpop=0.;
     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=0; line[j] != '\n';j++){  /* Untabifies line */
           if(line[j] == '\t')
             line[j] = ' ';
         }
         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 parameters 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 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           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,strstart);
   
     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]));
   
   lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
      
        for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
      
         for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
   
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
   
    tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
          }
      
      
          printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
   
       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,agemortsup);
   
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* 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, "#Local time at start: %s", strstart);
       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, "#Local time at start: %s", strstart);
       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,strstart);
   
       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, strstart);  
    
           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, strstart);
           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, strstart);
           }
   
           fprintf(ficrest, "#Local time at start: %s", strstart);
           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,strstart);
           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\nLocal time 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.1.5  
changed lines
  Added in v.1.106


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