Diff for /imach/src/imach.c between versions 1.32 and 1.106

version 1.32, 2002/03/11 14:17:15 version 1.106, 2006/01/19 13:24:36
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.106  2006/01/19 13:24:36  brouard
      Some cleaning and links added in html output
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.105  2006/01/05 20:23:19  lievre
   first survey ("cross") where individuals from different ages are    *** empty log message ***
   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    Revision 1.104  2005/09/30 16:11:43  lievre
   second wave of interviews ("longitudinal") which measure each change    (Module): sump fixed, loop imx fixed, and simplifications.
   (if any) in individual health status.  Health expectancies are    (Module): If the status is missing at the last wave but we know
   computed from the time spent in each health state according to a    that the person is alive, then we can code his/her status as -2
   model. More health states you consider, more time is necessary to reach the    (instead of missing=-1 in earlier versions) and his/her
   Maximum Likelihood of the parameters involved in the model.  The    contributions to the likelihood is 1 - Prob of dying from last
   simplest model is the multinomial logistic model where pij is the    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   probabibility to be observed in state j at the second wave    the healthy state at last known wave). Version is 0.98
   conditional to be observed in state i at the first wave. Therefore  
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Revision 1.103  2005/09/30 15:54:49  lievre
   'age' is age and 'sex' is a covariate. If you want to have a more    (Module): sump fixed, loop imx fixed, and simplifications.
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.102  2004/09/15 17:31:30  brouard
   you to do it.  More covariates you add, slower the    Add the possibility to read data file including tab characters.
   convergence.  
     Revision 1.101  2004/09/15 10:38:38  brouard
   The advantage of this computer programme, compared to a simple    Fix on curr_time
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.100  2004/07/12 18:29:06  brouard
   intermediate interview, the information is lost, but taken into    Add version for Mac OS X. Just define UNIX in Makefile
   account using an interpolation or extrapolation.    
     Revision 1.99  2004/06/05 08:57:40  brouard
   hPijx is the probability to be observed in state i at age x+h    *** empty log message ***
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Revision 1.98  2004/05/16 15:05:56  brouard
   states. This elementary transition (by month or quarter trimester,    New version 0.97 . First attempt to estimate force of mortality
   semester or year) is model as a multinomial logistic.  The hPx    directly from the data i.e. without the need of knowing the health
   matrix is simply the matrix product of nh*stepm elementary matrices    state at each age, but using a Gompertz model: log u =a + b*age .
   and the contribution of each individual to the likelihood is simply    This is the basic analysis of mortality and should be done before any
   hPijx.    other analysis, in order to test if the mortality estimated from the
     cross-longitudinal survey is different from the mortality estimated
   Also this programme outputs the covariance matrix of the parameters but also    from other sources like vital statistic data.
   of the life expectancies. It also computes the prevalence limits.  
      The same imach parameter file can be used but the option for mle should be -3.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Agnès, who wrote this part of the code, tried to keep most of the
   This software have been partly granted by Euro-REVES, a concerted action    former routines in order to include the new code within the former code.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    The output is very simple: only an estimate of the intercept and of
   software can be distributed freely for non commercial use. Latest version    the slope with 95% confident intervals.
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Current limitations:
      A) Even if you enter covariates, i.e. with the
 #include <math.h>    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #include <stdio.h>    B) There is no computation of Life Expectancy nor Life Table.
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
 #define MAXLINE 256    suppressed.
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"  
 #define FILENAMELENGTH 80    Revision 1.96  2003/07/15 15:38:55  brouard
 /*#define DEBUG*/    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #define windows    rewritten within the same printf. Workaround: many printfs.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.95  2003/07/08 07:54:34  brouard
     * imach.c (Repository):
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    (Repository): Using imachwizard code to output a more meaningful covariance
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    matrix (cov(a12,c31) instead of numbers.
   
 #define NINTERVMAX 8    Revision 1.94  2003/06/27 13:00:02  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Just cleaning
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.93  2003/06/25 16:33:55  brouard
 #define MAXN 20000    (Module): On windows (cygwin) function asctime_r doesn't
 #define YEARM 12. /* Number of months per year */    exist so I changed back to asctime which exists.
 #define AGESUP 130    (Module): Version 0.96b
 #define AGEBASE 40  
     Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 int erreur; /* Error number */    exist so I changed back to asctime which exists.
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.91  2003/06/25 15:30:29  brouard
 int npar=NPARMAX;    * imach.c (Repository): Duplicated warning errors corrected.
 int nlstate=2; /* Number of live states */    (Repository): Elapsed time after each iteration is now output. It
 int ndeath=1; /* Number of dead states */    helps to forecast when convergence will be reached. Elapsed time
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    is stamped in powell.  We created a new html file for the graphs
 int popbased=0;    concerning matrix of covariance. It has extension -cov.htm.
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.90  2003/06/24 12:34:15  brouard
 int maxwav; /* Maxim number of waves */    (Module): Some bugs corrected for windows. Also, when
 int jmin, jmax; /* min, max spacing between 2 waves */    mle=-1 a template is output in file "or"mypar.txt with the design
 int mle, weightopt;    of the covariance matrix to be input.
 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 */    Revision 1.89  2003/06/24 12:30:52  brouard
 double jmean; /* Mean space between 2 waves */    (Module): Some bugs corrected for windows. Also, when
 double **oldm, **newm, **savm; /* Working pointers to matrices */    mle=-1 a template is output in file "or"mypar.txt with the design
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    of the covariance matrix to be input.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficgp,*ficresprob,*ficpop;    Revision 1.88  2003/06/23 17:54:56  brouard
 FILE *ficreseij;    * 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.
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.87  2003/06/18 12:26:01  brouard
   char fileresv[FILENAMELENGTH];    Version 0.96
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
 #define NR_END 1    routine fileappend.
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
 #define NRANSI    current date of interview. It may happen when the death was just
 #define ITMAX 200    prior to the death. In this case, dh was negative and likelihood
     was wrong (infinity). We still send an "Error" but patch by
 #define TOL 2.0e-4    assuming that the date of death was just one stepm after the
     interview.
 #define CGOLD 0.3819660    (Repository): Because some people have very long ID (first column)
 #define ZEPS 1.0e-10    we changed int to long in num[] and we added a new lvector for
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    memory allocation. But we also truncated to 8 characters (left
     truncation)
 #define GOLD 1.618034    (Repository): No more line truncation errors.
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
 static double maxarg1,maxarg2;    place. It differs from routine "prevalence" which may be called
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    many times. Probs is memory consuming and must be used with
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    parcimony.
      Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.82  2003/06/05 15:57:20  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Add log in  imach.c and  fullversion number is now printed.
   
 int imx;  */
 int stepm;  /*
 /* Stepm, step in month: minimum step interpolation*/     Interpolated Markov Chain
   
 int m,nb;    Short summary of the programme:
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    This program computes Healthy Life Expectancies from
 double **pmmij, ***probs, ***mobaverage;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 double dateintmean=0;    first survey ("cross") where individuals from different ages are
     interviewed on their health status or degree of disability (in the
 double *weight;    case of a health survey which is our main interest) -2- at least a
 int **s; /* Status */    second wave of interviews ("longitudinal") which measure each change
 double *agedc, **covar, idx;    (if any) in individual health status.  Health expectancies are
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    computed from the time spent in each health state according to a
     model. More health states you consider, more time is necessary to reach the
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Maximum Likelihood of the parameters involved in the model.  The
 double ftolhess; /* Tolerance for computing hessian */    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
 /**************** split *************************/    conditional to be observed in state i at the first wave. Therefore
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 {    'age' is age and 'sex' is a covariate. If you want to have a more
    char *s;                             /* pointer */    complex model than "constant and age", you should modify the program
    int  l1, l2;                         /* length counters */    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
    l1 = strlen( path );                 /* length of path */    convergence.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows    The advantage of this computer programme, compared to a simple
    s = strrchr( path, '\\' );           /* find last / */    multinomial logistic model, is clear when the delay between waves is not
 #else    identical for each individual. Also, if a individual missed an
    s = strrchr( path, '/' );            /* find last / */    intermediate interview, the information is lost, but taken into
 #endif    account using an interpolation or extrapolation.  
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */    hPijx is the probability to be observed in state i at age x+h
       extern char       *getwd( );    conditional to the observed state i at age x. The delay 'h' can be
     split into an exact number (nh*stepm) of unobserved intermediate
       if ( getwd( dirc ) == NULL ) {    states. This elementary transition (by month, quarter,
 #else    semester or year) is modelled as a multinomial logistic.  The hPx
       extern char       *getcwd( );    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    hPijx.
 #endif  
          return( GLOCK_ERROR_GETCWD );    Also this programme outputs the covariance matrix of the parameters but also
       }    of the life expectancies. It also computes the stable prevalence. 
       strcpy( name, path );             /* we've got it */    
    } else {                             /* strip direcotry from path */    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
       s++;                              /* after this, the filename */             Institut national d'études démographiques, Paris.
       l2 = strlen( s );                 /* length of filename */    This software have been partly granted by Euro-REVES, a concerted action
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    from the European Union.
       strcpy( name, s );                /* save file name */    It is copyrighted identically to a GNU software product, ie programme and
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    software can be distributed freely for non commercial use. Latest version
       dirc[l1-l2] = 0;                  /* add zero */    can be accessed at http://euroreves.ined.fr/imach .
    }  
    l1 = strlen( dirc );                 /* length of directory */    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #ifdef windows    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    
 #else    **********************************************************************/
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  /*
 #endif    main
    s = strrchr( name, '.' );            /* find last / */    read parameterfile
    s++;    read datafile
    strcpy(ext,s);                       /* save extension */    concatwav
    l1= strlen( name);    freqsummary
    l2= strlen( s)+1;    if (mle >= 1)
    strncpy( finame, name, l1-l2);      mlikeli
    finame[l1-l2]= 0;    print results files
    return( 0 );                         /* we're done */    if mle==1 
 }       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 /******************************************/    open gnuplot file
     open html file
 void replace(char *s, char*t)    stable prevalence
 {     for age prevalim()
   int i;    h Pij x
   int lg=20;    variance of p varprob
   i=0;    forecasting if prevfcast==1 prevforecast call prevalence()
   lg=strlen(t);    health expectancies
   for(i=0; i<= lg; i++) {    Variance-covariance of DFLE
     (s[i] = t[i]);    prevalence()
     if (t[i]== '\\') s[i]='/';     movingaverage()
   }    varevsij() 
 }    if popbased==1 varevsij(,popbased)
     total life expectancies
 int nbocc(char *s, char occ)    Variance of stable prevalence
 {   end
   int i,j=0;  */
   int lg=20;  
   i=0;  
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {   
   if  (s[i] == occ ) j++;  #include <math.h>
   }  #include <stdio.h>
   return j;  #include <stdlib.h>
 }  #include <string.h>
   #include <unistd.h>
 void cutv(char *u,char *v, char*t, char occ)  
 {  /* #include <sys/time.h> */
   int i,lg,j,p=0;  #include <time.h>
   i=0;  #include "timeval.h"
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  /* #include <libintl.h> */
   }  /* #define _(String) gettext (String) */
   
   lg=strlen(t);  #define MAXLINE 256
   for(j=0; j<p; j++) {  #define GNUPLOTPROGRAM "gnuplot"
     (u[j] = t[j]);  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   }  #define FILENAMELENGTH 132
      u[p]='\0';  /*#define DEBUG*/
   /*#define windows*/
    for(j=0; j<= lg; j++) {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
     if (j>=(p+1))(v[j-p-1] = t[j]);  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   }  
 }  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 /********************** nrerror ********************/  
   #define NINTERVMAX 8
 void nrerror(char error_text[])  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 {  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   fprintf(stderr,"ERREUR ...\n");  #define NCOVMAX 8 /* Maximum number of covariates */
   fprintf(stderr,"%s\n",error_text);  #define MAXN 20000
   exit(1);  #define YEARM 12. /* Number of months per year */
 }  #define AGESUP 130
 /*********************** vector *******************/  #define AGEBASE 40
 double *vector(int nl, int nh)  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
 {  #ifdef UNIX
   double *v;  #define DIRSEPARATOR '/'
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #define ODIRSEPARATOR '\\'
   if (!v) nrerror("allocation failure in vector");  #else
   return v-nl+NR_END;  #define DIRSEPARATOR '\\'
 }  #define ODIRSEPARATOR '/'
   #endif
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)  /* $Id$ */
 {  /* $State$ */
   free((FREE_ARG)(v+nl-NR_END));  
 }  char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";
   char fullversion[]="$Revision$ $Date$"; 
 /************************ivector *******************************/  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 int *ivector(long nl,long nh)  int nvar;
 {  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   int *v;  int npar=NPARMAX;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  int nlstate=2; /* Number of live states */
   if (!v) nrerror("allocation failure in ivector");  int ndeath=1; /* Number of dead states */
   return v-nl+NR_END;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 }  int popbased=0;
   
 /******************free ivector **************************/  int *wav; /* Number of waves for this individuual 0 is possible */
 void free_ivector(int *v, long nl, long nh)  int maxwav; /* Maxim number of waves */
 {  int jmin, jmax; /* min, max spacing between 2 waves */
   free((FREE_ARG)(v+nl-NR_END));  int gipmx, gsw; /* Global variables on the number of contributions 
 }                     to the likelihood and the sum of weights (done by funcone)*/
   int mle, weightopt;
 /******************* imatrix *******************************/  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 int **imatrix(long nrl, long nrh, long ncl, long nch)  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 {             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  double jmean; /* Mean space between 2 waves */
   int **m;  double **oldm, **newm, **savm; /* Working pointers to matrices */
    double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   /* allocate pointers to rows */  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  FILE *ficlog, *ficrespow;
   if (!m) nrerror("allocation failure 1 in matrix()");  int globpr; /* Global variable for printing or not */
   m += NR_END;  double fretone; /* Only one call to likelihood */
   m -= nrl;  long ipmx; /* Number of contributions */
    double sw; /* Sum of weights */
    char filerespow[FILENAMELENGTH];
   /* allocate rows and set pointers to them */  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  FILE *ficresilk;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   m[nrl] += NR_END;  FILE *ficresprobmorprev;
   m[nrl] -= ncl;  FILE *fichtm, *fichtmcov; /* Html File */
    FILE *ficreseij;
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  char filerese[FILENAMELENGTH];
    FILE  *ficresvij;
   /* return pointer to array of pointers to rows */  char fileresv[FILENAMELENGTH];
   return m;  FILE  *ficresvpl;
 }  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
 /****************** free_imatrix *************************/  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 void free_imatrix(m,nrl,nrh,ncl,nch)  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
       int **m;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       long nch,ncl,nrh,nrl;  char command[FILENAMELENGTH];
      /* free an int matrix allocated by imatrix() */  int  outcmd=0;
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   free((FREE_ARG) (m+nrl-NR_END));  
 }  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
 /******************* matrix *******************************/  char fileregp[FILENAMELENGTH];
 double **matrix(long nrl, long nrh, long ncl, long nch)  char popfile[FILENAMELENGTH];
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   double **m;  
   struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  struct timezone tzp;
   if (!m) nrerror("allocation failure 1 in matrix()");  extern int gettimeofday();
   m += NR_END;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   m -= nrl;  long time_value;
   extern long time();
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  char strcurr[80], strfor[80];
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  #define NR_END 1
   m[nrl] -= ncl;  #define FREE_ARG char*
   #define FTOL 1.0e-10
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;  #define NRANSI 
 }  #define ITMAX 200 
   
 /*************************free matrix ************************/  #define TOL 2.0e-4 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {  #define CGOLD 0.3819660 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define ZEPS 1.0e-10 
   free((FREE_ARG)(m+nrl-NR_END));  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 }  
   #define GOLD 1.618034 
 /******************* ma3x *******************************/  #define GLIMIT 100.0 
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  #define TINY 1.0e-20 
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  static double maxarg1,maxarg2;
   double ***m;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    
   if (!m) nrerror("allocation failure 1 in matrix()");  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   m += NR_END;  #define rint(a) floor(a+0.5)
   m -= nrl;  
   static double sqrarg;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   m[nrl] += NR_END;  int agegomp= AGEGOMP;
   m[nrl] -= ncl;  
   int imx; 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int stepm=1;
   /* Stepm, step in month: minimum step interpolation*/
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  int estepm;
   m[nrl][ncl] += NR_END;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)  int m,nb;
     m[nrl][j]=m[nrl][j-1]+nlay;  long *num;
    int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   for (i=nrl+1; i<=nrh; i++) {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  double **pmmij, ***probs;
     for (j=ncl+1; j<=nch; j++)  double *ageexmed,*agecens;
       m[i][j]=m[i][j-1]+nlay;  double dateintmean=0;
   }  
   return m;  double *weight;
 }  int **s; /* Status */
   double *agedc, **covar, idx;
 /*************************free ma3x ************************/  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  double *lsurv, *lpop, *tpop;
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  double ftolhess; /* Tolerance for computing hessian */
   free((FREE_ARG)(m+nrl-NR_END));  
 }  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 /***************** f1dim *************************/  {
 extern int ncom;    /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
 extern double *pcom,*xicom;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
 extern double (*nrfunc)(double []);    */ 
      char  *ss;                            /* pointer */
 double f1dim(double x)    int   l1, l2;                         /* length counters */
 {  
   int j;    l1 = strlen(path );                   /* length of path */
   double f;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   double *xt;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
      if ( ss == NULL ) {                   /* no directory, so use current */
   xt=vector(1,ncom);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   f=(*nrfunc)(xt);      /* get current working directory */
   free_vector(xt,1,ncom);      /*    extern  char* getcwd ( char *buf , int len);*/
   return f;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 }        return( GLOCK_ERROR_GETCWD );
       }
 /*****************brent *************************/      strcpy( name, path );               /* we've got it */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    } else {                              /* strip direcotry from path */
 {      ss++;                               /* after this, the filename */
   int iter;      l2 = strlen( ss );                  /* length of filename */
   double a,b,d,etemp;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   double fu,fv,fw,fx;      strcpy( name, ss );         /* save file name */
   double ftemp;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   double p,q,r,tol1,tol2,u,v,w,x,xm;      dirc[l1-l2] = 0;                    /* add zero */
   double e=0.0;    }
      l1 = strlen( dirc );                  /* length of directory */
   a=(ax < cx ? ax : cx);    /*#ifdef windows
   b=(ax > cx ? ax : cx);    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   x=w=v=bx;  #else
   fw=fv=fx=(*f)(x);    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   for (iter=1;iter<=ITMAX;iter++) {  #endif
     xm=0.5*(a+b);    */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    ss = strrchr( name, '.' );            /* find last / */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    if (ss >0){
     printf(".");fflush(stdout);      ss++;
 #ifdef DEBUG      strcpy(ext,ss);                     /* save extension */
     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);      l1= strlen( name);
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */      l2= strlen(ss)+1;
 #endif      strncpy( finame, name, l1-l2);
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){      finame[l1-l2]= 0;
       *xmin=x;    }
       return fx;    return( 0 );                          /* we're done */
     }  }
     ftemp=fu;  
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);  /******************************************/
       q=(x-v)*(fx-fw);  
       p=(x-v)*q-(x-w)*r;  void replace_back_to_slash(char *s, char*t)
       q=2.0*(q-r);  {
       if (q > 0.0) p = -p;    int i;
       q=fabs(q);    int lg=0;
       etemp=e;    i=0;
       e=d;    lg=strlen(t);
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    for(i=0; i<= lg; i++) {
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      (s[i] = t[i]);
       else {      if (t[i]== '\\') s[i]='/';
         d=p/q;    }
         u=x+d;  }
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  int nbocc(char *s, char occ)
       }  {
     } else {    int i,j=0;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    int lg=20;
     }    i=0;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    lg=strlen(s);
     fu=(*f)(u);    for(i=0; i<= lg; i++) {
     if (fu <= fx) {    if  (s[i] == occ ) j++;
       if (u >= x) a=x; else b=x;    }
       SHFT(v,w,x,u)    return j;
         SHFT(fv,fw,fx,fu)  }
         } else {  
           if (u < x) a=u; else b=u;  void cutv(char *u,char *v, char*t, char occ)
           if (fu <= fw || w == x) {  {
             v=w;    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
             w=u;       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
             fv=fw;       gives u="abcedf" and v="ghi2j" */
             fw=fu;    int i,lg,j,p=0;
           } else if (fu <= fv || v == x || v == w) {    i=0;
             v=u;    for(j=0; j<=strlen(t)-1; j++) {
             fv=fu;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
           }    }
         }  
   }    lg=strlen(t);
   nrerror("Too many iterations in brent");    for(j=0; j<p; j++) {
   *xmin=x;      (u[j] = t[j]);
   return fx;    }
 }       u[p]='\0';
   
 /****************** mnbrak ***********************/     for(j=0; j<= lg; j++) {
       if (j>=(p+1))(v[j-p-1] = t[j]);
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    }
             double (*func)(double))  }
 {  
   double ulim,u,r,q, dum;  /********************** nrerror ********************/
   double fu;  
    void nrerror(char error_text[])
   *fa=(*func)(*ax);  {
   *fb=(*func)(*bx);    fprintf(stderr,"ERREUR ...\n");
   if (*fb > *fa) {    fprintf(stderr,"%s\n",error_text);
     SHFT(dum,*ax,*bx,dum)    exit(EXIT_FAILURE);
       SHFT(dum,*fb,*fa,dum)  }
       }  /*********************** vector *******************/
   *cx=(*bx)+GOLD*(*bx-*ax);  double *vector(int nl, int nh)
   *fc=(*func)(*cx);  {
   while (*fb > *fc) {    double *v;
     r=(*bx-*ax)*(*fb-*fc);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     q=(*bx-*cx)*(*fb-*fa);    if (!v) nrerror("allocation failure in vector");
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    return v-nl+NR_END;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  }
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {  /************************ free vector ******************/
       fu=(*func)(u);  void free_vector(double*v, int nl, int nh)
     } else if ((*cx-u)*(u-ulim) > 0.0) {  {
       fu=(*func)(u);    free((FREE_ARG)(v+nl-NR_END));
       if (fu < *fc) {  }
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  /************************ivector *******************************/
           }  int *ivector(long nl,long nh)
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  {
       u=ulim;    int *v;
       fu=(*func)(u);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     } else {    if (!v) nrerror("allocation failure in ivector");
       u=(*cx)+GOLD*(*cx-*bx);    return v-nl+NR_END;
       fu=(*func)(u);  }
     }  
     SHFT(*ax,*bx,*cx,u)  /******************free ivector **************************/
       SHFT(*fa,*fb,*fc,fu)  void free_ivector(int *v, long nl, long nh)
       }  {
 }    free((FREE_ARG)(v+nl-NR_END));
   }
 /*************** linmin ************************/  
   /************************lvector *******************************/
 int ncom;  long *lvector(long nl,long nh)
 double *pcom,*xicom;  {
 double (*nrfunc)(double []);    long *v;
      v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    if (!v) nrerror("allocation failure in ivector");
 {    return v-nl+NR_END;
   double brent(double ax, double bx, double cx,  }
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);  /******************free lvector **************************/
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  void free_lvector(long *v, long nl, long nh)
               double *fc, double (*func)(double));  {
   int j;    free((FREE_ARG)(v+nl-NR_END));
   double xx,xmin,bx,ax;  }
   double fx,fb,fa;  
    /******************* imatrix *******************************/
   ncom=n;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   pcom=vector(1,n);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   xicom=vector(1,n);  { 
   nrfunc=func;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   for (j=1;j<=n;j++) {    int **m; 
     pcom[j]=p[j];    
     xicom[j]=xi[j];    /* allocate pointers to rows */ 
   }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   ax=0.0;    if (!m) nrerror("allocation failure 1 in matrix()"); 
   xx=1.0;    m += NR_END; 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    m -= nrl; 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    
 #ifdef DEBUG    
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    /* allocate rows and set pointers to them */ 
 #endif    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   for (j=1;j<=n;j++) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     xi[j] *= xmin;    m[nrl] += NR_END; 
     p[j] += xi[j];    m[nrl] -= ncl; 
   }    
   free_vector(xicom,1,n);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   free_vector(pcom,1,n);    
 }    /* return pointer to array of pointers to rows */ 
     return m; 
 /*************** powell ************************/  } 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  
             double (*func)(double []))  /****************** free_imatrix *************************/
 {  void free_imatrix(m,nrl,nrh,ncl,nch)
   void linmin(double p[], double xi[], int n, double *fret,        int **m;
               double (*func)(double []));        long nch,ncl,nrh,nrl; 
   int i,ibig,j;       /* free an int matrix allocated by imatrix() */ 
   double del,t,*pt,*ptt,*xit;  { 
   double fp,fptt;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   double *xits;    free((FREE_ARG) (m+nrl-NR_END)); 
   pt=vector(1,n);  } 
   ptt=vector(1,n);  
   xit=vector(1,n);  /******************* matrix *******************************/
   xits=vector(1,n);  double **matrix(long nrl, long nrh, long ncl, long nch)
   *fret=(*func)(p);  {
   for (j=1;j<=n;j++) pt[j]=p[j];    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   for (*iter=1;;++(*iter)) {    double **m;
     fp=(*fret);  
     ibig=0;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     del=0.0;    if (!m) nrerror("allocation failure 1 in matrix()");
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    m += NR_END;
     for (i=1;i<=n;i++)    m -= nrl;
       printf(" %d %.12f",i, p[i]);  
     printf("\n");    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     for (i=1;i<=n;i++) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    m[nrl] += NR_END;
       fptt=(*fret);    m[nrl] -= ncl;
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 #endif    return m;
       printf("%d",i);fflush(stdout);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       linmin(p,xit,n,fret,func);     */
       if (fabs(fptt-(*fret)) > del) {  }
         del=fabs(fptt-(*fret));  
         ibig=i;  /*************************free matrix ************************/
       }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
 #ifdef DEBUG  {
       printf("%d %.12e",i,(*fret));    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       for (j=1;j<=n;j++) {    free((FREE_ARG)(m+nrl-NR_END));
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  }
         printf(" x(%d)=%.12e",j,xit[j]);  
       }  /******************* ma3x *******************************/
       for(j=1;j<=n;j++)  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
         printf(" p=%.12e",p[j]);  {
       printf("\n");    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
 #endif    double ***m;
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 #ifdef DEBUG    if (!m) nrerror("allocation failure 1 in matrix()");
       int k[2],l;    m += NR_END;
       k[0]=1;    m -= nrl;
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       for (j=1;j<=n;j++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         printf(" %.12e",p[j]);    m[nrl] += NR_END;
       printf("\n");    m[nrl] -= ncl;
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
           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]);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         }    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    m[nrl][ncl] += NR_END;
       }    m[nrl][ncl] -= nll;
 #endif    for (j=ncl+1; j<=nch; j++) 
       m[nrl][j]=m[nrl][j-1]+nlay;
     
       free_vector(xit,1,n);    for (i=nrl+1; i<=nrh; i++) {
       free_vector(xits,1,n);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       free_vector(ptt,1,n);      for (j=ncl+1; j<=nch; j++) 
       free_vector(pt,1,n);        m[i][j]=m[i][j-1]+nlay;
       return;    }
     }    return m; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     for (j=1;j<=n;j++) {             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       ptt[j]=2.0*p[j]-pt[j];    */
       xit[j]=p[j]-pt[j];  }
       pt[j]=p[j];  
     }  /*************************free ma3x ************************/
     fptt=(*func)(ptt);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     if (fptt < fp) {  {
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       if (t < 0.0) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         linmin(p,xit,n,fret,func);    free((FREE_ARG)(m+nrl-NR_END));
         for (j=1;j<=n;j++) {  }
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];  /*************** function subdirf ***********/
         }  char *subdirf(char fileres[])
 #ifdef DEBUG  {
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    /* Caution optionfilefiname is hidden */
         for(j=1;j<=n;j++)    strcpy(tmpout,optionfilefiname);
           printf(" %.12e",xit[j]);    strcat(tmpout,"/"); /* Add to the right */
         printf("\n");    strcat(tmpout,fileres);
 #endif    return tmpout;
       }  }
     }  
   }  /*************** function subdirf2 ***********/
 }  char *subdirf2(char fileres[], char *preop)
   {
 /**** Prevalence limit ****************/    
     /* Caution optionfilefiname is hidden */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    strcpy(tmpout,optionfilefiname);
 {    strcat(tmpout,"/");
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    strcat(tmpout,preop);
      matrix by transitions matrix until convergence is reached */    strcat(tmpout,fileres);
     return tmpout;
   int i, ii,j,k;  }
   double min, max, maxmin, maxmax,sumnew=0.;  
   double **matprod2();  /*************** function subdirf3 ***********/
   double **out, cov[NCOVMAX], **pmij();  char *subdirf3(char fileres[], char *preop, char *preop2)
   double **newm;  {
   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,"/");
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    strcat(tmpout,preop);
     }    strcat(tmpout,preop2);
     strcat(tmpout,fileres);
    cov[1]=1.;    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){  /***************** f1dim *************************/
     newm=savm;  extern int ncom; 
     /* Covariates have to be included here again */  extern double *pcom,*xicom;
      cov[2]=agefin;  extern double (*nrfunc)(double []); 
     
       for (k=1; k<=cptcovn;k++) {  double f1dim(double x) 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  { 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    int j; 
       }    double f;
       for (k=1; k<=cptcovage;k++)    double *xt; 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];   
       for (k=1; k<=cptcovprod;k++)    xt=vector(1,ncom); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    free_vector(xt,1,ncom); 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    return f; 
   } 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  
   /*****************brent *************************/
     savm=oldm;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     oldm=newm;  { 
     maxmax=0.;    int iter; 
     for(j=1;j<=nlstate;j++){    double a,b,d,etemp;
       min=1.;    double fu,fv,fw,fx;
       max=0.;    double ftemp;
       for(i=1; i<=nlstate; i++) {    double p,q,r,tol1,tol2,u,v,w,x,xm; 
         sumnew=0;    double e=0.0; 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];   
         prlim[i][j]= newm[i][j]/(1-sumnew);    a=(ax < cx ? ax : cx); 
         max=FMAX(max,prlim[i][j]);    b=(ax > cx ? ax : cx); 
         min=FMIN(min,prlim[i][j]);    x=w=v=bx; 
       }    fw=fv=fx=(*f)(x); 
       maxmin=max-min;    for (iter=1;iter<=ITMAX;iter++) { 
       maxmax=FMAX(maxmax,maxmin);      xm=0.5*(a+b); 
     }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     if(maxmax < ftolpl){      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       return prlim;      printf(".");fflush(stdout);
     }      fprintf(ficlog,".");fflush(ficlog);
   }  #ifdef DEBUG
 }      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 /*************** transition probabilities ***************/      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   #endif
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 {        *xmin=x; 
   double s1, s2;        return fx; 
   /*double t34;*/      } 
   int i,j,j1, nc, ii, jj;      ftemp=fu;
       if (fabs(e) > tol1) { 
     for(i=1; i<= nlstate; i++){        r=(x-w)*(fx-fv); 
     for(j=1; j<i;j++){        q=(x-v)*(fx-fw); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        p=(x-v)*q-(x-w)*r; 
         /*s2 += param[i][j][nc]*cov[nc];*/        q=2.0*(q-r); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        if (q > 0.0) p = -p; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/        q=fabs(q); 
       }        etemp=e; 
       ps[i][j]=s2;        e=d; 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        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)); 
     for(j=i+1; j<=nlstate+ndeath;j++){        else { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          d=p/q; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          u=x+d; 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/          if (u-a < tol2 || b-u < tol2) 
       }            d=SIGN(tol1,xm-x); 
       ps[i][j]=s2;        } 
     }      } else { 
   }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     /*ps[3][2]=1;*/      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   for(i=1; i<= nlstate; i++){      fu=(*f)(u); 
      s1=0;      if (fu <= fx) { 
     for(j=1; j<i; j++)        if (u >= x) a=x; else b=x; 
       s1+=exp(ps[i][j]);        SHFT(v,w,x,u) 
     for(j=i+1; j<=nlstate+ndeath; j++)          SHFT(fv,fw,fx,fu) 
       s1+=exp(ps[i][j]);          } else { 
     ps[i][i]=1./(s1+1.);            if (u < x) a=u; else b=u; 
     for(j=1; j<i; j++)            if (fu <= fw || w == x) { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];              v=w; 
     for(j=i+1; j<=nlstate+ndeath; j++)              w=u; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];              fv=fw; 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */              fw=fu; 
   } /* end i */            } else if (fu <= fv || v == x || v == w) { 
               v=u; 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){              fv=fu; 
     for(jj=1; jj<= nlstate+ndeath; jj++){            } 
       ps[ii][jj]=0;          } 
       ps[ii][ii]=1;    } 
     }    nrerror("Too many iterations in brent"); 
   }    *xmin=x; 
     return fx; 
   } 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  /****************** mnbrak ***********************/
      printf("%lf ",ps[ii][jj]);  
    }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     printf("\n ");              double (*func)(double)) 
     }  { 
     printf("\n ");printf("%lf ",cov[2]);*/    double ulim,u,r,q, dum;
 /*    double fu; 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);   
   goto end;*/    *fa=(*func)(*ax); 
     return ps;    *fb=(*func)(*bx); 
 }    if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
 /**************** Product of 2 matrices ******************/        SHFT(dum,*fb,*fa,dum) 
         } 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    *cx=(*bx)+GOLD*(*bx-*ax); 
 {    *fc=(*func)(*cx); 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    while (*fb > *fc) { 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      r=(*bx-*ax)*(*fb-*fc); 
   /* in, b, out are matrice of pointers which should have been initialized      q=(*bx-*cx)*(*fb-*fa); 
      before: only the contents of out is modified. The function returns      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
      a pointer to pointers identical to out */        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   long i, j, k;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   for(i=nrl; i<= nrh; i++)      if ((*bx-u)*(u-*cx) > 0.0) { 
     for(k=ncolol; k<=ncoloh; k++)        fu=(*func)(u); 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         out[i][k] +=in[i][j]*b[j][k];        fu=(*func)(u); 
         if (fu < *fc) { 
   return out;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
 }            SHFT(*fb,*fc,fu,(*func)(u)) 
             } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 /************* Higher Matrix Product ***************/        u=ulim; 
         fu=(*func)(u); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      } else { 
 {        u=(*cx)+GOLD*(*cx-*bx); 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        fu=(*func)(u); 
      duration (i.e. until      } 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      SHFT(*ax,*bx,*cx,u) 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        SHFT(*fa,*fb,*fc,fu) 
      (typically every 2 years instead of every month which is too big).        } 
      Model is determined by parameters x and covariates have to be  } 
      included manually here.  
   /*************** linmin ************************/
      */  
   int ncom; 
   int i, j, d, h, k;  double *pcom,*xicom;
   double **out, cov[NCOVMAX];  double (*nrfunc)(double []); 
   double **newm;   
   void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   /* Hstepm could be zero and should return the unit matrix */  { 
   for (i=1;i<=nlstate+ndeath;i++)    double brent(double ax, double bx, double cx, 
     for (j=1;j<=nlstate+ndeath;j++){                 double (*f)(double), double tol, double *xmin); 
       oldm[i][j]=(i==j ? 1.0 : 0.0);    double f1dim(double x); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     }                double *fc, double (*func)(double)); 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    int j; 
   for(h=1; h <=nhstepm; h++){    double xx,xmin,bx,ax; 
     for(d=1; d <=hstepm; d++){    double fx,fb,fa;
       newm=savm;   
       /* Covariates have to be included here again */    ncom=n; 
       cov[1]=1.;    pcom=vector(1,n); 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    xicom=vector(1,n); 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    nrfunc=func; 
       for (k=1; k<=cptcovage;k++)    for (j=1;j<=n;j++) { 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      pcom[j]=p[j]; 
       for (k=1; k<=cptcovprod;k++)      xicom[j]=xi[j]; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    } 
     ax=0.0; 
     xx=1.0; 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  #ifdef DEBUG
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       savm=oldm;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       oldm=newm;  #endif
     }    for (j=1;j<=n;j++) { 
     for(i=1; i<=nlstate+ndeath; i++)      xi[j] *= xmin; 
       for(j=1;j<=nlstate+ndeath;j++) {      p[j] += xi[j]; 
         po[i][j][h]=newm[i][j];    } 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    free_vector(xicom,1,n); 
          */    free_vector(pcom,1,n); 
       }  } 
   } /* end h */  
   return po;  char *asc_diff_time(long time_sec, char ascdiff[])
 }  {
     long sec_left, days, hours, minutes;
     days = (time_sec) / (60*60*24);
 /*************** log-likelihood *************/    sec_left = (time_sec) % (60*60*24);
 double func( double *x)    hours = (sec_left) / (60*60) ;
 {    sec_left = (sec_left) %(60*60);
   int i, ii, j, k, mi, d, kk;    minutes = (sec_left) /60;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    sec_left = (sec_left) % (60);
   double **out;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   double sw; /* Sum of weights */    return ascdiff;
   double lli; /* Individual log likelihood */  }
   long ipmx;  
   /*extern weight */  /*************** powell ************************/
   /* We are differentiating ll according to initial status */  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/              double (*func)(double [])) 
   /*for(i=1;i<imx;i++)  { 
     printf(" %d\n",s[4][i]);    void linmin(double p[], double xi[], int n, double *fret, 
   */                double (*func)(double [])); 
   cov[1]=1.;    int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
   for(k=1; k<=nlstate; k++) ll[k]=0.;    double fp,fptt;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    double *xits;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    int niterf, itmp;
     for(mi=1; mi<= wav[i]-1; mi++){  
       for (ii=1;ii<=nlstate+ndeath;ii++)    pt=vector(1,n); 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    ptt=vector(1,n); 
       for(d=0; d<dh[mi][i]; d++){    xit=vector(1,n); 
         newm=savm;    xits=vector(1,n); 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    *fret=(*func)(p); 
         for (kk=1; kk<=cptcovage;kk++) {    for (j=1;j<=n;j++) pt[j]=p[j]; 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    for (*iter=1;;++(*iter)) { 
         }      fp=(*fret); 
              ibig=0; 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      del=0.0; 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      last_time=curr_time;
         savm=oldm;      (void) gettimeofday(&curr_time,&tzp);
         oldm=newm;      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
              /*    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
              fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       } /* end mult */      */
           for (i=1;i<=n;i++) {
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        printf(" %d %.12f",i, p[i]);
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        fprintf(ficlog," %d %.12lf",i, p[i]);
       ipmx +=1;        fprintf(ficrespow," %.12lf", p[i]);
       sw += weight[i];      }
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      printf("\n");
     } /* end of wave */      fprintf(ficlog,"\n");
   } /* end of individual */      fprintf(ficrespow,"\n");fflush(ficrespow);
       if(*iter <=3){
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        tm = *localtime(&curr_time.tv_sec);
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        strcpy(strcurr,asctime(&tm));
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  /*       asctime_r(&tm,strcurr); */
   return -l;        forecast_time=curr_time; 
 }        itmp = strlen(strcurr);
         if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           strcurr[itmp-1]='\0';
 /*********** Maximum Likelihood Estimation ***************/        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        for(niterf=10;niterf<=30;niterf+=10){
 {          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   int i,j, iter;          tmf = *localtime(&forecast_time.tv_sec);
   double **xi,*delti;  /*      asctime_r(&tmf,strfor); */
   double fret;          strcpy(strfor,asctime(&tmf));
   xi=matrix(1,npar,1,npar);          itmp = strlen(strfor);
   for (i=1;i<=npar;i++)          if(strfor[itmp-1]=='\n')
     for (j=1;j<=npar;j++)          strfor[itmp-1]='\0';
       xi[i][j]=(i==j ? 1.0 : 0.0);          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);
   printf("Powell\n");          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);
   powell(p,xi,npar,ftol,&iter,&fret,func);        }
       }
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      for (i=1;i<=n;i++) { 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         fptt=(*fret); 
 }  #ifdef DEBUG
         printf("fret=%lf \n",*fret);
 /**** Computes Hessian and covariance matrix ***/        fprintf(ficlog,"fret=%lf \n",*fret);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  #endif
 {        printf("%d",i);fflush(stdout);
   double  **a,**y,*x,pd;        fprintf(ficlog,"%d",i);fflush(ficlog);
   double **hess;        linmin(p,xit,n,fret,func); 
   int i, j,jk;        if (fabs(fptt-(*fret)) > del) { 
   int *indx;          del=fabs(fptt-(*fret)); 
           ibig=i; 
   double hessii(double p[], double delta, int theta, double delti[]);        } 
   double hessij(double p[], double delti[], int i, int j);  #ifdef DEBUG
   void lubksb(double **a, int npar, int *indx, double b[]) ;        printf("%d %.12e",i,(*fret));
   void ludcmp(double **a, int npar, int *indx, double *d) ;        fprintf(ficlog,"%d %.12e",i,(*fret));
         for (j=1;j<=n;j++) {
   hess=matrix(1,npar,1,npar);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           printf(" x(%d)=%.12e",j,xit[j]);
   printf("\nCalculation of the hessian matrix. Wait...\n");          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   for (i=1;i<=npar;i++){        }
     printf("%d",i);fflush(stdout);        for(j=1;j<=n;j++) {
     hess[i][i]=hessii(p,ftolhess,i,delti);          printf(" p=%.12e",p[j]);
     /*printf(" %f ",p[i]);*/          fprintf(ficlog," p=%.12e",p[j]);
     /*printf(" %lf ",hess[i][i]);*/        }
   }        printf("\n");
          fprintf(ficlog,"\n");
   for (i=1;i<=npar;i++) {  #endif
     for (j=1;j<=npar;j++)  {      } 
       if (j>i) {      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
         printf(".%d%d",i,j);fflush(stdout);  #ifdef DEBUG
         hess[i][j]=hessij(p,delti,i,j);        int k[2],l;
         hess[j][i]=hess[i][j];            k[0]=1;
         /*printf(" %lf ",hess[i][j]);*/        k[1]=-1;
       }        printf("Max: %.12e",(*func)(p));
     }        fprintf(ficlog,"Max: %.12e",(*func)(p));
   }        for (j=1;j<=n;j++) {
   printf("\n");          printf(" %.12e",p[j]);
           fprintf(ficlog," %.12e",p[j]);
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        }
          printf("\n");
   a=matrix(1,npar,1,npar);        fprintf(ficlog,"\n");
   y=matrix(1,npar,1,npar);        for(l=0;l<=1;l++) {
   x=vector(1,npar);          for (j=1;j<=n;j++) {
   indx=ivector(1,npar);            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   for (i=1;i<=npar;i++)            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][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]);
   ludcmp(a,npar,indx,&pd);          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   for (j=1;j<=npar;j++) {          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for (i=1;i<=npar;i++) x[i]=0;        }
     x[j]=1;  #endif
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){  
       matcov[i][j]=x[i];        free_vector(xit,1,n); 
     }        free_vector(xits,1,n); 
   }        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
   printf("\n#Hessian matrix#\n");        return; 
   for (i=1;i<=npar;i++) {      } 
     for (j=1;j<=npar;j++) {      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       printf("%.3e ",hess[i][j]);      for (j=1;j<=n;j++) { 
     }        ptt[j]=2.0*p[j]-pt[j]; 
     printf("\n");        xit[j]=p[j]-pt[j]; 
   }        pt[j]=p[j]; 
       } 
   /* Recompute Inverse */      fptt=(*func)(ptt); 
   for (i=1;i<=npar;i++)      if (fptt < fp) { 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   ludcmp(a,npar,indx,&pd);        if (t < 0.0) { 
           linmin(p,xit,n,fret,func); 
   /*  printf("\n#Hessian matrix recomputed#\n");          for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; 
   for (j=1;j<=npar;j++) {            xi[j][n]=xit[j]; 
     for (i=1;i<=npar;i++) x[i]=0;          }
     x[j]=1;  #ifdef DEBUG
     lubksb(a,npar,indx,x);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for (i=1;i<=npar;i++){          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       y[i][j]=x[i];          for(j=1;j<=n;j++){
       printf("%.3e ",y[i][j]);            printf(" %.12e",xit[j]);
     }            fprintf(ficlog," %.12e",xit[j]);
     printf("\n");          }
   }          printf("\n");
   */          fprintf(ficlog,"\n");
   #endif
   free_matrix(a,1,npar,1,npar);        }
   free_matrix(y,1,npar,1,npar);      } 
   free_vector(x,1,npar);    } 
   free_ivector(indx,1,npar);  } 
   free_matrix(hess,1,npar,1,npar);  
   /**** Prevalence limit (stable prevalence)  ****************/
   
 }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   {
 /*************** hessian matrix ****************/    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
 double hessii( double x[], double delta, int theta, double delti[])       matrix by transitions matrix until convergence is reached */
 {  
   int i;    int i, ii,j,k;
   int l=1, lmax=20;    double min, max, maxmin, maxmax,sumnew=0.;
   double k1,k2;    double **matprod2();
   double p2[NPARMAX+1];    double **out, cov[NCOVMAX], **pmij();
   double res;    double **newm;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    double agefin, delaymax=50 ; /* Max number of years to converge */
   double fx;  
   int k=0,kmax=10;    for (ii=1;ii<=nlstate+ndeath;ii++)
   double l1;      for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   fx=func(x);      }
   for (i=1;i<=npar;i++) p2[i]=x[i];  
   for(l=0 ; l <=lmax; l++){     cov[1]=1.;
     l1=pow(10,l);   
     delts=delt;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(k=1 ; k <kmax; k=k+1){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       delt = delta*(l1*k);      newm=savm;
       p2[theta]=x[theta] +delt;      /* Covariates have to be included here again */
       k1=func(p2)-fx;       cov[2]=agefin;
       p2[theta]=x[theta]-delt;    
       k2=func(p2)-fx;        for (k=1; k<=cptcovn;k++) {
       /*res= (k1-2.0*fx+k2)/delt/delt; */          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          /*      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]]);*/
              }
 #ifdef DEBUG        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       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);        for (k=1; k<=cptcovprod;k++)
 #endif          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         k=kmax;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       }        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
         k=kmax; l=lmax*10.;  
       }      savm=oldm;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      oldm=newm;
         delts=delt;      maxmax=0.;
       }      for(j=1;j<=nlstate;j++){
     }        min=1.;
   }        max=0.;
   delti[theta]=delts;        for(i=1; i<=nlstate; i++) {
   return res;          sumnew=0;
            for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
 }          prlim[i][j]= newm[i][j]/(1-sumnew);
           max=FMAX(max,prlim[i][j]);
 double hessij( double x[], double delti[], int thetai,int thetaj)          min=FMIN(min,prlim[i][j]);
 {        }
   int i;        maxmin=max-min;
   int l=1, l1, lmax=20;        maxmax=FMAX(maxmax,maxmin);
   double k1,k2,k3,k4,res,fx;      }
   double p2[NPARMAX+1];      if(maxmax < ftolpl){
   int k;        return prlim;
       }
   fx=func(x);    }
   for (k=1; k<=2; k++) {  }
     for (i=1;i<=npar;i++) p2[i]=x[i];  
     p2[thetai]=x[thetai]+delti[thetai]/k;  /*************** transition probabilities ***************/ 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k1=func(p2)-fx;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
    {
     p2[thetai]=x[thetai]+delti[thetai]/k;    double s1, s2;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    /*double t34;*/
     k2=func(p2)-fx;    int i,j,j1, nc, ii, jj;
    
     p2[thetai]=x[thetai]-delti[thetai]/k;      for(i=1; i<= nlstate; i++){
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        for(j=1; j<i;j++){
     k3=func(p2)-fx;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
              /*s2 += param[i][j][nc]*cov[nc];*/
     p2[thetai]=x[thetai]-delti[thetai]/k;            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
     k4=func(p2)-fx;          }
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          ps[i][j]=s2;
 #ifdef DEBUG  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
     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        for(j=i+1; j<=nlstate+ndeath;j++){
   }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   return res;            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 }  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
           }
 /************** Inverse of matrix **************/          ps[i][j]=s2;
 void ludcmp(double **a, int n, int *indx, double *d)        }
 {      }
   int i,imax,j,k;      /*ps[3][2]=1;*/
   double big,dum,sum,temp;      
   double *vv;      for(i=1; i<= nlstate; i++){
          s1=0;
   vv=vector(1,n);        for(j=1; j<i; j++)
   *d=1.0;          s1+=exp(ps[i][j]);
   for (i=1;i<=n;i++) {        for(j=i+1; j<=nlstate+ndeath; j++)
     big=0.0;          s1+=exp(ps[i][j]);
     for (j=1;j<=n;j++)        ps[i][i]=1./(s1+1.);
       if ((temp=fabs(a[i][j])) > big) big=temp;        for(j=1; j<i; j++)
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          ps[i][j]= exp(ps[i][j])*ps[i][i];
     vv[i]=1.0/big;        for(j=i+1; j<=nlstate+ndeath; j++)
   }          ps[i][j]= exp(ps[i][j])*ps[i][i];
   for (j=1;j<=n;j++) {        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     for (i=1;i<j;i++) {      } /* end i */
       sum=a[i][j];      
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       a[i][j]=sum;        for(jj=1; jj<= nlstate+ndeath; jj++){
     }          ps[ii][jj]=0;
     big=0.0;          ps[ii][ii]=1;
     for (i=j;i<=n;i++) {        }
       sum=a[i][j];      }
       for (k=1;k<j;k++)      
         sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
       if ( (dum=vv[i]*fabs(sum)) >= big) {  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
         big=dum;  /*         printf("ddd %lf ",ps[ii][jj]); */
         imax=i;  /*       } */
       }  /*       printf("\n "); */
     }  /*        } */
     if (j != imax) {  /*        printf("\n ");printf("%lf ",cov[2]); */
       for (k=1;k<=n;k++) {         /*
         dum=a[imax][k];        for(i=1; i<= npar; i++) printf("%f ",x[i]);
         a[imax][k]=a[j][k];        goto end;*/
         a[j][k]=dum;      return ps;
       }  }
       *d = -(*d);  
       vv[imax]=vv[j];  /**************** Product of 2 matrices ******************/
     }  
     indx[j]=imax;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     if (a[j][j] == 0.0) a[j][j]=TINY;  {
     if (j != n) {    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       dum=1.0/(a[j][j]);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    /* in, b, out are matrice of pointers which should have been initialized 
     }       before: only the contents of out is modified. The function returns
   }       a pointer to pointers identical to out */
   free_vector(vv,1,n);  /* Doesn't work */    long i, j, k;
 ;    for(i=nrl; i<= nrh; i++)
 }      for(k=ncolol; k<=ncoloh; k++)
         for(j=ncl,out[i][k]=0.; j<=nch; j++)
 void lubksb(double **a, int n, int *indx, double b[])          out[i][k] +=in[i][j]*b[j][k];
 {  
   int i,ii=0,ip,j;    return out;
   double sum;  }
    
   for (i=1;i<=n;i++) {  
     ip=indx[i];  /************* Higher Matrix Product ***************/
     sum=b[ip];  
     b[ip]=b[i];  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     if (ii)  {
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    /* Computes the transition matrix starting at age 'age' over 
     else if (sum) ii=i;       'nhstepm*hstepm*stepm' months (i.e. until
     b[i]=sum;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   }       nhstepm*hstepm matrices. 
   for (i=n;i>=1;i--) {       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     sum=b[i];       (typically every 2 years instead of every month which is too big 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];       for the memory).
     b[i]=sum/a[i][i];       Model is determined by parameters x and covariates have to be 
   }       included manually here. 
 }  
        */
 /************ Frequencies ********************/  
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)    int i, j, d, h, k;
 {  /* Some frequencies */    double **out, cov[NCOVMAX];
      double **newm;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */    /* Hstepm could be zero and should return the unit matrix */
   double *pp;    for (i=1;i<=nlstate+ndeath;i++)
   double pos, k2, dateintsum=0,k2cpt=0;      for (j=1;j<=nlstate+ndeath;j++){
   FILE *ficresp;        oldm[i][j]=(i==j ? 1.0 : 0.0);
   char fileresp[FILENAMELENGTH];        po[i][j][0]=(i==j ? 1.0 : 0.0);
        }
   pp=vector(1,nlstate);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    for(h=1; h <=nhstepm; h++){
   strcpy(fileresp,"p");      for(d=1; d <=hstepm; d++){
   strcat(fileresp,fileres);        newm=savm;
   if((ficresp=fopen(fileresp,"w"))==NULL) {        /* Covariates have to be included here again */
     printf("Problem with prevalence resultfile: %s\n", fileresp);        cov[1]=1.;
     exit(0);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   }        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        for (k=1; k<=cptcovage;k++)
   j1=0;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
   j=cptcoveff;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
   
   for(k1=1; k1<=j;k1++){        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
    for(i1=1; i1<=ncodemax[k1];i1++){        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
        j1++;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
          scanf("%d", i);*/        savm=oldm;
         for (i=-1; i<=nlstate+ndeath; i++)          oldm=newm;
          for (jk=-1; jk<=nlstate+ndeath; jk++)        }
            for(m=agemin; m <= agemax+3; m++)      for(i=1; i<=nlstate+ndeath; i++)
              freq[i][jk][m]=0;        for(j=1;j<=nlstate+ndeath;j++) {
           po[i][j][h]=newm[i][j];
         dateintsum=0;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
         k2cpt=0;           */
        for (i=1; i<=imx; i++) {        }
          bool=1;    } /* end h */
          if  (cptcovn>0) {    return po;
            for (z1=1; z1<=cptcoveff; z1++)  }
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
                bool=0;  
          }  /*************** log-likelihood *************/
          if (bool==1) {  double func( double *x)
            for(m=firstpass; m<=lastpass; m++){  {
              k2=anint[m][i]+(mint[m][i]/12.);    int i, ii, j, k, mi, d, kk;
              if ((k2>=dateprev1) && (k2<=dateprev2)) {    double l, ll[NLSTATEMAX], cov[NCOVMAX];
                if(agev[m][i]==0) agev[m][i]=agemax+1;    double **out;
                if(agev[m][i]==1) agev[m][i]=agemax+2;    double sw; /* Sum of weights */
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    double lli; /* Individual log likelihood */
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    int s1, s2;
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    double bbh, survp;
                  dateintsum=dateintsum+k2;    long ipmx;
                  k2cpt++;    /*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++) 
            }      printf(" %d\n",s[4][i]);
          }    */
        }    cov[1]=1.;
          
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
         if  (cptcovn>0) {    if(mle==1){
          fprintf(ficresp, "\n#********** Variable ");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          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++) cov[2+k]=covar[Tvar[k]][i];
        fprintf(ficresp, "**********\n#");        for(mi=1; mi<= wav[i]-1; mi++){
         }          for (ii=1;ii<=nlstate+ndeath;ii++)
        for(i=1; i<=nlstate;i++)            for (j=1;j<=nlstate+ndeath;j++){
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
        fprintf(ficresp, "\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                    }
   for(i=(int)agemin; i <= (int)agemax+3; i++){          for(d=0; d<dh[mi][i]; d++){
     if(i==(int)agemax+3)            newm=savm;
       printf("Total");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     else            for (kk=1; kk<=cptcovage;kk++) {
       printf("Age %d", i);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(jk=1; jk <=nlstate ; jk++){            }
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         pp[jk] += freq[jk][m][i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
     for(jk=1; jk <=nlstate ; jk++){            oldm=newm;
       for(m=-1, pos=0; m <=0 ; m++)          } /* end mult */
         pos += freq[jk][m][i];        
       if(pp[jk]>=1.e-10)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          /* 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 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);           * (in months) between two waves is not a multiple of stepm, we rounded to 
     }           * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
      for(jk=1; jk <=nlstate ; jk++){           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)           * probability in order to take into account the bias as a fraction of the way
         pp[jk] += freq[jk][m][i];           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
      }           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
     for(jk=1,pos=0; jk <=nlstate ; jk++)           * For stepm > 1 the results are less biased than in previous versions. 
       pos += pp[jk];           */
     for(jk=1; jk <=nlstate ; jk++){          s1=s[mw[mi][i]][i];
       if(pos>=1.e-5)          s2=s[mw[mi+1][i]][i];
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          bbh=(double)bh[mi][i]/(double)stepm; 
       else          /* bias bh is positive if real duration
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);           * is higher than the multiple of stepm and negative otherwise.
       if( i <= (int) agemax){           */
         if(pos>=1.e-5){          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          if( s2 > nlstate){ 
           probs[i][jk][j1]= pp[jk]/pos;            /* i.e. if s2 is a death state and if the date of death is known 
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/               then the contribution to the likelihood is the probability to 
         }               die between last step unit time and current  step unit time, 
       else               which is also equal to probability to die before dh 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);               minus probability to die before dh-stepm . 
       }               In version up to 0.92 likelihood was computed
     }          as if date of death was unknown. Death was treated as any other
     for(jk=-1; jk <=nlstate+ndeath; jk++)          health state: the date of the interview describes the actual state
       for(m=-1; m <=nlstate+ndeath; m++)          and not the date of a change in health state. The former idea was
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          to consider that at each interview the state was recorded
     if(i <= (int) agemax)          (healthy, disable or death) and IMaCh was corrected; but when we
       fprintf(ficresp,"\n");          introduced the exact date of death then we should have modified
     printf("\n");          the contribution of an exact death to the likelihood. This new
     }          contribution is smaller and very dependent of the step unit
     }          stepm. It is no more the probability to die between last interview
  }          and month of death but the probability to survive from last
   dateintmean=dateintsum/k2cpt;          interview up to one month before death multiplied by the
            probability to die within a month. Thanks to Chris
   fclose(ficresp);          Jackson for correcting this bug.  Former versions increased
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          mortality artificially. The bad side is that we add another loop
   free_vector(pp,1,nlstate);          which slows down the processing. The difference can be up to 10%
           lower mortality.
   /* End of Freq */            */
 }            lli=log(out[s1][s2] - savm[s1][s2]);
   
 /************ Prevalence ********************/  
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)          } else if  (s2==-2) {
 {  /* Some frequencies */            for (j=1,survp=0. ; j<=nlstate; j++) 
                survp += out[s1][j];
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;            lli= survp;
   double ***freq; /* Frequencies */          }
   double *pp;          
   double pos, k2;          else if  (s2==-4) {
             for (j=3,survp=0. ; j<=nlstate; j++) 
   pp=vector(1,nlstate);              survp += out[s1][j];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            lli= survp;
            }
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          
   j1=0;          else if  (s2==-5) {
              for (j=1,survp=0. ; j<=2; j++) 
   j=cptcoveff;              survp += out[s1][j];
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            lli= survp;
            }
  for(k1=1; k1<=j;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){  
       j1++;          else{
              lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       for (i=-1; i<=nlstate+ndeath; i++)              /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
         for (jk=-1; jk<=nlstate+ndeath; jk++)            } 
           for(m=agemin; m <= agemax+3; m++)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
             freq[i][jk][m]=0;          /*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); */
       for (i=1; i<=imx; i++) {          ipmx +=1;
         bool=1;          sw += weight[i];
         if  (cptcovn>0) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           for (z1=1; z1<=cptcoveff; z1++)        } /* end of wave */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      } /* end of individual */
               bool=0;    }  else if(mle==2){
         }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         if (bool==1) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           for(m=firstpass; m<=lastpass; m++){        for(mi=1; mi<= wav[i]-1; mi++){
             k2=anint[m][i]+(mint[m][i]/12.);          for (ii=1;ii<=nlstate+ndeath;ii++)
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            for (j=1;j<=nlstate+ndeath;j++){
               if(agev[m][i]==0) agev[m][i]=agemax+1;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               if(agev[m][i]==1) agev[m][i]=agemax+2;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];            }
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */          for(d=0; d<=dh[mi][i]; d++){
             }            newm=savm;
           }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         }            for (kk=1; kk<=cptcovage;kk++) {
       }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for(i=(int)agemin; i <= (int)agemax+3; i++){            }
           for(jk=1; jk <=nlstate ; jk++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
               pp[jk] += freq[jk][m][i];            savm=oldm;
           }            oldm=newm;
           for(jk=1; jk <=nlstate ; jk++){          } /* end mult */
             for(m=-1, pos=0; m <=0 ; m++)        
             pos += freq[jk][m][i];          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
                  bbh=(double)bh[mi][i]/(double)stepm; 
          for(jk=1; jk <=nlstate ; jk++){          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          ipmx +=1;
              pp[jk] += freq[jk][m][i];          sw += weight[i];
          }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                  } /* end of wave */
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      } /* end of individual */
     }  else if(mle==3){  /* exponential inter-extrapolation */
          for(jk=1; jk <=nlstate ; jk++){                for (i=1,ipmx=0, sw=0.; i<=imx; i++){
            if( i <= (int) agemax){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
              if(pos>=1.e-5){        for(mi=1; mi<= wav[i]-1; mi++){
                probs[i][jk][j1]= pp[jk]/pos;          for (ii=1;ii<=nlstate+ndeath;ii++)
              }            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(d=0; d<dh[mi][i]; d++){
     }            newm=savm;
   }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            }
   free_vector(pp,1,nlstate);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }  /* End of Freq */            savm=oldm;
             oldm=newm;
 /************* Waves Concatenation ***************/          } /* end mult */
         
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          s1=s[mw[mi][i]][i];
 {          s2=s[mw[mi+1][i]][i];
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          bbh=(double)bh[mi][i]/(double)stepm; 
      Death is a valid wave (if date is known).          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 */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          ipmx +=1;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          sw += weight[i];
      and mw[mi+1][i]. dh depends on stepm.          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      */        } /* end of wave */
       } /* end of individual */
   int i, mi, m;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      double sum=0., jmean=0.;*/        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   int j, k=0,jk, ju, jl;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double sum=0.;            for (j=1;j<=nlstate+ndeath;j++){
   jmin=1e+5;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   jmax=-1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   jmean=0.;            }
   for(i=1; i<=imx; i++){          for(d=0; d<dh[mi][i]; d++){
     mi=0;            newm=savm;
     m=firstpass;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     while(s[m][i] <= nlstate){            for (kk=1; kk<=cptcovage;kk++) {
       if(s[m][i]>=1)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         mw[++mi][i]=m;            }
       if(m >=lastpass)          
         break;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       else                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         m++;            savm=oldm;
     }/* end while */            oldm=newm;
     if (s[m][i] > nlstate){          } /* end mult */
       mi++;     /* Death is another wave */        
       /* if(mi==0)  never been interviewed correctly before death */          s1=s[mw[mi][i]][i];
          /* Only death is a correct wave */          s2=s[mw[mi+1][i]][i];
       mw[mi][i]=m;          if( s2 > nlstate){ 
     }            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
     wav[i]=mi;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     if(mi==0)          }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          ipmx +=1;
   }          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for(i=1; i<=imx; i++){  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     for(mi=1; mi<wav[i];mi++){        } /* end of wave */
       if (stepm <=0)      } /* end of individual */
         dh[mi][i]=1;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       else{      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         if (s[mw[mi+1][i]][i] > nlstate) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           if (agedc[i] < 2*AGESUP) {        for(mi=1; mi<= wav[i]-1; mi++){
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          for (ii=1;ii<=nlstate+ndeath;ii++)
           if(j==0) j=1;  /* Survives at least one month after exam */            for (j=1;j<=nlstate+ndeath;j++){
           k=k+1;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           if (j >= jmax) jmax=j;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           if (j <= jmin) jmin=j;            }
           sum=sum+j;          for(d=0; d<dh[mi][i]; d++){
           /*if (j<0) printf("j=%d num=%d \n",j,i); */            newm=savm;
           }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         }            for (kk=1; kk<=cptcovage;kk++) {
         else{              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            }
           k=k+1;          
           if (j >= jmax) jmax=j;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           else if (j <= jmin)jmin=j;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            savm=oldm;
           sum=sum+j;            oldm=newm;
         }          } /* end mult */
         jk= j/stepm;        
         jl= j -jk*stepm;          s1=s[mw[mi][i]][i];
         ju= j -(jk+1)*stepm;          s2=s[mw[mi+1][i]][i];
         if(jl <= -ju)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           dh[mi][i]=jk;          ipmx +=1;
         else          sw += weight[i];
           dh[mi][i]=jk+1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         if(dh[mi][i]==0)          /*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]);*/
           dh[mi][i]=1; /* At least one step */        } /* end of wave */
       }      } /* end of individual */
     }    } /* End of if */
   }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   jmean=sum/k;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
  }    return -l;
 /*********** Tricode ****************************/  }
 void tricode(int *Tvar, int **nbcode, int imx)  
 {  /*************** log-likelihood *************/
   int Ndum[20],ij=1, k, j, i;  double funcone( double *x)
   int cptcode=0;  {
   cptcoveff=0;    /* Same as likeli but slower because of a lot of printf and if */
      int i, ii, j, k, mi, d, kk;
   for (k=0; k<19; k++) Ndum[k]=0;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   for (k=1; k<=7; k++) ncodemax[k]=0;    double **out;
     double lli; /* Individual log likelihood */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    double llt;
     for (i=1; i<=imx; i++) {    int s1, s2;
       ij=(int)(covar[Tvar[j]][i]);    double bbh, survp;
       Ndum[ij]++;    /*extern weight */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    /* We are differentiating ll according to initial status */
       if (ij > cptcode) cptcode=ij;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     }    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
     for (i=0; i<=cptcode; i++) {    */
       if(Ndum[i]!=0) ncodemax[j]++;    cov[1]=1.;
     }  
     ij=1;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (i=1; i<=ncodemax[j]; i++) {      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for (k=0; k<=19; k++) {      for(mi=1; mi<= wav[i]-1; mi++){
         if (Ndum[k] != 0) {        for (ii=1;ii<=nlstate+ndeath;ii++)
           nbcode[Tvar[j]][ij]=k;          for (j=1;j<=nlstate+ndeath;j++){
           ij++;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
         if (ij > ncodemax[j]) break;          }
       }          for(d=0; d<dh[mi][i]; d++){
     }          newm=savm;
   }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {
  for (k=0; k<19; k++) Ndum[k]=0;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           }
  for (i=1; i<=ncovmodel-2; i++) {          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       ij=Tvar[i];                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       Ndum[ij]++;          savm=oldm;
     }          oldm=newm;
         } /* end mult */
  ij=1;        
  for (i=1; i<=10; i++) {        s1=s[mw[mi][i]][i];
    if((Ndum[i]!=0) && (i<=ncov)){        s2=s[mw[mi+1][i]][i];
      Tvaraff[ij]=i;        bbh=(double)bh[mi][i]/(double)stepm; 
      ij++;        /* bias is positive if real duration
    }         * is higher than the multiple of stepm and negative otherwise.
  }         */
          if( s2 > nlstate && (mle <5) ){  /* Jackson */
     cptcoveff=ij-1;          lli=log(out[s1][s2] - savm[s1][s2]);
 }        } else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 /*********** Health Expectancies ****************/        } else if(mle==2){
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        } else if(mle==3){  /* exponential inter-extrapolation */
 {          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   /* Health expectancies */        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   int i, j, nhstepm, hstepm, h, nstepm, k;          lli=log(out[s1][s2]); /* Original formula */
   double age, agelim,hf;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   double ***p3mat;          lli=log(out[s1][s2]); /* Original formula */
          } /* End of if */
   fprintf(ficreseij,"# Health expectancies\n");        ipmx +=1;
   fprintf(ficreseij,"# Age");        sw += weight[i];
   for(i=1; i<=nlstate;i++)        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]); */
       fprintf(ficreseij," %1d-%1d",i,j);        if(globpr){
   fprintf(ficreseij,"\n");          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
    %10.6f %10.6f %10.6f ", \
   k=1;             /* For example stepm=6 months */                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.            llt +=ll[k]*gipmx/gsw;
      nhstepm is the number of hstepm from age to agelim            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
      nstepm is the number of stepm from age to agelin.          }
      Look at hpijx to understand the reason of that which relies in memory size          fprintf(ficresilk," %10.6f\n", -llt);
      and note for a fixed period like k years */        }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      } /* end of wave */
      survival function given by stepm (the optimization length). Unfortunately it    } /* end of individual */
      means that if the survival funtion is printed only each two years of age and if    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
      results. So we changed our mind and took the option of the best precision.    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 */
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */      gipmx=ipmx;
       gsw=sw;
   agelim=AGESUP;    }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    return -l;
     /* nhstepm age range expressed in number of stepm */  }
     nstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */  
     if (stepm >= YEARM) hstepm=1;  /*************** function likelione ***********/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  {
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    /* This routine should help understanding what is done with 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */       the selection of individuals/waves and
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);         to check the exact contribution to the likelihood.
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */       Plotting could be done.
     for(i=1; i<=nlstate;i++)     */
       for(j=1; j<=nlstate;j++)    int k;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){  
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    if(*globpri !=0){ /* Just counts and sums, no printings */
           /* 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]);*/      strcpy(fileresilk,"ilk"); 
         }      strcat(fileresilk,fileres);
     fprintf(ficreseij,"%3.0f",age );      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     for(i=1; i<=nlstate;i++)        printf("Problem with resultfile: %s\n", fileresilk);
       for(j=1; j<=nlstate;j++){        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);      }
       }      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");
     fprintf(ficreseij,"\n");      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /*  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");
 /************ Variance ******************/    }
 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)  
 {    *fretone=(*funcone)(p);
   /* Variance of health expectancies */    if(*globpri !=0){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      fclose(ficresilk);
   double **newm;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   double **dnewm,**doldm;      fflush(fichtm); 
   int i, j, nhstepm, hstepm, h;    } 
   int k, cptcode;    return;
   double *xp;  }
   double **gp, **gm;  
   double ***gradg, ***trgradg;  
   double ***p3mat;  /*********** Maximum Likelihood Estimation ***************/
   double age,agelim;  
   int theta;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
    fprintf(ficresvij,"# Covariances of life expectancies\n");    int i,j, iter;
   fprintf(ficresvij,"# Age");    double **xi;
   for(i=1; i<=nlstate;i++)    double fret;
     for(j=1; j<=nlstate;j++)    double fretone; /* Only one call to likelihood */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    /*  char filerespow[FILENAMELENGTH];*/
   fprintf(ficresvij,"\n");    xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
   xp=vector(1,npar);      for (j=1;j<=npar;j++)
   dnewm=matrix(1,nlstate,1,npar);        xi[i][j]=(i==j ? 1.0 : 0.0);
   doldm=matrix(1,nlstate,1,nlstate);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
      strcpy(filerespow,"pow"); 
   hstepm=1*YEARM; /* Every year of age */    strcat(filerespow,fileres);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   agelim = AGESUP;      printf("Problem with resultfile: %s\n", filerespow);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    }
     if (stepm >= YEARM) hstepm=1;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    for (i=1;i<=nlstate;i++)
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(j=1;j<=nlstate+ndeath;j++)
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     gp=matrix(0,nhstepm,1,nlstate);    fprintf(ficrespow,"\n");
     gm=matrix(0,nhstepm,1,nlstate);  
     powell(p,xi,npar,ftol,&iter,&fret,func);
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */    fclose(ficrespow);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       }    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
   }
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)  /**** Computes Hessian and covariance matrix ***/
           prlim[i][i]=probs[(int)age][i][ij];  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       }  {
      double  **a,**y,*x,pd;
       for(j=1; j<= nlstate; j++){    double **hess;
         for(h=0; h<=nhstepm; h++){    int i, j,jk;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    int *indx;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
       }    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[]) ;
       for(i=1; i<=npar; i++) /* Computes gradient */    void ludcmp(double **a, int npar, int *indx, double *d) ;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double gompertz(double p[]);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      hess=matrix(1,npar,1,npar);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
      printf("\nCalculation of the hessian matrix. Wait...\n");
       if (popbased==1) {    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         for(i=1; i<=nlstate;i++)    for (i=1;i<=npar;i++){
           prlim[i][i]=probs[(int)age][i][ij];      printf("%d",i);fflush(stdout);
       }      fprintf(ficlog,"%d",i);fflush(ficlog);
      
       for(j=1; j<= nlstate; j++){       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
         for(h=0; h<=nhstepm; h++){      
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      /*  printf(" %f ",p[i]);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
         }    }
       }    
     for (i=1;i<=npar;i++) {
       for(j=1; j<= nlstate; j++)      for (j=1;j<=npar;j++)  {
         for(h=0; h<=nhstepm; h++){        if (j>i) { 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          printf(".%d%d",i,j);fflush(stdout);
         }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     } /* End theta */          hess[i][j]=hessij(p,delti,i,j,func,npar);
           
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
     for(h=0; h<=nhstepm; h++)        }
       for(j=1; j<=nlstate;j++)      }
         for(theta=1; theta <=npar; theta++)    }
           trgradg[h][j][theta]=gradg[h][theta][j];    printf("\n");
     fprintf(ficlog,"\n");
     for(i=1;i<=nlstate;i++)  
       for(j=1;j<=nlstate;j++)    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
         vareij[i][j][(int)age] =0.;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     for(h=0;h<=nhstepm;h++){    
       for(k=0;k<=nhstepm;k++){    a=matrix(1,npar,1,npar);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    y=matrix(1,npar,1,npar);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    x=vector(1,npar);
         for(i=1;i<=nlstate;i++)    indx=ivector(1,npar);
           for(j=1;j<=nlstate;j++)    for (i=1;i<=npar;i++)
             vareij[i][j][(int)age] += doldm[i][j];      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       }    ludcmp(a,npar,indx,&pd);
     }  
     h=1;    for (j=1;j<=npar;j++) {
     if (stepm >= YEARM) h=stepm/YEARM;      for (i=1;i<=npar;i++) x[i]=0;
     fprintf(ficresvij,"%.0f ",age );      x[j]=1;
     for(i=1; i<=nlstate;i++)      lubksb(a,npar,indx,x);
       for(j=1; j<=nlstate;j++){      for (i=1;i<=npar;i++){ 
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);        matcov[i][j]=x[i];
       }      }
     fprintf(ficresvij,"\n");    }
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);    printf("\n#Hessian matrix#\n");
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    fprintf(ficlog,"\n#Hessian matrix#\n");
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    for (i=1;i<=npar;i++) { 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (j=1;j<=npar;j++) { 
   } /* End age */        printf("%.3e ",hess[i][j]);
          fprintf(ficlog,"%.3e ",hess[i][j]);
   free_vector(xp,1,npar);      }
   free_matrix(doldm,1,nlstate,1,npar);      printf("\n");
   free_matrix(dnewm,1,nlstate,1,nlstate);      fprintf(ficlog,"\n");
     }
 }  
     /* Recompute Inverse */
 /************ Variance of prevlim ******************/    for (i=1;i<=npar;i++)
 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 (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
 {    ludcmp(a,npar,indx,&pd);
   /* Variance of prevalence limit */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    /*  printf("\n#Hessian matrix recomputed#\n");
   double **newm;  
   double **dnewm,**doldm;    for (j=1;j<=npar;j++) {
   int i, j, nhstepm, hstepm;      for (i=1;i<=npar;i++) x[i]=0;
   int k, cptcode;      x[j]=1;
   double *xp;      lubksb(a,npar,indx,x);
   double *gp, *gm;      for (i=1;i<=npar;i++){ 
   double **gradg, **trgradg;        y[i][j]=x[i];
   double age,agelim;        printf("%.3e ",y[i][j]);
   int theta;        fprintf(ficlog,"%.3e ",y[i][j]);
          }
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      printf("\n");
   fprintf(ficresvpl,"# Age");      fprintf(ficlog,"\n");
   for(i=1; i<=nlstate;i++)    }
       fprintf(ficresvpl," %1d-%1d",i,i);    */
   fprintf(ficresvpl,"\n");  
     free_matrix(a,1,npar,1,npar);
   xp=vector(1,npar);    free_matrix(y,1,npar,1,npar);
   dnewm=matrix(1,nlstate,1,npar);    free_vector(x,1,npar);
   doldm=matrix(1,nlstate,1,nlstate);    free_ivector(indx,1,npar);
      free_matrix(hess,1,npar,1,npar);
   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 */  /*************** hessian matrix ****************/
     if (stepm >= YEARM) hstepm=1;  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  {
     gradg=matrix(1,npar,1,nlstate);    int i;
     gp=vector(1,nlstate);    int l=1, lmax=20;
     gm=vector(1,nlstate);    double k1,k2;
     double p2[NPARMAX+1];
     for(theta=1; theta <=npar; theta++){    double res;
       for(i=1; i<=npar; i++){ /* Computes gradient */    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double fx;
       }    int k=0,kmax=10;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double l1;
       for(i=1;i<=nlstate;i++)  
         gp[i] = prlim[i][i];    fx=func(x);
        for (i=1;i<=npar;i++) p2[i]=x[i];
       for(i=1; i<=npar; i++) /* Computes gradient */    for(l=0 ; l <=lmax; l++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      l1=pow(10,l);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      delts=delt;
       for(i=1;i<=nlstate;i++)      for(k=1 ; k <kmax; k=k+1){
         gm[i] = prlim[i][i];        delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
       for(i=1;i<=nlstate;i++)        k1=func(p2)-fx;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        p2[theta]=x[theta]-delt;
     } /* End theta */        k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
     trgradg =matrix(1,nlstate,1,npar);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
     for(j=1; j<=nlstate;j++)  #ifdef DEBUG
       for(theta=1; theta <=npar; theta++)        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);
         trgradg[j][theta]=gradg[theta][j];        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);
   #endif
     for(i=1;i<=nlstate;i++)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       varpl[i][(int)age] =0.;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          k=kmax;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        }
     for(i=1;i<=nlstate;i++)        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          k=kmax; l=lmax*10.;
         }
     fprintf(ficresvpl,"%.0f ",age );        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     for(i=1; i<=nlstate;i++)          delts=delt;
       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);    delti[theta]=delts;
     free_matrix(gradg,1,npar,1,nlstate);    return res; 
     free_matrix(trgradg,1,nlstate,1,npar);    
   } /* End age */  }
   
   free_vector(xp,1,npar);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   free_matrix(doldm,1,nlstate,1,npar);  {
   free_matrix(dnewm,1,nlstate,1,nlstate);    int i;
     int l=1, l1, lmax=20;
 }    double k1,k2,k3,k4,res,fx;
     double p2[NPARMAX+1];
 /************ Variance of one-step probabilities  ******************/    int k;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)  
 {    fx=func(x);
   int i, j;    for (k=1; k<=2; k++) {
   int k=0, cptcode;      for (i=1;i<=npar;i++) p2[i]=x[i];
   double **dnewm,**doldm;      p2[thetai]=x[thetai]+delti[thetai]/k;
   double *xp;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double *gp, *gm;      k1=func(p2)-fx;
   double **gradg, **trgradg;    
   double age,agelim, cov[NCOVMAX];      p2[thetai]=x[thetai]+delti[thetai]/k;
   int theta;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   char fileresprob[FILENAMELENGTH];      k2=func(p2)-fx;
     
   strcpy(fileresprob,"prob");      p2[thetai]=x[thetai]-delti[thetai]/k;
   strcat(fileresprob,fileres);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      k3=func(p2)-fx;
     printf("Problem with resultfile: %s\n", fileresprob);    
   }      p2[thetai]=x[thetai]-delti[thetai]/k;
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        k4=func(p2)-fx;
       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   xp=vector(1,npar);  #ifdef DEBUG
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      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);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      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);
    #endif
   cov[1]=1;    }
   for (age=bage; age<=fage; age ++){    return res;
     cov[2]=age;  }
     gradg=matrix(1,npar,1,9);  
     trgradg=matrix(1,9,1,npar);  /************** Inverse of matrix **************/
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  void ludcmp(double **a, int n, int *indx, double *d) 
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  { 
        int i,imax,j,k; 
     for(theta=1; theta <=npar; theta++){    double big,dum,sum,temp; 
       for(i=1; i<=npar; i++)    double *vv; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);   
          vv=vector(1,n); 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    *d=1.0; 
        for (i=1;i<=n;i++) { 
       k=0;      big=0.0; 
       for(i=1; i<= (nlstate+ndeath); i++){      for (j=1;j<=n;j++) 
         for(j=1; j<=(nlstate+ndeath);j++){        if ((temp=fabs(a[i][j])) > big) big=temp; 
            k=k+1;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           gp[k]=pmmij[i][j];      vv[i]=1.0/big; 
         }    } 
       }    for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
       for(i=1; i<=npar; i++)        sum=a[i][j]; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
            a[i][j]=sum; 
       } 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      big=0.0; 
       k=0;      for (i=j;i<=n;i++) { 
       for(i=1; i<=(nlstate+ndeath); i++){        sum=a[i][j]; 
         for(j=1; j<=(nlstate+ndeath);j++){        for (k=1;k<j;k++) 
           k=k+1;          sum -= a[i][k]*a[k][j]; 
           gm[k]=pmmij[i][j];        a[i][j]=sum; 
         }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       }          big=dum; 
                imax=i; 
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        } 
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        } 
     }      if (j != imax) { 
         for (k=1;k<=n;k++) { 
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          dum=a[imax][k]; 
       for(theta=1; theta <=npar; theta++)          a[imax][k]=a[j][k]; 
       trgradg[j][theta]=gradg[theta][j];          a[j][k]=dum; 
          } 
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        *d = -(*d); 
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);        vv[imax]=vv[j]; 
       } 
      pmij(pmmij,cov,ncovmodel,x,nlstate);      indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
      k=0;      if (j != n) { 
      for(i=1; i<=(nlstate+ndeath); i++){        dum=1.0/(a[j][j]); 
        for(j=1; j<=(nlstate+ndeath);j++){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
          k=k+1;      } 
          gm[k]=pmmij[i][j];    } 
         }    free_vector(vv,1,n);  /* Doesn't work */
      }  ;
        } 
      /*printf("\n%d ",(int)age);  
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  void lubksb(double **a, int n, int *indx, double b[]) 
          { 
     int i,ii=0,ip,j; 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    double sum; 
      }*/   
     for (i=1;i<=n;i++) { 
   fprintf(ficresprob,"\n%d ",(int)age);      ip=indx[i]; 
       sum=b[ip]; 
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      b[ip]=b[i]; 
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      if (ii) 
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   }      else if (sum) ii=i; 
       b[i]=sum; 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    } 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    for (i=n;i>=1;i--) { 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      sum=b[i]; 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
 }      b[i]=sum/a[i][i]; 
  free_vector(xp,1,npar);    } 
 fclose(ficresprob);  } 
   
 }  /************ 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[])
 /******************* Printing html file ***********/  {  /* Some frequencies */
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){    
   int jj1, k1, i1, cpt;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   FILE *fichtm;    int first;
   /*char optionfilehtm[FILENAMELENGTH];*/    double ***freq; /* Frequencies */
     double *pp, **prop;
   strcpy(optionfilehtm,optionfile);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   strcat(optionfilehtm,".htm");    FILE *ficresp;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    char fileresp[FILENAMELENGTH];
     printf("Problem with %s \n",optionfilehtm), exit(0);    
   }    pp=vector(1,nlstate);
     prop=matrix(1,nlstate,iagemin,iagemax+3);
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71c </font> <hr size=\"2\" color=\"#EC5E5E\">    strcpy(fileresp,"p");
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
 Total number of observations=%d <br>      printf("Problem with prevalence resultfile: %s\n", fileresp);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 <hr  size=\"2\" color=\"#EC5E5E\">      exit(0);
 <li>Outputs files<br><br>\n    }
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    j1=0;
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    j=cptcoveff;
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>  
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    first=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>    for(k1=1; k1<=j;k1++){
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>      for(i1=1; i1<=ncodemax[k1];i1++){
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>        j1++;
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
            scanf("%d", i);*/
 fprintf(fichtm," <li>Graphs</li><p>");        for (i=-5; i<=nlstate+ndeath; i++)  
           for (jk=-5; jk<=nlstate+ndeath; jk++)  
  m=cptcoveff;            for(m=iagemin; m <= iagemax+3; m++)
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}              freq[i][jk][m]=0;
   
  jj1=0;      for (i=1; i<=nlstate; i++)  
  for(k1=1; k1<=m;k1++){        for(m=iagemin; m <= iagemax+3; m++)
    for(i1=1; i1<=ncodemax[k1];i1++){          prop[i][m]=0;
        jj1++;        
        if (cptcovn > 0) {        dateintsum=0;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        k2cpt=0;
          for (cpt=1; cpt<=cptcoveff;cpt++)        for (i=1; i<=imx; i++) {
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);          bool=1;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          if  (cptcovn>0) {
        }            for (z1=1; z1<=cptcoveff; z1++) 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                    bool=0;
        for(cpt=1; cpt<nlstate;cpt++){          }
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>          if (bool==1){
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            for(m=firstpass; m<=lastpass; m++){
        }              k2=anint[m][i]+(mint[m][i]/12.);
     for(cpt=1; cpt<=nlstate;cpt++) {              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 interval) in state (%d): v%s%d%d.gif <br>                if(agev[m][i]==1) agev[m][i]=iagemax+2;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                  if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
      }                if (m<lastpass) {
      for(cpt=1; cpt<=nlstate;cpt++) {                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                }
      }                
      fprintf(fichtm,"\n<br>- Total life expectancy by age and                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
 health expectancies in states (1) and (2): e%s%d.gif<br>                  dateintsum=dateintsum+k2;
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                  k2cpt++;
 fprintf(fichtm,"\n</body>");                }
    }                /*}*/
    }            }
 fclose(fichtm);          }
 }        }
          
 /******************* Gnuplot file **************/        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){  fprintf(ficresp, "#Local time at start: %s", strstart);
         if  (cptcovn>0) {
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   strcpy(optionfilegnuplot,optionfilefiname);          fprintf(ficresp, "**********\n#");
   strcat(optionfilegnuplot,".plt");        }
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        for(i=1; i<=nlstate;i++) 
     printf("Problem with file %s",optionfilegnuplot);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   }        fprintf(ficresp, "\n");
         
 #ifdef windows        for(i=iagemin; i <= iagemax+3; i++){
     fprintf(ficgp,"cd \"%s\" \n",pathc);          if(i==iagemax+3){
 #endif            fprintf(ficlog,"Total");
 m=pow(2,cptcoveff);          }else{
              if(first==1){
  /* 1eme*/              first=0;
   for (cpt=1; cpt<= nlstate ; cpt ++) {              printf("See log file for details...\n");
    for (k1=1; k1<= m ; k1 ++) {            }
             fprintf(ficlog,"Age %d", i);
 #ifdef windows          }
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);          for(jk=1; jk <=nlstate ; jk++){
 #endif            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 #ifdef unix              pp[jk] += freq[jk][m][i]; 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);          }
 #endif          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
 for (i=1; i<= nlstate ; i ++) {              pos += freq[jk][m][i];
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            if(pp[jk]>=1.e-10){
   else fprintf(ficgp," \%%*lf (\%%*lf)");              if(first==1){
 }              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);              }
     for (i=1; i<= nlstate ; i ++) {              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            }else{
   else fprintf(ficgp," \%%*lf (\%%*lf)");              if(first==1)
 }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
      for (i=1; i<= nlstate ; i ++) {            }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }            for(jk=1; jk <=nlstate ; jk++){
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 #ifdef unix              pp[jk] += freq[jk][m][i];
 fprintf(ficgp,"\nset ter gif small size 400,300");          }       
 #endif          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            pos += pp[jk];
    }            posprop += prop[jk][i];
   }          }
   /*2 eme*/          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
   for (k1=1; k1<= m ; k1 ++) {              if(first==1)
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                  fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for (i=1; i<= nlstate+1 ; i ++) {            }else{
       k=2*i;              if(first==1)
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       for (j=1; j<= nlstate+1 ; j ++) {              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            }
   else fprintf(ficgp," \%%*lf (\%%*lf)");            if( i <= iagemax){
 }                if(pos>=1.e-5){
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);                /*probs[i][jk][j1]= pp[jk]/pos;*/
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       for (j=1; j<= nlstate+1 ; j ++) {              }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              else
         else fprintf(ficgp," \%%*lf (\%%*lf)");                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
 }              }
       fprintf(ficgp,"\" t\"\" w l 0,");          }
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          
       for (j=1; j<= nlstate+1 ; j ++) {          for(jk=-1; jk <=nlstate+ndeath; jk++)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            for(m=-1; m <=nlstate+ndeath; m++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");              if(freq[jk][m][i] !=0 ) {
 }                if(first==1)
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
       else fprintf(ficgp,"\" t\"\" w l 0,");                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     }              }
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          if(i <= iagemax)
   }            fprintf(ficresp,"\n");
            if(first==1)
   /*3eme*/            printf("Others in log...\n");
           fprintf(ficlog,"\n");
   for (k1=1; k1<= m ; k1 ++) {        }
     for (cpt=1; cpt<= nlstate ; cpt ++) {      }
       k=2+nlstate*(cpt-1);    }
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);    dateintmean=dateintsum/k2cpt; 
       for (i=1; i< nlstate ; i ++) {   
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);    fclose(ficresp);
       }    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    free_vector(pp,1,nlstate);
     }    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     }    /* End of Freq */
    }
   /* CV preval stat */  
     for (k1=1; k1<= m ; k1 ++) {  /************ Prevalence ********************/
     for (cpt=1; cpt<nlstate ; cpt ++) {  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)
       k=3;  {  
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
       for (i=1; i< nlstate ; i ++)       We still use firstpass and lastpass as another selection.
         fprintf(ficgp,"+$%d",k+i+1);    */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);   
          int i, m, jk, k1, i1, j1, bool, z1,z2,j;
       l=3+(nlstate+ndeath)*cpt;    double ***freq; /* Frequencies */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    double *pp, **prop;
       for (i=1; i< nlstate ; i ++) {    double pos,posprop; 
         l=3+(nlstate+ndeath)*cpt;    double  y2; /* in fractional years */
         fprintf(ficgp,"+$%d",l+i+1);    int iagemin, iagemax;
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      iagemin= (int) agemin;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    iagemax= (int) agemax;
     }    /*pp=vector(1,nlstate);*/
   }      prop=matrix(1,nlstate,iagemin,iagemax+3); 
      /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   /* proba elementaires */    j1=0;
    for(i=1,jk=1; i <=nlstate; i++){    
     for(k=1; k <=(nlstate+ndeath); k++){    j=cptcoveff;
       if (k != i) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         for(j=1; j <=ncovmodel; j++){    
            for(k1=1; k1<=j;k1++){
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      for(i1=1; i1<=ncodemax[k1];i1++){
           jk++;        j1++;
           fprintf(ficgp,"\n");        
         }        for (i=1; i<=nlstate; i++)  
       }          for(m=iagemin; m <= iagemax+3; m++)
     }            prop[i][m]=0.0;
     }       
         for (i=1; i<=imx; i++) { /* Each individual */
     for(jk=1; jk <=m; jk++) {          bool=1;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);          if  (cptcovn>0) {
    i=1;            for (z1=1; z1<=cptcoveff; z1++) 
    for(k2=1; k2<=nlstate; k2++) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
      k3=i;                bool=0;
      for(k=1; k<=(nlstate+ndeath); k++) {          } 
        if (k != k2){          if (bool==1) { 
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
 ij=1;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
         for(j=3; j <=ncovmodel; j++) {              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
             ij++;                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
           }                if (s[m][i]>0 && s[m][i]<=nlstate) { 
           else                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
         }                  prop[s[m][i]][iagemax+3] += weight[i]; 
           fprintf(ficgp,")/(1");                } 
                      }
         for(k1=1; k1 <=nlstate; k1++){              } /* end selection of waves */
           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++){        for(i=iagemin; i <= iagemax+3; i++){  
           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]]]);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             ij++;            posprop += prop[jk][i]; 
           }          } 
           else  
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          for(jk=1; jk <=nlstate ; jk++){     
           }            if( i <=  iagemax){ 
           fprintf(ficgp,")");              if(posprop>=1.e-5){ 
         }                probs[i][jk][j1]= prop[jk][i]/posprop;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);              } 
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");            } 
         i=i+ncovmodel;          }/* end jk */ 
        }        }/* end i */ 
      }      } /* end i1 */
    }    } /* end k1 */
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    
    }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
        /*free_vector(pp,1,nlstate);*/
   fclose(ficgp);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
 }  /* end gnuplot */  }  /* End of prevalence */
   
   /************* Waves Concatenation ***************/
 /*************** Moving average **************/  
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){  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)
   {
   int i, cpt, cptcod;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     for (agedeb=agemin; agedeb<=fage; agedeb++)       Death is a valid wave (if date is known).
       for (i=1; i<=nlstate;i++)       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
           mobaverage[(int)agedeb][i][cptcod]=0.;       and mw[mi+1][i]. dh depends on stepm.
           */
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){  
       for (i=1; i<=nlstate;i++){    int i, mi, m;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           for (cpt=0;cpt<=4;cpt++){       double sum=0., jmean=0.;*/
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    int first;
           }    int j, k=0,jk, ju, jl;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    double sum=0.;
         }    first=0;
       }    jmin=1e+5;
     }    jmax=-1;
        jmean=0.;
 }    for(i=1; i<=imx; i++){
       mi=0;
       m=firstpass;
 /************** Forecasting ******************/      while(s[m][i] <= nlstate){
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
            mw[++mi][i]=m;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        if(m >=lastpass)
   int *popage;          break;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        else
   double *popeffectif,*popcount;          m++;
   double ***p3mat;      }/* end while */
   char fileresf[FILENAMELENGTH];      if (s[m][i] > nlstate){
         mi++;     /* Death is another wave */
  agelim=AGESUP;        /* if(mi==0)  never been interviewed correctly before death */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;           /* Only death is a correct wave */
         mw[mi][i]=m;
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      }
    
        wav[i]=mi;
   strcpy(fileresf,"f");      if(mi==0){
   strcat(fileresf,fileres);        nbwarn++;
   if((ficresf=fopen(fileresf,"w"))==NULL) {        if(first==0){
     printf("Problem with forecast resultfile: %s\n", fileresf);          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   }          first=1;
   printf("Computing forecasting: result on file '%s' \n", fileresf);        }
         if(first==1){
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
         }
   if (mobilav==1) {      } /* end mi==0 */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    } /* End individuals */
     movingaverage(agedeb, fage, agemin, mobaverage);  
   }    for(i=1; i<=imx; i++){
       for(mi=1; mi<wav[i];mi++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;        if (stepm <=0)
   if (stepm<=12) stepsize=1;          dh[mi][i]=1;
          else{
   agelim=AGESUP;          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
              if (agedc[i] < 2*AGESUP) {
   hstepm=1;              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   hstepm=hstepm/stepm;              if(j==0) j=1;  /* Survives at least one month after exam */
   yp1=modf(dateintmean,&yp);              else if(j<0){
   anprojmean=yp;                nberr++;
   yp2=modf((yp1*12),&yp);                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]);
   mprojmean=yp;                j=1; /* Temporary Dangerous patch */
   yp1=modf((yp2*30.5),&yp);                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);
   jprojmean=yp;                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]);
   if(jprojmean==0) jprojmean=1;                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);
   if(mprojmean==0) jprojmean=1;              }
                k=k+1;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);              if (j >= jmax) jmax=j;
                if (j <= jmin) jmin=j;
   for(cptcov=1;cptcov<=i2;cptcov++){              sum=sum+j;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       k=k+1;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       fprintf(ficresf,"\n#******");            }
       for(j=1;j<=cptcoveff;j++) {          }
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          else{
       }            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       fprintf(ficresf,"******\n");  /*        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]); */
       fprintf(ficresf,"# StartingAge FinalAge");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);            k=k+1;
                  if (j >= jmax) jmax=j;
                  else if (j <= jmin)jmin=j;
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
         fprintf(ficresf,"\n");            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);              if(j<0){
               nberr++;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){              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]);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              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]);
           nhstepm = nhstepm/hstepm;            }
                      sum=sum+j;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
           oldm=oldms;savm=savms;          jk= j/stepm;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            jl= j -jk*stepm;
                  ju= j -(jk+1)*stepm;
           for (h=0; h<=nhstepm; h++){          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             if (h==(int) (calagedate+YEARM*cpt)) {            if(jl==0){
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);              dh[mi][i]=jk;
             }              bh[mi][i]=0;
             for(j=1; j<=nlstate+ndeath;j++) {            }else{ /* We want a negative bias in order to only have interpolation ie
               kk1=0.;kk2=0;                    * at the price of an extra matrix product in likelihood */
               for(i=1; i<=nlstate;i++) {                            dh[mi][i]=jk+1;
                 if (mobilav==1)              bh[mi][i]=ju;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            }
                 else {          }else{
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            if(jl <= -ju){
                 }              dh[mi][i]=jk;
                              bh[mi][i]=jl;       /* bias is positive if real duration
               }                                   * is higher than the multiple of stepm and negative otherwise.
               if (h==(int)(calagedate+12*cpt)){                                   */
                 fprintf(ficresf," %.3f", kk1);            }
                                    else{
               }              dh[mi][i]=jk+1;
             }              bh[mi][i]=ju;
           }            }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            if(dh[mi][i]==0){
         }              dh[mi][i]=1; /* At least one step */
       }              bh[mi][i]=ju; /* At least one step */
     }              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
   }            }
                  } /* end if mle */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }
       } /* end wave */
   fclose(ficresf);    }
 }    jmean=sum/k;
 /************** Forecasting ******************/    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     }
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  
   int *popage;  /*********** Tricode ****************************/
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  void tricode(int *Tvar, int **nbcode, int imx)
   double *popeffectif,*popcount;  {
   double ***p3mat,***tabpop,***tabpopprev;    
   char filerespop[FILENAMELENGTH];    int Ndum[20],ij=1, k, j, i, maxncov=19;
     int cptcode=0;
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    cptcoveff=0; 
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   
   agelim=AGESUP;    for (k=0; k<maxncov; k++) Ndum[k]=0;
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    for (k=1; k<=7; k++) ncodemax[k]=0;
    
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
        for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                   modality*/ 
   strcpy(filerespop,"pop");        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   strcat(filerespop,fileres);        Ndum[ij]++; /*store the modality */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     printf("Problem with forecast resultfile: %s\n", filerespop);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   }                                         Tvar[j]. If V=sex and male is 0 and 
   printf("Computing forecasting: result on file '%s' \n", filerespop);                                         female is 1, then  cptcode=1.*/
       }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
       for (i=0; i<=cptcode; i++) {
   if (mobilav==1) {        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 */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      }
     movingaverage(agedeb, fage, agemin, mobaverage);  
   }      ij=1; 
       for (i=1; i<=ncodemax[j]; i++) {
   stepsize=(int) (stepm+YEARM-1)/YEARM;        for (k=0; k<= maxncov; k++) {
   if (stepm<=12) stepsize=1;          if (Ndum[k] != 0) {
              nbcode[Tvar[j]][ij]=k; 
   agelim=AGESUP;            /* 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; */
              
   hstepm=1;            ij++;
   hstepm=hstepm/stepm;          }
            if (ij > ncodemax[j]) break; 
   if (popforecast==1) {        }  
     if((ficpop=fopen(popfile,"r"))==NULL) {      } 
       printf("Problem with population file : %s\n",popfile);exit(0);    }  
     }  
     popage=ivector(0,AGESUP);   for (k=0; k< maxncov; k++) Ndum[k]=0;
     popeffectif=vector(0,AGESUP);  
     popcount=vector(0,AGESUP);   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.*/
     i=1;       ij=Tvar[i];
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;     Ndum[ij]++;
       }
     imx=i;  
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];   ij=1;
   }   for (i=1; i<= maxncov; i++) {
      if((Ndum[i]!=0) && (i<=ncovcol)){
   for(cptcov=1;cptcov<=i2;cptcov++){       Tvaraff[ij]=i; /*For printing */
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       ij++;
       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]]);   cptcoveff=ij-1; /*Number of simple covariates*/
       }  }
       fprintf(ficrespop,"******\n");  
       fprintf(ficrespop,"# Age");  /*********** Health Expectancies ****************/
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  
       if (popforecast==1)  fprintf(ficrespop," [Population]");  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[] )
        
       for (cpt=0; cpt<=0;cpt++) {  {
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      /* Health expectancies */
            int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){    double age, agelim, hf;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    double ***p3mat,***varhe;
           nhstepm = nhstepm/hstepm;    double **dnewm,**doldm;
              double *xp;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **gp, **gm;
           oldm=oldms;savm=savms;    double ***gradg, ***trgradg;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      int theta;
          
           for (h=0; h<=nhstepm; h++){    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
             if (h==(int) (calagedate+YEARM*cpt)) {    xp=vector(1,npar);
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    dnewm=matrix(1,nlstate*nlstate,1,npar);
             }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
             for(j=1; j<=nlstate+ndeath;j++) {    
               kk1=0.;kk2=0;    fprintf(ficreseij,"# Local time at start: %s", strstart);
               for(i=1; i<=nlstate;i++) {                  fprintf(ficreseij,"# Health expectancies\n");
                 if (mobilav==1)    fprintf(ficreseij,"# Age");
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    for(i=1; i<=nlstate;i++)
                 else {      for(j=1; j<=nlstate;j++)
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        fprintf(ficreseij," %1d-%1d (SE)",i,j);
                 }    fprintf(ficreseij,"\n");
               }  
               if (h==(int)(calagedate+12*cpt)){    if(estepm < stepm){
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      printf ("Problem %d lower than %d\n",estepm, stepm);
                   /*fprintf(ficrespop," %.3f", kk1);    }
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    else  hstepm=estepm;   
               }    /* We compute the life expectancy from trapezoids spaced every estepm months
             }     * This is mainly to measure the difference between two models: for example
             for(i=1; i<=nlstate;i++){     * if stepm=24 months pijx are given only every 2 years and by summing them
               kk1=0.;     * we are calculating an estimate of the Life Expectancy assuming a linear 
                 for(j=1; j<=nlstate;j++){     * progression in between and thus overestimating or underestimating according
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];     * to the curvature of the survival function. If, for the same date, we 
                 }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];     * to compare the new estimate of Life expectancy with the same linear 
             }     * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)  
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    /* 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. 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       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 estepm months */
   /******/    /* 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
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {       means that if the survival funtion is printed only each two years of age and if
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);         you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){       results. So we changed our mind and took the option of the best precision.
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    */
           nhstepm = nhstepm/hstepm;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    agelim=AGESUP;
           oldm=oldms;savm=savms;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        /* nhstepm age range expressed in number of stepm */
           for (h=0; h<=nhstepm; h++){      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
             if (h==(int) (calagedate+YEARM*cpt)) {      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      /* if (stepm >= YEARM) hstepm=1;*/
             }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
             for(j=1; j<=nlstate+ndeath;j++) {      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               kk1=0.;kk2=0;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
               for(i=1; i<=nlstate;i++) {                    gp=matrix(0,nhstepm,1,nlstate*nlstate);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];          gm=matrix(0,nhstepm,1,nlstate*nlstate);
               }  
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
             }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
           }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   
         }  
       }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    }  
   }      /* Computing  Variances of health expectancies */
    
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
   if (popforecast==1) {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     free_ivector(popage,0,AGESUP);        }
     free_vector(popeffectif,0,AGESUP);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     free_vector(popcount,0,AGESUP);    
   }        cptj=0;
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(j=1; j<= nlstate; j++){
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(i=1; i<=nlstate; i++){
   fclose(ficrespop);            cptj=cptj+1;
 }            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
               gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
 /***********************************************/            }
 /**************** Main Program *****************/          }
 /***********************************************/        }
        
 int main(int argc, char *argv[])       
 {        for(i=1; i<=npar; i++) 
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   double agedeb, agefin,hf;        
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;        cptj=0;
         for(j=1; j<= nlstate; j++){
   double fret;          for(i=1;i<=nlstate;i++){
   double **xi,tmp,delta;            cptj=cptj+1;
             for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   double dum; /* Dummy variable */  
   double ***p3mat;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   int *indx;            }
   char line[MAXLINE], linepar[MAXLINE];          }
   char title[MAXLINE];        }
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];        for(j=1; j<= nlstate*nlstate; j++)
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];          for(h=0; h<=nhstepm-1; h++){
              gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];          }
        } 
   char filerest[FILENAMELENGTH];     
   char fileregp[FILENAMELENGTH];  /* End theta */
   char popfile[FILENAMELENGTH];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   int firstobs=1, lastobs=10;  
   int sdeb, sfin; /* Status at beginning and end */       for(h=0; h<=nhstepm-1; h++)
   int c,  h , cpt,l;        for(j=1; j<=nlstate*nlstate;j++)
   int ju,jl, mi;          for(theta=1; theta <=npar; theta++)
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            trgradg[h][j][theta]=gradg[h][theta][j];
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;       
   int mobilav=0,popforecast=0;  
   int hstepm, nhstepm;       for(i=1;i<=nlstate*nlstate;i++)
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;        for(j=1;j<=nlstate*nlstate;j++)
           varhe[i][j][(int)age] =0.;
   double bage, fage, age, agelim, agebase;  
   double ftolpl=FTOL;       printf("%d|",(int)age);fflush(stdout);
   double **prlim;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   double *severity;       for(h=0;h<=nhstepm-1;h++){
   double ***param; /* Matrix of parameters */        for(k=0;k<=nhstepm-1;k++){
   double  *p;          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   double **matcov; /* Matrix of covariance */          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   double ***delti3; /* Scale */          for(i=1;i<=nlstate*nlstate;i++)
   double *delti; /* Scale */            for(j=1;j<=nlstate*nlstate;j++)
   double ***eij, ***vareij;              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   double **varpl; /* Variances of prevalence limits by age */        }
   double *epj, vepp;      }
   double kk1, kk2;      /* Computing expectancies */
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;      for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   char version[80]="Imach version 0.71c, March 2002, INED-EUROREVES ";            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   char *alph[]={"a","a","b","c","d","e"}, str[4];            
   /* 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]);*/
   
   char z[1]="c", occ;          }
 #include <sys/time.h>  
 #include <time.h>      fprintf(ficreseij,"%3.0f",age );
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      cptj=0;
        for(i=1; i<=nlstate;i++)
   /* long total_usecs;        for(j=1; j<=nlstate;j++){
   struct timeval start_time, end_time;          cptj++;
            fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        }
       fprintf(ficreseij,"\n");
      
   printf("\n%s",version);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   if(argc <=1){      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     printf("\nEnter the parameter file name: ");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     scanf("%s",pathtot);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   else{    }
     strcpy(pathtot,argv[1]);    printf("\n");
   }    fprintf(ficlog,"\n");
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/  
   /*cygwin_split_path(pathtot,path,optionfile);    free_vector(xp,1,npar);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   /* cutv(path,optionfile,pathtot,'\\');*/    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  }
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  
   chdir(path);  /************ Variance ******************/
   replace(pathc,path);  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[])
   {
 /*-------- arguments in the command line --------*/    /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   strcpy(fileres,"r");    /* double **newm;*/
   strcat(fileres, optionfilefiname);    double **dnewm,**doldm;
   strcat(fileres,".txt");    /* Other files have txt extension */    double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
   /*---------arguments file --------*/    int k, cptcode;
     double *xp;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    double **gp, **gm;  /* for var eij */
     printf("Problem with optionfile %s\n",optionfile);    double ***gradg, ***trgradg; /*for var eij */
     goto end;    double **gradgp, **trgradgp; /* for var p point j */
   }    double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   strcpy(filereso,"o");    double ***p3mat;
   strcat(filereso,fileres);    double age,agelim, hf;
   if((ficparo=fopen(filereso,"w"))==NULL) {    double ***mobaverage;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    int theta;
   }    char digit[4];
     char digitp[25];
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    char fileresprobmorprev[FILENAMELENGTH];
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    if(popbased==1){
     puts(line);      if(mobilav!=0)
     fputs(line,ficparo);        strcpy(digitp,"-populbased-mobilav-");
   }      else strcpy(digitp,"-populbased-nomobil-");
   ungetc(c,ficpar);    }
     else 
   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);      strcpy(digitp,"-stablbased-");
   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);  
   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);    if (mobilav!=0) {
 while((c=getc(ficpar))=='#' && c!= EOF){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     ungetc(c,ficpar);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     fgets(line, MAXLINE, ficpar);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     puts(line);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     fputs(line,ficparo);      }
   }    }
   ungetc(c,ficpar);  
      strcpy(fileresprobmorprev,"prmorprev"); 
        sprintf(digit,"%-d",ij);
   covar=matrix(0,NCOVMAX,1,n);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   cptcovn=0;    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
   ncovmodel=2+cptcovn;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      printf("Problem with resultfile: %s\n", fileresprobmorprev);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   /* Read guess parameters */    }
   /* Reads comments: lines beginning with '#' */    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   while((c=getc(ficpar))=='#' && c!= EOF){   
     ungetc(c,ficpar);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     fgets(line, MAXLINE, ficpar);    fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
     puts(line);    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);
     fputs(line,ficparo);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   }    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   ungetc(c,ficpar);      fprintf(ficresprobmorprev," p.%-d SE",j);
        for(i=1; i<=nlstate;i++)
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     for(i=1; i <=nlstate; i++)    }  
     for(j=1; j <=nlstate+ndeath-1; j++){    fprintf(ficresprobmorprev,"\n");
       fscanf(ficpar,"%1d%1d",&i1,&j1);    fprintf(ficgp,"\n# Routine varevsij");
       fprintf(ficparo,"%1d%1d",i1,j1);    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
       printf("%1d%1d",i,j);    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");
       for(k=1; k<=ncovmodel;k++){    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
         fscanf(ficpar," %lf",&param[i][j][k]);  /*   } */
         printf(" %lf",param[i][j][k]);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         fprintf(ficparo," %lf",param[i][j][k]);   fprintf(ficresvij, "#Local time at start: %s", strstart);
       }    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");
       fscanf(ficpar,"\n");    fprintf(ficresvij,"# Age");
       printf("\n");    for(i=1; i<=nlstate;i++)
       fprintf(ficparo,"\n");      for(j=1; j<=nlstate;j++)
     }        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
      fprintf(ficresvij,"\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  
     xp=vector(1,npar);
   p=param[1][1];    dnewm=matrix(1,nlstate,1,npar);
      doldm=matrix(1,nlstate,1,nlstate);
   /* Reads comments: lines beginning with '#' */    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     puts(line);    gpp=vector(nlstate+1,nlstate+ndeath);
     fputs(line,ficparo);    gmp=vector(nlstate+1,nlstate+ndeath);
   }    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   ungetc(c,ficpar);    
     if(estepm < stepm){
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      printf ("Problem %d lower than %d\n",estepm, stepm);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    }
   for(i=1; i <=nlstate; i++){    else  hstepm=estepm;   
     for(j=1; j <=nlstate+ndeath-1; j++){    /* For example we decided to compute the life expectancy with the smallest unit */
       fscanf(ficpar,"%1d%1d",&i1,&j1);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       printf("%1d%1d",i,j);       nhstepm is the number of hstepm from age to agelim 
       fprintf(ficparo,"%1d%1d",i1,j1);       nstepm is the number of stepm from age to agelin. 
       for(k=1; k<=ncovmodel;k++){       Look at hpijx to understand the reason of that which relies in memory size
         fscanf(ficpar,"%le",&delti3[i][j][k]);       and note for a fixed period like k years */
         printf(" %le",delti3[i][j][k]);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         fprintf(ficparo," %le",delti3[i][j][k]);       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
       fscanf(ficpar,"\n");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       printf("\n");       results. So we changed our mind and took the option of the best precision.
       fprintf(ficparo,"\n");    */
     }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   }    agelim = AGESUP;
   delti=delti3[1][1];    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   /* Reads comments: lines beginning with '#' */      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   while((c=getc(ficpar))=='#' && c!= EOF){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     ungetc(c,ficpar);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     fgets(line, MAXLINE, ficpar);      gp=matrix(0,nhstepm,1,nlstate);
     puts(line);      gm=matrix(0,nhstepm,1,nlstate);
     fputs(line,ficparo);  
   }  
   ungetc(c,ficpar);      for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   matcov=matrix(1,npar,1,npar);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   for(i=1; i <=npar; i++){        }
     fscanf(ficpar,"%s",&str);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     printf("%s",str);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     fprintf(ficparo,"%s",str);  
     for(j=1; j <=i; j++){        if (popbased==1) {
       fscanf(ficpar," %le",&matcov[i][j]);          if(mobilav ==0){
       printf(" %.5le",matcov[i][j]);            for(i=1; i<=nlstate;i++)
       fprintf(ficparo," %.5le",matcov[i][j]);              prlim[i][i]=probs[(int)age][i][ij];
     }          }else{ /* mobilav */ 
     fscanf(ficpar,"\n");            for(i=1; i<=nlstate;i++)
     printf("\n");              prlim[i][i]=mobaverage[(int)age][i][ij];
     fprintf(ficparo,"\n");          }
   }        }
   for(i=1; i <=npar; i++)    
     for(j=i+1;j<=npar;j++)        for(j=1; j<= nlstate; j++){
       matcov[i][j]=matcov[j][i];          for(h=0; h<=nhstepm; h++){
                for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   printf("\n");              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
     /*-------- Rewriting paramater file ----------*/        /* This for computing probability of death (h=1 means
      strcpy(rfileres,"r");    /* "Rparameterfile */           computed over hstepm matrices product = hstepm*stepm months) 
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/           as a weighted average of prlim.
      strcat(rfileres,".");    /* */        */
      strcat(rfileres,optionfilext);    /* Other files have txt extension */        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     if((ficres =fopen(rfileres,"w"))==NULL) {          for(i=1,gpp[j]=0.; i<= nlstate; i++)
       printf("Problem writing new parameter file: %s\n", fileres);goto end;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     }        }    
     fprintf(ficres,"#%s\n",version);        /* end probability of death */
      
     /*-------- data file ----------*/        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     if((fic=fopen(datafile,"r"))==NULL)    {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       printf("Problem with datafile: %s\n", datafile);goto end;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
     n= lastobs;        if (popbased==1) {
     severity = vector(1,maxwav);          if(mobilav ==0){
     outcome=imatrix(1,maxwav+1,1,n);            for(i=1; i<=nlstate;i++)
     num=ivector(1,n);              prlim[i][i]=probs[(int)age][i][ij];
     moisnais=vector(1,n);          }else{ /* mobilav */ 
     annais=vector(1,n);            for(i=1; i<=nlstate;i++)
     moisdc=vector(1,n);              prlim[i][i]=mobaverage[(int)age][i][ij];
     andc=vector(1,n);          }
     agedc=vector(1,n);        }
     cod=ivector(1,n);  
     weight=vector(1,n);        for(j=1; j<= nlstate; j++){
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          for(h=0; h<=nhstepm; h++){
     mint=matrix(1,maxwav,1,n);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     anint=matrix(1,maxwav,1,n);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     s=imatrix(1,maxwav+1,1,n);          }
     adl=imatrix(1,maxwav+1,1,n);            }
     tab=ivector(1,NCOVMAX);        /* This for computing probability of death (h=1 means
     ncodemax=ivector(1,8);           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
     i=1;        */
     while (fgets(line, MAXLINE, fic) != NULL)    {        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       if ((i >= firstobs) && (i <=lastobs)) {          for(i=1,gmp[j]=0.; i<= nlstate; i++)
                   gmp[j] += prlim[i][i]*p3mat[i][j][1];
         for (j=maxwav;j>=1;j--){        }    
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        /* end probability of death */
           strcpy(line,stra);  
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        for(j=1; j<= nlstate; j++) /* vareij */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          for(h=0; h<=nhstepm; h++){
         }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                  }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        }
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  
       } /* End theta */
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  
         for (j=ncov;j>=1;j--){      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }      for(h=0; h<=nhstepm; h++) /* veij */
         num[i]=atol(stra);        for(j=1; j<=nlstate;j++)
                  for(theta=1; theta <=npar; theta++)
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){            trgradg[h][j][theta]=gradg[h][theta][j];
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/  
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         i=i+1;        for(theta=1; theta <=npar; theta++)
       }          trgradgp[j][theta]=gradgp[theta][j];
     }    
     /* printf("ii=%d", ij);  
        scanf("%d",i);*/      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   imx=i-1; /* Number of individuals */      for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
   /* for (i=1; i<=imx; i++){          vareij[i][j][(int)age] =0.;
     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;      for(h=0;h<=nhstepm;h++){
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;        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<=imx; i++)          for(i=1;i<=nlstate;i++)
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/            for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   /* Calculation of the number of parameter from char model*/        }
   Tvar=ivector(1,15);      }
   Tprod=ivector(1,15);    
   Tvaraff=ivector(1,15);      /* pptj */
   Tvard=imatrix(1,15,1,2);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   Tage=ivector(1,15);            matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
          for(j=nlstate+1;j<=nlstate+ndeath;j++)
   if (strlen(model) >1){        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     j=0, j1=0, k1=1, k2=1;          varppt[j][i]=doldmp[j][i];
     j=nbocc(model,'+');      /* end ppptj */
     j1=nbocc(model,'*');      /*  x centered again */
     cptcovn=j+1;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     cptcovprod=j1;      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
       
          if (popbased==1) {
     strcpy(modelsav,model);        if(mobilav ==0){
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          for(i=1; i<=nlstate;i++)
       printf("Error. Non available option model=%s ",model);            prlim[i][i]=probs[(int)age][i][ij];
       goto end;        }else{ /* mobilav */ 
     }          for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
     for(i=(j+1); i>=1;i--){        }
       cutv(stra,strb,modelsav,'+');      }
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);               
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      /* This for computing probability of death (h=1 means
       /*scanf("%d",i);*/         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       if (strchr(strb,'*')) {         as a weighted average of prlim.
         cutv(strd,strc,strb,'*');      */
         if (strcmp(strc,"age")==0) {      for(j=nlstate+1;j<=nlstate+ndeath;j++){
           cptcovprod--;        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           cutv(strb,stre,strd,'V');          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           Tvar[i]=atoi(stre);      }    
           cptcovage++;      /* end probability of death */
             Tage[cptcovage]=i;  
             /*printf("stre=%s ", stre);*/      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
         }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         else if (strcmp(strd,"age")==0) {        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
           cptcovprod--;        for(i=1; i<=nlstate;i++){
           cutv(strb,stre,strc,'V');          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
           Tvar[i]=atoi(stre);        }
           cptcovage++;      } 
           Tage[cptcovage]=i;      fprintf(ficresprobmorprev,"\n");
         }  
         else {      fprintf(ficresvij,"%.0f ",age );
           cutv(strb,stre,strc,'V');      for(i=1; i<=nlstate;i++)
           Tvar[i]=ncov+k1;        for(j=1; j<=nlstate;j++){
           cutv(strb,strc,strd,'V');          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
           Tprod[k1]=i;        }
           Tvard[k1][1]=atoi(strc);      fprintf(ficresvij,"\n");
           Tvard[k1][2]=atoi(stre);      free_matrix(gp,0,nhstepm,1,nlstate);
           Tvar[cptcovn+k2]=Tvard[k1][1];      free_matrix(gm,0,nhstepm,1,nlstate);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
           for (k=1; k<=lastobs;k++)      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           k1++;    } /* End age */
           k2=k2+2;    free_vector(gpp,nlstate+1,nlstate+ndeath);
         }    free_vector(gmp,nlstate+1,nlstate+ndeath);
       }    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
       else {    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
        /*  scanf("%d",i);*/    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       cutv(strd,strc,strb,'V');    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       Tvar[i]=atoi(strc);  /*   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); */
       strcpy(modelsav,stra);    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
         scanf("%d",i);*/    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);
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    /*  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);
   printf("cptcovprod=%d ", cptcovprod);  */
   scanf("%d ",i);*/  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fclose(fic);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     /*  if(mle==1){*/    free_vector(xp,1,npar);
     if (weightopt != 1) { /* Maximisation without weights*/    free_matrix(doldm,1,nlstate,1,nlstate);
       for(i=1;i<=n;i++) weight[i]=1.0;    free_matrix(dnewm,1,nlstate,1,npar);
     }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     /*-calculation of age at interview from date of interview and age at death -*/    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     agev=matrix(1,maxwav,1,imx);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    for (i=1; i<=imx; i++)    fclose(ficresprobmorprev);
      for(m=2; (m<= maxwav); m++)    fflush(ficgp);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    fflush(fichtm); 
          anint[m][i]=9999;  }  /* end varevsij */
          s[m][i]=-1;  
        }  /************ 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[])
     for (i=1; i<=imx; i++)  {  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    /* Variance of prevalence limit */
       for(m=1; (m<= maxwav); m++){    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
         if(s[m][i] >0){    double **newm;
           if (s[m][i] == nlstate+1) {    double **dnewm,**doldm;
             if(agedc[i]>0)    int i, j, nhstepm, hstepm;
               if(moisdc[i]!=99 && andc[i]!=9999)    int k, cptcode;
               agev[m][i]=agedc[i];    double *xp;
             else {    double *gp, *gm;
               if (andc[i]!=9999){    double **gradg, **trgradg;
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    double age,agelim;
               agev[m][i]=-1;    int theta;
               }    fprintf(ficresvpl, "#Local time at start: %s", strstart); 
             }    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
           }    fprintf(ficresvpl,"# Age");
           else if(s[m][i] !=9){ /* Should no more exist */    for(i=1; i<=nlstate;i++)
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        fprintf(ficresvpl," %1d-%1d",i,i);
             if(mint[m][i]==99 || anint[m][i]==9999)    fprintf(ficresvpl,"\n");
               agev[m][i]=1;  
             else if(agev[m][i] <agemin){    xp=vector(1,npar);
               agemin=agev[m][i];    dnewm=matrix(1,nlstate,1,npar);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    doldm=matrix(1,nlstate,1,nlstate);
             }    
             else if(agev[m][i] >agemax){    hstepm=1*YEARM; /* Every year of age */
               agemax=agev[m][i];    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    agelim = AGESUP;
             }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
             /*agev[m][i]=anint[m][i]-annais[i];*/      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             /*   agev[m][i] = age[i]+2*m;*/      if (stepm >= YEARM) hstepm=1;
           }      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           else { /* =9 */      gradg=matrix(1,npar,1,nlstate);
             agev[m][i]=1;      gp=vector(1,nlstate);
             s[m][i]=-1;      gm=vector(1,nlstate);
           }  
         }      for(theta=1; theta <=npar; theta++){
         else /*= 0 Unknown */        for(i=1; i<=npar; i++){ /* Computes gradient */
           agev[m][i]=1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }        }
            prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     }        for(i=1;i<=nlstate;i++)
     for (i=1; i<=imx; i++)  {          gp[i] = prlim[i][i];
       for(m=1; (m<= maxwav); m++){      
         if (s[m][i] > (nlstate+ndeath)) {        for(i=1; i<=npar; i++) /* Computes gradient */
           printf("Error: Wrong value in nlstate or ndeath\n");            xp[i] = x[i] - (i==theta ?delti[theta]:0);
           goto end;        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++)
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
     free_vector(severity,1,maxwav);  
     free_imatrix(outcome,1,maxwav+1,1,n);      trgradg =matrix(1,nlstate,1,npar);
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);      for(j=1; j<=nlstate;j++)
     /* free_matrix(mint,1,maxwav,1,n);        for(theta=1; theta <=npar; theta++)
        free_matrix(anint,1,maxwav,1,n);*/          trgradg[j][theta]=gradg[theta][j];
     free_vector(moisdc,1,n);  
     free_vector(andc,1,n);      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
          matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     wav=ivector(1,imx);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      for(i=1;i<=nlstate;i++)
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
      
     /* Concatenates waves */      fprintf(ficresvpl,"%.0f ",age );
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       Tcode=ivector(1,100);      free_vector(gp,1,nlstate);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      free_vector(gm,1,nlstate);
       ncodemax[1]=1;      free_matrix(gradg,1,npar,1,nlstate);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      free_matrix(trgradg,1,nlstate,1,npar);
          } /* End age */
    codtab=imatrix(1,100,1,10);  
    h=0;    free_vector(xp,1,npar);
    m=pow(2,cptcoveff);    free_matrix(doldm,1,nlstate,1,npar);
      free_matrix(dnewm,1,nlstate,1,nlstate);
    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++){  /************ Variance of one-step probabilities  ******************/
            h++;  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[])
            if (h>m) h=1;codtab[h][k]=j;  {
          }    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;
    /*for(i=1; i <=m ;i++){    double *xp;
      for(k=1; k <=cptcovn; k++){    double *gp, *gm;
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);    double **gradg, **trgradg;
      }    double **mu;
      printf("\n");    double age,agelim, cov[NCOVMAX];
    }    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
    scanf("%d",i);*/    int theta;
        char fileresprob[FILENAMELENGTH];
    /* Calculates basic frequencies. Computes observed prevalence at single age    char fileresprobcov[FILENAMELENGTH];
        and prints on file fileres'p'. */    char fileresprobcor[FILENAMELENGTH];
   
        double ***varpij;
      
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    strcpy(fileresprob,"prob"); 
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    strcat(fileresprob,fileres);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      printf("Problem with resultfile: %s\n", fileresprob);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
          }
     /* For Powell, parameters are in a vector p[] starting at p[1]    strcpy(fileresprobcov,"probcov"); 
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    strcat(fileresprobcov,fileres);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
     if(mle==1){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    }
     }    strcpy(fileresprobcor,"probcor"); 
        strcat(fileresprobcor,fileres);
     /*--------- results files --------------*/    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);      printf("Problem with resultfile: %s\n", fileresprobcor);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
    jk=1;    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
    fprintf(ficres,"# Parameters\n");    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
    printf("# Parameters\n");    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
    for(i=1,jk=1; i <=nlstate; i++){    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      for(k=1; k <=(nlstate+ndeath); k++){    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
        if (k != i)    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
          {    fprintf(ficresprob, "#Local time at start: %s", strstart);
            printf("%d%d ",i,k);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
            fprintf(ficres,"%1d%1d ",i,k);    fprintf(ficresprob,"# Age");
            for(j=1; j <=ncovmodel; j++){    fprintf(ficresprobcov, "#Local time at start: %s", strstart);
              printf("%f ",p[jk]);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
              fprintf(ficres,"%f ",p[jk]);    fprintf(ficresprobcov,"# Age");
              jk++;    fprintf(ficresprobcor, "#Local time at start: %s", strstart);
            }    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
            printf("\n");    fprintf(ficresprobcov,"# Age");
            fprintf(ficres,"\n");  
          }  
      }    for(i=1; i<=nlstate;i++)
    }      for(j=1; j<=(nlstate+ndeath);j++){
  if(mle==1){        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
     /* Computing hessian and covariance matrix */        fprintf(ficresprobcov," p%1d-%1d ",i,j);
     ftolhess=ftol; /* Usually correct */        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     hesscov(matcov, p, npar, delti, ftolhess, func);      }  
  }   /* fprintf(ficresprob,"\n");
     fprintf(ficres,"# Scales\n");    fprintf(ficresprobcov,"\n");
     printf("# Scales\n");    fprintf(ficresprobcor,"\n");
      for(i=1,jk=1; i <=nlstate; i++){   */
       for(j=1; j <=nlstate+ndeath; j++){   xp=vector(1,npar);
         if (j!=i) {    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           fprintf(ficres,"%1d%1d",i,j);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
           printf("%1d%1d",i,j);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
           for(k=1; k<=ncovmodel;k++){    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
             printf(" %.5e",delti[jk]);    first=1;
             fprintf(ficres," %.5e",delti[jk]);    fprintf(ficgp,"\n# Routine varprob");
             jk++;    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
           }    fprintf(fichtm,"\n");
           printf("\n");  
           fprintf(ficres,"\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.\
     k=1;   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(ficres,"# Covariance\n");    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
     printf("# Covariance\n");  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
     for(i=1;i<=npar;i++){  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
       /*  if (k>nlstate) k=1;  standard deviations wide on each axis. <br>\
       i1=(i-1)/(ncovmodel*nlstate)+1;   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
       printf("%s%d%d",alph[k],i1,tab[i]);*/  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
       fprintf(ficres,"%3d",i);  
       printf("%3d",i);    cov[1]=1;
       for(j=1; j<=i;j++){    tj=cptcoveff;
         fprintf(ficres," %.5e",matcov[i][j]);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
         printf(" %.5e",matcov[i][j]);    j1=0;
       }    for(t=1; t<=tj;t++){
       fprintf(ficres,"\n");      for(i1=1; i1<=ncodemax[t];i1++){ 
       printf("\n");        j1++;
       k++;        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]]);
     while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresprob, "**********\n#\n");
       ungetc(c,ficpar);          fprintf(ficresprobcov, "\n#********** Variable "); 
       fgets(line, MAXLINE, ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       puts(line);          fprintf(ficresprobcov, "**********\n#\n");
       fputs(line,ficparo);          
     }          fprintf(ficgp, "\n#********** Variable "); 
     ungetc(c,ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficgp, "**********\n#\n");
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);          
              
     if (fage <= 2) {          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       bage = agemin;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fage = agemaxpar;          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     }          
              fprintf(ficresprobcor, "\n#********** Variable ");    
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);          fprintf(ficresprobcor, "**********\n#");    
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);        }
          
     while((c=getc(ficpar))=='#' && c!= EOF){        for (age=bage; age<=fage; age ++){ 
     ungetc(c,ficpar);          cov[2]=age;
     fgets(line, MAXLINE, ficpar);          for (k=1; k<=cptcovn;k++) {
     puts(line);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     fputs(line,ficparo);          }
   }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   ungetc(c,ficpar);          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]]];
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);          
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
                gp=vector(1,(nlstate)*(nlstate+ndeath));
   while((c=getc(ficpar))=='#' && c!= EOF){          gm=vector(1,(nlstate)*(nlstate+ndeath));
     ungetc(c,ficpar);      
     fgets(line, MAXLINE, ficpar);          for(theta=1; theta <=npar; theta++){
     puts(line);            for(i=1; i<=npar; i++)
     fputs(line,ficparo);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   }            
   ungetc(c,ficpar);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
              
             k=0;
    dateprev1=anprev1+mprev1/12.+jprev1/365.;            for(i=1; i<= (nlstate); i++){
    dateprev2=anprev2+mprev2/12.+jprev2/365.;              for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
   fscanf(ficpar,"pop_based=%d\n",&popbased);                gp[k]=pmmij[i][j];
   fprintf(ficparo,"pop_based=%d\n",popbased);                }
   fprintf(ficres,"pop_based=%d\n",popbased);              }
              
   while((c=getc(ficpar))=='#' && c!= EOF){            for(i=1; i<=npar; i++)
     ungetc(c,ficpar);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     fgets(line, MAXLINE, ficpar);      
     puts(line);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     fputs(line,ficparo);            k=0;
   }            for(i=1; i<=(nlstate); i++){
   ungetc(c,ficpar);              for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);                gm[k]=pmmij[i][j];
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);              }
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);            }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
 while((c=getc(ficpar))=='#' && c!= EOF){              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);  
     puts(line);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     fputs(line,ficparo);            for(theta=1; theta <=npar; theta++)
   }              trgradg[j][theta]=gradg[theta][j];
   ungetc(c,ficpar);          
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
 /*------------ gnuplot -------------*/          pmij(pmmij,cov,ncovmodel,x,nlstate);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);          
            k=0;
 /*------------ free_vector  -------------*/          for(i=1; i<=(nlstate); i++){
  chdir(path);            for(j=1; j<=(nlstate+ndeath);j++){
                k=k+1;
  free_ivector(wav,1,imx);              mu[k][(int) age]=pmmij[i][j];
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);            }
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            }
  free_ivector(num,1,n);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
  free_vector(agedc,1,n);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
  /*free_matrix(covar,1,NCOVMAX,1,n);*/              varpij[i][j][(int)age] = doldm[i][j];
  fclose(ficparo);  
  fclose(ficres);          /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
 /*--------- index.htm --------*/            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]));
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);            }*/
   
            fprintf(ficresprob,"\n%d ",(int)age);
   /*--------------- Prevalence limit --------------*/          fprintf(ficresprobcov,"\n%d ",(int)age);
            fprintf(ficresprobcor,"\n%d ",(int)age);
   strcpy(filerespl,"pl");  
   strcat(filerespl,fileres);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   if((ficrespl=fopen(filerespl,"w"))==NULL) {            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   }            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   fprintf(ficrespl,"#Prevalence limit\n");          }
   fprintf(ficrespl,"#Age ");          i=0;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);          for (k=1; k<=(nlstate);k++){
   fprintf(ficrespl,"\n");            for (l=1; l<=(nlstate+ndeath);l++){ 
                i=i++;
   prlim=matrix(1,nlstate,1,nlstate);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              for (j=1; j<=i;j++){
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              }
   k=0;            }
   agebase=agemin;          }/* end of loop for state */
   agelim=agemaxpar;        } /* end of loop for age */
   ftolpl=1.e-10;  
   i1=cptcoveff;        /* Confidence intervalle of pij  */
   if (cptcovn < 1){i1=1;}        /*
           fprintf(ficgp,"\nset noparametric;unset label");
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
         k=k+1;          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
         fprintf(ficrespl,"\n#******");          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
         for(j=1;j<=cptcoveff;j++)          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        */
         fprintf(ficrespl,"******\n");  
                /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         for (age=agebase; age<=agelim; age++){        first1=1;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        for (k2=1; k2<=(nlstate);k2++){
           fprintf(ficrespl,"%.0f",age );          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
           for(i=1; i<=nlstate;i++)            if(l2==k2) continue;
           fprintf(ficrespl," %.5f", prlim[i][i]);            j=(k2-1)*(nlstate+ndeath)+l2;
           fprintf(ficrespl,"\n");            for (k1=1; k1<=(nlstate);k1++){
         }              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
       }                if(l1==k1) continue;
     }                i=(k1-1)*(nlstate+ndeath)+l1;
   fclose(ficrespl);                if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
   /*------------- h Pij x at various ages ------------*/                  if ((int)age %5==0){
                      v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                    mu1=mu[i][(int) age]/stepm*YEARM ;
   }                    mu2=mu[j][(int) age]/stepm*YEARM;
   printf("Computing pij: result on file '%s' \n", filerespij);                    c12=cv12/sqrt(v1*v2);
                      /* Computing eigen value of matrix of covariance */
   stepsize=(int) (stepm+YEARM-1)/YEARM;                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   /*if (stepm<=24) stepsize=2;*/                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
   agelim=AGESUP;                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   hstepm=stepsize*YEARM; /* Every year of age */                    /*v21=sqrt(1.-v11*v11); *//* error */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */                    v21=(lc1-v1)/cv12*v11;
                      v12=-v21;
   k=0;                    v22=v11;
   for(cptcov=1;cptcov<=i1;cptcov++){                    tnalp=v21/v11;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    if(first1==1){
       k=k+1;                      first1=0;
         fprintf(ficrespij,"\n#****** ");                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
         for(j=1;j<=cptcoveff;j++)                    }
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
         fprintf(ficrespij,"******\n");                    /*printf(fignu*/
                            /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                    if(first==1){
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                      first=0;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                      fprintf(ficgp,"\nset parametric;unset label");
           oldm=oldms;savm=savms;                      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);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(ficrespij,"# Age");                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
           for(i=1; i<=nlstate;i++)   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
             for(j=1; j<=nlstate+ndeath;j++)  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
               fprintf(ficrespij," %1d-%1d",i,j);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
           fprintf(ficrespij,"\n");                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           for (h=0; h<=nhstepm; h++){                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
             for(i=1; i<=nlstate;i++)                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
               for(j=1; j<=nlstate+ndeath;j++)                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
             fprintf(ficrespij,"\n");                      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),\
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
           fprintf(ficrespij,"\n");                    }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);
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/                      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),\
   fclose(ficrespij);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
   /*---------- Forecasting ------------------*/                } /* end loop age */
   if((stepm == 1) && (strcmp(model,".")==0)){                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);                first=1;
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);              } /*l12 */
     free_matrix(mint,1,maxwav,1,n);            } /* k12 */
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);          } /*l1 */
     free_vector(weight,1,n);}        }/* k1 */
   else{      } /* loop covariates */
     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);    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);
   /*---------- Health expectancies and variances ------------*/    fclose(ficresprobcov);
     fclose(ficresprobcor);
   strcpy(filerest,"t");    fflush(ficgp);
   strcat(filerest,fileres);    fflush(fichtmcov);
   if((ficrest=fopen(filerest,"w"))==NULL) {  }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
   strcpy(filerese,"e");                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   strcat(filerese,fileres);                    int popforecast, int estepm ,\
   if((ficreseij=fopen(filerese,"w"))==NULL) {                    double jprev1, double mprev1,double anprev1, \
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                    double jprev2, double mprev2,double anprev2){
   }    int jj1, k1, i1, cpt;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
      fprintf(fichtm,"<ul><li><a> href="#firstorder">Result files (first order: no variance)</a>\n \
  strcpy(fileresv,"v");     <li><a> href="#secondorder">Result files (second order (variance)</a>\n \
   strcat(fileresv,fileres);  </ul>");
   if((ficresvij=fopen(fileresv,"w"))==NULL) {     fprintf(fichtm,"<ul><li><h4><a name="firstorder">Result files (first order: no variance)</a></h4>\n \
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);   - 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"));
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);     fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
   k=0;             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
   for(cptcov=1;cptcov<=i1;cptcov++){     fprintf(fichtm,"\
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
       k=k+1;             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
       fprintf(ficrest,"\n#****** ");     fprintf(fichtm,"\
       for(j=1;j<=cptcoveff;j++)   - Life expectancies by age and initial health status (estepm=%2d months): \
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     <a href=\"%s\">%s</a> <br>\n</li>",
       fprintf(ficrest,"******\n");             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   
       fprintf(ficreseij,"\n#****** ");  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);   m=cptcoveff;
       fprintf(ficreseij,"******\n");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
       fprintf(ficresvij,"\n#****** ");   jj1=0;
       for(j=1;j<=cptcoveff;j++)   for(k1=1; k1<=m;k1++){
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);     for(i1=1; i1<=ncodemax[k1];i1++){
       fprintf(ficresvij,"******\n");       jj1++;
        if (cptcovn > 0) {
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       oldm=oldms;savm=savms;         for (cpt=1; cpt<=cptcoveff;cpt++) 
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);             fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       oldm=oldms;savm=savms;       }
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);       /* 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(ficrest,"#Total LEs with variances: e.. (std) ");       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
       fprintf(ficrest,"\n");  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Stable prevalence in each health state */
       hf=1;         for(cpt=1; cpt<nlstate;cpt++){
       if (stepm >= YEARM) hf=stepm/YEARM;           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
       epj=vector(1,nlstate+1);  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
       for(age=bage; age <=fage ;age++){         }
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);       for(cpt=1; cpt<=nlstate;cpt++) {
         if (popbased==1) {          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
           for(i=1; i<=nlstate;i++)  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
             prlim[i][i]=probs[(int)age][i][k];       }
         }     } /* end i1 */
           }/* End k1 */
         fprintf(ficrest," %.0f",age);   fprintf(fichtm,"</ul>");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];   fprintf(fichtm,"\
           }  \n<br><li><h4> <a name="secondorder">Result files (second order: variances)</a></h4>\n\
           epj[nlstate+1] +=epj[j];   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
         }  
         for(i=1, vepp=0.;i <=nlstate;i++)   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
           for(j=1;j <=nlstate;j++)           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
             vepp += vareij[i][j][(int)age];   fprintf(fichtm,"\
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
         for(j=1;j <=nlstate;j++){           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));  
         }   fprintf(fichtm,"\
         fprintf(ficrest,"\n");   - 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"));
   fclose(ficreseij);   fprintf(fichtm,"\
   fclose(ficresvij);   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
   fclose(ficrest);           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
   fclose(ficpar);   fprintf(fichtm,"\
   free_vector(epj,1,nlstate+1);   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
             subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   /*------- Variance limit prevalence------*/    
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   strcpy(fileresvpl,"vpl");  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   strcat(fileresvpl,fileres);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  /*      <br>",fileres,fileres,fileres,fileres); */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  /*  else  */
     exit(0);  /*    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);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
   k=0;   m=cptcoveff;
   for(cptcov=1;cptcov<=i1;cptcov++){   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;   jj1=0;
       fprintf(ficresvpl,"\n#****** ");   for(k1=1; k1<=m;k1++){
       for(j=1;j<=cptcoveff;j++)     for(i1=1; i1<=ncodemax[k1];i1++){
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       jj1++;
       fprintf(ficresvpl,"******\n");       if (cptcovn > 0) {
               fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       varpl=matrix(1,nlstate,(int) bage, (int) fage);         for (cpt=1; cpt<=cptcoveff;cpt++) 
       oldm=oldms;savm=savms;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     }       }
  }       for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   fclose(ficresvpl);  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);  
   /*---------- End : free ----------------*/       }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
    health expectancies in states (1) and (2): %s%d.png<br>\
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);     } /* end i1 */
     }/* End k1 */
     fprintf(fichtm,"</ul>");
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);   fflush(fichtm);
   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);  /******************* Gnuplot file **************/
    void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);    char dirfileres[132],optfileres[132];
   free_matrix(agev,1,maxwav,1,imx);    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   if(erreur >0)  /*     printf("Problem with file %s",optionfilegnuplot); */
     printf("End of Imach with error %d\n",erreur);  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   else   printf("End of Imach\n");  /*   } */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
      /*#ifdef windows */
   /* 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(ficgp,"cd \"%s\" \n",pathc);
   /*printf("Total time was %d uSec.\n", total_usecs);*/      /*#endif */
   /*------ End -----------*/    m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
  end:    strcpy(optfileres,"vpl");
 #ifdef windows   /* 1eme*/
   /* chdir(pathcd);*/    for (cpt=1; cpt<= nlstate ; cpt ++) {
 #endif     for (k1=1; k1<= m ; k1 ++) {
  /*system("wgnuplot graph.plt");*/       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
  /*system("../gp37mgw/wgnuplot graph.plt");*/       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
  /*system("cd ../gp37mgw");*/       fprintf(ficgp,"set xlabel \"Age\" \n\
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  set ylabel \"Probability\" \n\
  strcpy(plotcmd,GNUPLOTPROGRAM);  set ter png small\n\
  strcat(plotcmd," ");  set size 0.65,0.65\n\
  strcat(plotcmd,optionfilegnuplot);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
  system(plotcmd);  
        for (i=1; i<= nlstate ; i ++) {
 #ifdef windows         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   while (z[0] != 'q') {         else fprintf(ficgp," \%%*lf (\%%*lf)");
     chdir(path);       }
     printf("\nType e to edit output files, c to start again, and q for exiting: ");       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);
     scanf("%s",z);       for (i=1; i<= nlstate ; i ++) {
     if (z[0] == 'c') system("./imach");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     else if (z[0] == 'e') {         else fprintf(ficgp," \%%*lf (\%%*lf)");
       chdir(path);       } 
       system(optionfilehtm);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
     }       for (i=1; i<= nlstate ; i ++) {
     else if (z[0] == 'q') exit(0);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   }         else fprintf(ficgp," \%%*lf (\%%*lf)");
 #endif       }  
 }       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%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.1.32  
changed lines
  Added in v.1.106


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