Diff for /imach/src/imach.c between versions 1.51 and 1.104

version 1.51, 2002/07/19 12:22:25 version 1.104, 2005/09/30 16:11:43
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.104  2005/09/30 16:11:43  lievre
      (Module): sump fixed, loop imx fixed, and simplifications.
   This program computes Healthy Life Expectancies from    (Module): If the status is missing at the last wave but we know
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    that the person is alive, then we can code his/her status as -2
   first survey ("cross") where individuals from different ages are    (instead of missing=-1 in earlier versions) and his/her
   interviewed on their health status or degree of disability (in the    contributions to the likelihood is 1 - Prob of dying from last
   case of a health survey which is our main interest) -2- at least a    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   second wave of interviews ("longitudinal") which measure each change    the healthy state at last known wave). Version is 0.98
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.103  2005/09/30 15:54:49  lievre
   model. More health states you consider, more time is necessary to reach the    (Module): sump fixed, loop imx fixed, and simplifications.
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.102  2004/09/15 17:31:30  brouard
   probability to be observed in state j at the second wave    Add the possibility to read data file including tab characters.
   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 1.101  2004/09/15 10:38:38  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    Fix on curr_time
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.100  2004/07/12 18:29:06  brouard
   you to do it.  More covariates you add, slower the    Add version for Mac OS X. Just define UNIX in Makefile
   convergence.  
     Revision 1.99  2004/06/05 08:57:40  brouard
   The advantage of this computer programme, compared to a simple    *** empty log message ***
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.98  2004/05/16 15:05:56  brouard
   intermediate interview, the information is lost, but taken into    New version 0.97 . First attempt to estimate force of mortality
   account using an interpolation or extrapolation.      directly from the data i.e. without the need of knowing the health
     state at each age, but using a Gompertz model: log u =a + b*age .
   hPijx is the probability to be observed in state i at age x+h    This is the basic analysis of mortality and should be done before any
   conditional to the observed state i at age x. The delay 'h' can be    other analysis, in order to test if the mortality estimated from the
   split into an exact number (nh*stepm) of unobserved intermediate    cross-longitudinal survey is different from the mortality estimated
   states. This elementary transition (by month or quarter trimester,    from other sources like vital statistic data.
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    The same imach parameter file can be used but the option for mle should be -3.
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Agnès, who wrote this part of the code, tried to keep most of the
     former routines in order to include the new code within the former code.
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    The output is very simple: only an estimate of the intercept and of
      the slope with 95% confident intervals.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Current limitations:
   This software have been partly granted by Euro-REVES, a concerted action    A) Even if you enter covariates, i.e. with the
   from the European Union.    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   It is copyrighted identically to a GNU software product, ie programme and    B) There is no computation of Life Expectancy nor Life Table.
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Revision 1.97  2004/02/20 13:25:42  lievre
   **********************************************************************/    Version 0.96d. Population forecasting command line is (temporarily)
      suppressed.
 #include <math.h>  
 #include <stdio.h>    Revision 1.96  2003/07/15 15:38:55  brouard
 #include <stdlib.h>    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #include <unistd.h>    rewritten within the same printf. Workaround: many printfs.
   
 #define MAXLINE 256    Revision 1.95  2003/07/08 07:54:34  brouard
 #define GNUPLOTPROGRAM "gnuplot"    * imach.c (Repository):
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    (Repository): Using imachwizard code to output a more meaningful covariance
 #define FILENAMELENGTH 80    matrix (cov(a12,c31) instead of numbers.
 /*#define DEBUG*/  
 #define windows    Revision 1.94  2003/06/27 13:00:02  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Just cleaning
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.93  2003/06/25 16:33:55  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    (Module): On windows (cygwin) function asctime_r doesn't
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    exist so I changed back to asctime which exists.
     (Module): Version 0.96b
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.92  2003/06/25 16:30:45  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    (Module): On windows (cygwin) function asctime_r doesn't
 #define NCOVMAX 8 /* Maximum number of covariates */    exist so I changed back to asctime which exists.
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.91  2003/06/25 15:30:29  brouard
 #define AGESUP 130    * imach.c (Repository): Duplicated warning errors corrected.
 #define AGEBASE 40    (Repository): Elapsed time after each iteration is now output. It
 #ifdef windows    helps to forecast when convergence will be reached. Elapsed time
 #define DIRSEPARATOR '\\'    is stamped in powell.  We created a new html file for the graphs
 #define ODIRSEPARATOR '/'    concerning matrix of covariance. It has extension -cov.htm.
 #else  
 #define DIRSEPARATOR '/'    Revision 1.90  2003/06/24 12:34:15  brouard
 #define ODIRSEPARATOR '\\'    (Module): Some bugs corrected for windows. Also, when
 #endif    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";  
 int erreur; /* Error number */    Revision 1.89  2003/06/24 12:30:52  brouard
 int nvar;    (Module): Some bugs corrected for windows. Also, when
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    mle=-1 a template is output in file "or"mypar.txt with the design
 int npar=NPARMAX;    of the covariance matrix to be input.
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.88  2003/06/23 17:54:56  brouard
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    * 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.
 int popbased=0;  
     Revision 1.87  2003/06/18 12:26:01  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    Version 0.96
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.86  2003/06/17 20:04:08  brouard
 int mle, weightopt;    (Module): Change position of html and gnuplot routines and added
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    routine fileappend.
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Revision 1.85  2003/06/17 13:12:43  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    * imach.c (Repository): Check when date of death was earlier that
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    current date of interview. It may happen when the death was just
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    prior to the death. In this case, dh was negative and likelihood
 FILE *ficlog;    was wrong (infinity). We still send an "Error" but patch by
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    assuming that the date of death was just one stepm after the
 FILE *ficresprobmorprev;    interview.
 FILE *fichtm; /* Html File */    (Repository): Because some people have very long ID (first column)
 FILE *ficreseij;    we changed int to long in num[] and we added a new lvector for
 char filerese[FILENAMELENGTH];    memory allocation. But we also truncated to 8 characters (left
 FILE  *ficresvij;    truncation)
 char fileresv[FILENAMELENGTH];    (Repository): No more line truncation errors.
 FILE  *ficresvpl;  
 char fileresvpl[FILENAMELENGTH];    Revision 1.84  2003/06/13 21:44:43  brouard
 char title[MAXLINE];    * imach.c (Repository): Replace "freqsummary" at a correct
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    place. It differs from routine "prevalence" which may be called
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    many times. Probs is memory consuming and must be used with
     parcimony.
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 char filelog[FILENAMELENGTH]; /* Log file */  
 char filerest[FILENAMELENGTH];    Revision 1.83  2003/06/10 13:39:11  lievre
 char fileregp[FILENAMELENGTH];    *** empty log message ***
 char popfile[FILENAMELENGTH];  
     Revision 1.82  2003/06/05 15:57:20  brouard
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    Add log in  imach.c and  fullversion number is now printed.
   
 #define NR_END 1  */
 #define FREE_ARG char*  /*
 #define FTOL 1.0e-10     Interpolated Markov Chain
   
 #define NRANSI    Short summary of the programme:
 #define ITMAX 200    
     This program computes Healthy Life Expectancies from
 #define TOL 2.0e-4    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     first survey ("cross") where individuals from different ages are
 #define CGOLD 0.3819660    interviewed on their health status or degree of disability (in the
 #define ZEPS 1.0e-10    case of a health survey which is our main interest) -2- at least a
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
 #define GOLD 1.618034    computed from the time spent in each health state according to a
 #define GLIMIT 100.0    model. More health states you consider, more time is necessary to reach the
 #define TINY 1.0e-20    Maximum Likelihood of the parameters involved in the model.  The
     simplest model is the multinomial logistic model where pij is the
 static double maxarg1,maxarg2;    probability to be observed in state j at the second wave
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    conditional to be observed in state i at the first wave. Therefore
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    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
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    complex model than "constant and age", you should modify the program
 #define rint(a) floor(a+0.5)    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
 static double sqrarg;    convergence.
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    The advantage of this computer programme, compared to a simple
     multinomial logistic model, is clear when the delay between waves is not
 int imx;    identical for each individual. Also, if a individual missed an
 int stepm;    intermediate interview, the information is lost, but taken into
 /* Stepm, step in month: minimum step interpolation*/    account using an interpolation or extrapolation.  
   
 int estepm;    hPijx is the probability to be observed in state i at age x+h
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    conditional to the observed state i at age x. The delay 'h' can be
     split into an exact number (nh*stepm) of unobserved intermediate
 int m,nb;    states. This elementary transition (by month, quarter,
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    semester or year) is modelled as a multinomial logistic.  The hPx
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    matrix is simply the matrix product of nh*stepm elementary matrices
 double **pmmij, ***probs, ***mobaverage;    and the contribution of each individual to the likelihood is simply
 double dateintmean=0;    hPijx.
   
 double *weight;    Also this programme outputs the covariance matrix of the parameters but also
 int **s; /* Status */    of the life expectancies. It also computes the stable prevalence. 
 double *agedc, **covar, idx;    
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    This software have been partly granted by Euro-REVES, a concerted action
 double ftolhess; /* Tolerance for computing hessian */    from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
 /**************** split *************************/    software can be distributed freely for non commercial use. Latest version
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    can be accessed at http://euroreves.ined.fr/imach .
 {  
    char *s;                             /* pointer */    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
    int  l1, l2;                         /* length counters */    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     
    l1 = strlen( path );                 /* length of path */    **********************************************************************/
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  /*
    s= strrchr( path, DIRSEPARATOR );            /* find last / */    main
    if ( s == NULL ) {                   /* no directory, so use current */    read parameterfile
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)    read datafile
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/    concatwav
 #if     defined(__bsd__)                /* get current working directory */    freqsummary
       extern char       *getwd( );    if (mle >= 1)
       mlikeli
       if ( getwd( dirc ) == NULL ) {    print results files
 #else    if mle==1 
       extern char       *getcwd( );       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {        begin-prev-date,...
 #endif    open gnuplot file
          return( GLOCK_ERROR_GETCWD );    open html file
       }    stable prevalence
       strcpy( name, path );             /* we've got it */     for age prevalim()
    } else {                             /* strip direcotry from path */    h Pij x
       s++;                              /* after this, the filename */    variance of p varprob
       l2 = strlen( s );                 /* length of filename */    forecasting if prevfcast==1 prevforecast call prevalence()
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    health expectancies
       strcpy( name, s );                /* save file name */    Variance-covariance of DFLE
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    prevalence()
       dirc[l1-l2] = 0;                  /* add zero */     movingaverage()
    }    varevsij() 
    l1 = strlen( dirc );                 /* length of directory */    if popbased==1 varevsij(,popbased)
 #ifdef windows    total life expectancies
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Variance of stable prevalence
 #else   end
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  */
 #endif  
    s = strrchr( name, '.' );            /* find last / */  
    s++;  
    strcpy(ext,s);                       /* save extension */   
    l1= strlen( name);  #include <math.h>
    l2= strlen( s)+1;  #include <stdio.h>
    strncpy( finame, name, l1-l2);  #include <stdlib.h>
    finame[l1-l2]= 0;  #include <unistd.h>
    return( 0 );                         /* we're done */  
 }  /* #include <sys/time.h> */
   #include <time.h>
   #include "timeval.h"
 /******************************************/  
   /* #include <libintl.h> */
 void replace(char *s, char*t)  /* #define _(String) gettext (String) */
 {  
   int i;  #define MAXLINE 256
   int lg=20;  #define GNUPLOTPROGRAM "gnuplot"
   i=0;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   lg=strlen(t);  #define FILENAMELENGTH 132
   for(i=0; i<= lg; i++) {  /*#define DEBUG*/
     (s[i] = t[i]);  /*#define windows*/
     if (t[i]== '\\') s[i]='/';  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   }  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 }  
   #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 int nbocc(char *s, char occ)  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 {  
   int i,j=0;  #define NINTERVMAX 8
   int lg=20;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   i=0;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   lg=strlen(s);  #define NCOVMAX 8 /* Maximum number of covariates */
   for(i=0; i<= lg; i++) {  #define MAXN 20000
   if  (s[i] == occ ) j++;  #define YEARM 12. /* Number of months per year */
   }  #define AGESUP 130
   return j;  #define AGEBASE 40
 }  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   #ifdef UNIX
 void cutv(char *u,char *v, char*t, char occ)  #define DIRSEPARATOR '/'
 {  #define ODIRSEPARATOR '\\'
   /* cuts string t into u and v where u is ended by char occ excluding it  #else
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)  #define DIRSEPARATOR '\\'
      gives u="abcedf" and v="ghi2j" */  #define ODIRSEPARATOR '/'
   int i,lg,j,p=0;  #endif
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {  /* $Id$ */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  /* $State$ */
   }  
   char version[]="Imach version 0.98, September 2005, INED-EUROREVES ";
   lg=strlen(t);  char fullversion[]="$Revision$ $Date$"; 
   for(j=0; j<p; j++) {  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
     (u[j] = t[j]);  int nvar;
   }  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
      u[p]='\0';  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
    for(j=0; j<= lg; j++) {  int ndeath=1; /* Number of dead states */
     if (j>=(p+1))(v[j-p-1] = t[j]);  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   }  int popbased=0;
 }  
   int *wav; /* Number of waves for this individuual 0 is possible */
 /********************** nrerror ********************/  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
 void nrerror(char error_text[])  int gipmx, gsw; /* Global variables on the number of contributions 
 {                     to the likelihood and the sum of weights (done by funcone)*/
   fprintf(stderr,"ERREUR ...\n");  int mle, weightopt;
   fprintf(stderr,"%s\n",error_text);  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   exit(1);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 }  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 /*********************** vector *******************/             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 double *vector(int nl, int nh)  double jmean; /* Mean space between 2 waves */
 {  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double *v;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   if (!v) nrerror("allocation failure in vector");  FILE *ficlog, *ficrespow;
   return v-nl+NR_END;  int globpr; /* Global variable for printing or not */
 }  double fretone; /* Only one call to likelihood */
   long ipmx; /* Number of contributions */
 /************************ free vector ******************/  double sw; /* Sum of weights */
 void free_vector(double*v, int nl, int nh)  char filerespow[FILENAMELENGTH];
 {  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   free((FREE_ARG)(v+nl-NR_END));  FILE *ficresilk;
 }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 /************************ivector *******************************/  FILE *fichtm, *fichtmcov; /* Html File */
 int *ivector(long nl,long nh)  FILE *ficreseij;
 {  char filerese[FILENAMELENGTH];
   int *v;  FILE  *ficresvij;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  char fileresv[FILENAMELENGTH];
   if (!v) nrerror("allocation failure in ivector");  FILE  *ficresvpl;
   return v-nl+NR_END;  char fileresvpl[FILENAMELENGTH];
 }  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 /******************free ivector **************************/  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 void free_ivector(int *v, long nl, long nh)  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 {  char command[FILENAMELENGTH];
   free((FREE_ARG)(v+nl-NR_END));  int  outcmd=0;
 }  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)  char filelog[FILENAMELENGTH]; /* Log file */
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  char filerest[FILENAMELENGTH];
 {  char fileregp[FILENAMELENGTH];
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  char popfile[FILENAMELENGTH];
   int **m;  
    char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   if (!m) nrerror("allocation failure 1 in matrix()");  struct timezone tzp;
   m += NR_END;  extern int gettimeofday();
   m -= nrl;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
    long time_value;
    extern long time();
   /* allocate rows and set pointers to them */  char strcurr[80], strfor[80];
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define NR_END 1
   m[nrl] += NR_END;  #define FREE_ARG char*
   m[nrl] -= ncl;  #define FTOL 1.0e-10
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  #define NRANSI 
    #define ITMAX 200 
   /* return pointer to array of pointers to rows */  
   return m;  #define TOL 2.0e-4 
 }  
   #define CGOLD 0.3819660 
 /****************** free_imatrix *************************/  #define ZEPS 1.0e-10 
 void free_imatrix(m,nrl,nrh,ncl,nch)  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       int **m;  
       long nch,ncl,nrh,nrl;  #define GOLD 1.618034 
      /* free an int matrix allocated by imatrix() */  #define GLIMIT 100.0 
 {  #define TINY 1.0e-20 
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  static double maxarg1,maxarg2;
 }  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 /******************* matrix *******************************/    
 double **matrix(long nrl, long nrh, long ncl, long nch)  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 {  #define rint(a) floor(a+0.5)
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   if (!m) nrerror("allocation failure 1 in matrix()");  int agegomp= AGEGOMP;
   m += NR_END;  
   m -= nrl;  int imx; 
   int stepm=1;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  /* Stepm, step in month: minimum step interpolation*/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  int estepm;
   m[nrl] -= ncl;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int m,nb;
   return m;  long *num;
 }  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 /*************************free matrix ************************/  double **pmmij, ***probs;
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  double *ageexmed,*agecens;
 {  double dateintmean=0;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  double *weight;
 }  int **s; /* Status */
   double *agedc, **covar, idx;
 /******************* ma3x *******************************/  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  double ftolhess; /* Tolerance for computing hessian */
   double ***m;  
   /**************** split *************************/
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   if (!m) nrerror("allocation failure 1 in matrix()");  {
   m += NR_END;    /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
   m -= nrl;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     */ 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    char  *ss;                            /* pointer */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    int   l1, l2;                         /* length counters */
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if ( ss == NULL ) {                   /* no directory, so use current */
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   m[nrl][ncl] += NR_END;      /* get current working directory */
   m[nrl][ncl] -= nll;      /*    extern  char* getcwd ( char *buf , int len);*/
   for (j=ncl+1; j<=nch; j++)      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     m[nrl][j]=m[nrl][j-1]+nlay;        return( GLOCK_ERROR_GETCWD );
        }
   for (i=nrl+1; i<=nrh; i++) {      strcpy( name, path );               /* we've got it */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    } else {                              /* strip direcotry from path */
     for (j=ncl+1; j<=nch; j++)      ss++;                               /* after this, the filename */
       m[i][j]=m[i][j-1]+nlay;      l2 = strlen( ss );                  /* length of filename */
   }      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   return m;      strcpy( name, ss );         /* save file name */
 }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
 /*************************free ma3x ************************/    }
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    l1 = strlen( dirc );                  /* length of directory */
 {    /*#ifdef windows
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #else
   free((FREE_ARG)(m+nrl-NR_END));    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 }  #endif
     */
 /***************** f1dim *************************/    ss = strrchr( name, '.' );            /* find last / */
 extern int ncom;    if (ss >0){
 extern double *pcom,*xicom;      ss++;
 extern double (*nrfunc)(double []);      strcpy(ext,ss);                     /* save extension */
        l1= strlen( name);
 double f1dim(double x)      l2= strlen(ss)+1;
 {      strncpy( finame, name, l1-l2);
   int j;      finame[l1-l2]= 0;
   double f;    }
   double *xt;    return( 0 );                          /* we're done */
    }
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);  /******************************************/
   free_vector(xt,1,ncom);  
   return f;  void replace_back_to_slash(char *s, char*t)
 }  {
     int i;
 /*****************brent *************************/    int lg=0;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    i=0;
 {    lg=strlen(t);
   int iter;    for(i=0; i<= lg; i++) {
   double a,b,d,etemp;      (s[i] = t[i]);
   double fu,fv,fw,fx;      if (t[i]== '\\') s[i]='/';
   double ftemp;    }
   double p,q,r,tol1,tol2,u,v,w,x,xm;  }
   double e=0.0;  
    int nbocc(char *s, char occ)
   a=(ax < cx ? ax : cx);  {
   b=(ax > cx ? ax : cx);    int i,j=0;
   x=w=v=bx;    int lg=20;
   fw=fv=fx=(*f)(x);    i=0;
   for (iter=1;iter<=ITMAX;iter++) {    lg=strlen(s);
     xm=0.5*(a+b);    for(i=0; i<= lg; i++) {
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    if  (s[i] == occ ) j++;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    }
     printf(".");fflush(stdout);    return j;
     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);  void cutv(char *u,char *v, char*t, char occ)
     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);  {
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
 #endif       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){       gives u="abcedf" and v="ghi2j" */
       *xmin=x;    int i,lg,j,p=0;
       return fx;    i=0;
     }    for(j=0; j<=strlen(t)-1; j++) {
     ftemp=fu;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     if (fabs(e) > tol1) {    }
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);    lg=strlen(t);
       p=(x-v)*q-(x-w)*r;    for(j=0; j<p; j++) {
       q=2.0*(q-r);      (u[j] = t[j]);
       if (q > 0.0) p = -p;    }
       q=fabs(q);       u[p]='\0';
       etemp=e;  
       e=d;     for(j=0; j<= lg; j++) {
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))      if (j>=(p+1))(v[j-p-1] = t[j]);
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    }
       else {  }
         d=p/q;  
         u=x+d;  /********************** nrerror ********************/
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  void nrerror(char error_text[])
       }  {
     } else {    fprintf(stderr,"ERREUR ...\n");
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    fprintf(stderr,"%s\n",error_text);
     }    exit(EXIT_FAILURE);
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  }
     fu=(*f)(u);  /*********************** vector *******************/
     if (fu <= fx) {  double *vector(int nl, int nh)
       if (u >= x) a=x; else b=x;  {
       SHFT(v,w,x,u)    double *v;
         SHFT(fv,fw,fx,fu)    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
         } else {    if (!v) nrerror("allocation failure in vector");
           if (u < x) a=u; else b=u;    return v-nl+NR_END;
           if (fu <= fw || w == x) {  }
             v=w;  
             w=u;  /************************ free vector ******************/
             fv=fw;  void free_vector(double*v, int nl, int nh)
             fw=fu;  {
           } else if (fu <= fv || v == x || v == w) {    free((FREE_ARG)(v+nl-NR_END));
             v=u;  }
             fv=fu;  
           }  /************************ivector *******************************/
         }  int *ivector(long nl,long nh)
   }  {
   nrerror("Too many iterations in brent");    int *v;
   *xmin=x;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   return fx;    if (!v) nrerror("allocation failure in ivector");
 }    return v-nl+NR_END;
   }
 /****************** mnbrak ***********************/  
   /******************free ivector **************************/
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  void free_ivector(int *v, long nl, long nh)
             double (*func)(double))  {
 {    free((FREE_ARG)(v+nl-NR_END));
   double ulim,u,r,q, dum;  }
   double fu;  
    /************************lvector *******************************/
   *fa=(*func)(*ax);  long *lvector(long nl,long nh)
   *fb=(*func)(*bx);  {
   if (*fb > *fa) {    long *v;
     SHFT(dum,*ax,*bx,dum)    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       SHFT(dum,*fb,*fa,dum)    if (!v) nrerror("allocation failure in ivector");
       }    return v-nl+NR_END;
   *cx=(*bx)+GOLD*(*bx-*ax);  }
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  /******************free lvector **************************/
     r=(*bx-*ax)*(*fb-*fc);  void free_lvector(long *v, long nl, long nh)
     q=(*bx-*cx)*(*fb-*fa);  {
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    free((FREE_ARG)(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) {  /******************* imatrix *******************************/
       fu=(*func)(u);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     } else if ((*cx-u)*(u-ulim) > 0.0) {       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       fu=(*func)(u);  { 
       if (fu < *fc) {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    int **m; 
           SHFT(*fb,*fc,fu,(*func)(u))    
           }    /* allocate pointers to rows */ 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       u=ulim;    if (!m) nrerror("allocation failure 1 in matrix()"); 
       fu=(*func)(u);    m += NR_END; 
     } else {    m -= nrl; 
       u=(*cx)+GOLD*(*cx-*bx);    
       fu=(*func)(u);    
     }    /* allocate rows and set pointers to them */ 
     SHFT(*ax,*bx,*cx,u)    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       SHFT(*fa,*fb,*fc,fu)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       }    m[nrl] += NR_END; 
 }    m[nrl] -= ncl; 
     
 /*************** linmin ************************/    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     
 int ncom;    /* return pointer to array of pointers to rows */ 
 double *pcom,*xicom;    return m; 
 double (*nrfunc)(double []);  } 
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  /****************** free_imatrix *************************/
 {  void free_imatrix(m,nrl,nrh,ncl,nch)
   double brent(double ax, double bx, double cx,        int **m;
                double (*f)(double), double tol, double *xmin);        long nch,ncl,nrh,nrl; 
   double f1dim(double x);       /* free an int matrix allocated by imatrix() */ 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  { 
               double *fc, double (*func)(double));    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   int j;    free((FREE_ARG) (m+nrl-NR_END)); 
   double xx,xmin,bx,ax;  } 
   double fx,fb,fa;  
    /******************* matrix *******************************/
   ncom=n;  double **matrix(long nrl, long nrh, long ncl, long nch)
   pcom=vector(1,n);  {
   xicom=vector(1,n);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   nrfunc=func;    double **m;
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     xicom[j]=xi[j];    if (!m) nrerror("allocation failure 1 in matrix()");
   }    m += NR_END;
   ax=0.0;    m -= nrl;
   xx=1.0;  
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 #ifdef DEBUG    m[nrl] += NR_END;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    m[nrl] -= ncl;
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   for (j=1;j<=n;j++) {    return m;
     xi[j] *= xmin;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     p[j] += xi[j];     */
   }  }
   free_vector(xicom,1,n);  
   free_vector(pcom,1,n);  /*************************free matrix ************************/
 }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
 /*************** powell ************************/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    free((FREE_ARG)(m+nrl-NR_END));
             double (*func)(double []))  }
 {  
   void linmin(double p[], double xi[], int n, double *fret,  /******************* ma3x *******************************/
               double (*func)(double []));  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   int i,ibig,j;  {
   double del,t,*pt,*ptt,*xit;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   double fp,fptt;    double ***m;
   double *xits;  
   pt=vector(1,n);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   ptt=vector(1,n);    if (!m) nrerror("allocation failure 1 in matrix()");
   xit=vector(1,n);    m += NR_END;
   xits=vector(1,n);    m -= nrl;
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   for (*iter=1;;++(*iter)) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     fp=(*fret);    m[nrl] += NR_END;
     ibig=0;    m[nrl] -= ncl;
     del=0.0;  
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     for (i=1;i<=n;i++)    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       printf(" %d %.12f",i, p[i]);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     fprintf(ficlog," %d %.12f",i, p[i]);    m[nrl][ncl] += NR_END;
     printf("\n");    m[nrl][ncl] -= nll;
     fprintf(ficlog,"\n");    for (j=ncl+1; j<=nch; j++) 
     for (i=1;i<=n;i++) {      m[nrl][j]=m[nrl][j-1]+nlay;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    
       fptt=(*fret);    for (i=nrl+1; i<=nrh; i++) {
 #ifdef DEBUG      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       printf("fret=%lf \n",*fret);      for (j=ncl+1; j<=nch; j++) 
       fprintf(ficlog,"fret=%lf \n",*fret);        m[i][j]=m[i][j-1]+nlay;
 #endif    }
       printf("%d",i);fflush(stdout);    return m; 
       fprintf(ficlog,"%d",i);fflush(ficlog);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       linmin(p,xit,n,fret,func);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       if (fabs(fptt-(*fret)) > del) {    */
         del=fabs(fptt-(*fret));  }
         ibig=i;  
       }  /*************************free ma3x ************************/
 #ifdef DEBUG  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       printf("%d %.12e",i,(*fret));  {
       fprintf(ficlog,"%d %.12e",i,(*fret));    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       for (j=1;j<=n;j++) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    free((FREE_ARG)(m+nrl-NR_END));
         printf(" x(%d)=%.12e",j,xit[j]);  }
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);  
       }  /*************** function subdirf ***********/
       for(j=1;j<=n;j++) {  char *subdirf(char fileres[])
         printf(" p=%.12e",p[j]);  {
         fprintf(ficlog," p=%.12e",p[j]);    /* Caution optionfilefiname is hidden */
       }    strcpy(tmpout,optionfilefiname);
       printf("\n");    strcat(tmpout,"/"); /* Add to the right */
       fprintf(ficlog,"\n");    strcat(tmpout,fileres);
 #endif    return tmpout;
     }  }
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  
 #ifdef DEBUG  /*************** function subdirf2 ***********/
       int k[2],l;  char *subdirf2(char fileres[], char *preop)
       k[0]=1;  {
       k[1]=-1;    
       printf("Max: %.12e",(*func)(p));    /* Caution optionfilefiname is hidden */
       fprintf(ficlog,"Max: %.12e",(*func)(p));    strcpy(tmpout,optionfilefiname);
       for (j=1;j<=n;j++) {    strcat(tmpout,"/");
         printf(" %.12e",p[j]);    strcat(tmpout,preop);
         fprintf(ficlog," %.12e",p[j]);    strcat(tmpout,fileres);
       }    return tmpout;
       printf("\n");  }
       fprintf(ficlog,"\n");  
       for(l=0;l<=1;l++) {  /*************** function subdirf3 ***********/
         for (j=1;j<=n;j++) {  char *subdirf3(char fileres[], char *preop, char *preop2)
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  {
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    /* Caution optionfilefiname is hidden */
         }    strcpy(tmpout,optionfilefiname);
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    strcat(tmpout,"/");
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    strcat(tmpout,preop);
       }    strcat(tmpout,preop2);
 #endif    strcat(tmpout,fileres);
     return tmpout;
   }
       free_vector(xit,1,n);  
       free_vector(xits,1,n);  /***************** f1dim *************************/
       free_vector(ptt,1,n);  extern int ncom; 
       free_vector(pt,1,n);  extern double *pcom,*xicom;
       return;  extern double (*nrfunc)(double []); 
     }   
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  double f1dim(double x) 
     for (j=1;j<=n;j++) {  { 
       ptt[j]=2.0*p[j]-pt[j];    int j; 
       xit[j]=p[j]-pt[j];    double f;
       pt[j]=p[j];    double *xt; 
     }   
     fptt=(*func)(ptt);    xt=vector(1,ncom); 
     if (fptt < fp) {    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    f=(*nrfunc)(xt); 
       if (t < 0.0) {    free_vector(xt,1,ncom); 
         linmin(p,xit,n,fret,func);    return f; 
         for (j=1;j<=n;j++) {  } 
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];  /*****************brent *************************/
         }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
 #ifdef DEBUG  { 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    int iter; 
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    double a,b,d,etemp;
         for(j=1;j<=n;j++){    double fu,fv,fw,fx;
           printf(" %.12e",xit[j]);    double ftemp;
           fprintf(ficlog," %.12e",xit[j]);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
         }    double e=0.0; 
         printf("\n");   
         fprintf(ficlog,"\n");    a=(ax < cx ? ax : cx); 
 #endif    b=(ax > cx ? ax : cx); 
       }    x=w=v=bx; 
     }    fw=fv=fx=(*f)(x); 
   }    for (iter=1;iter<=ITMAX;iter++) { 
 }      xm=0.5*(a+b); 
       tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 /**** Prevalence limit ****************/      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       printf(".");fflush(stdout);
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      fprintf(ficlog,".");fflush(ficlog);
 {  #ifdef DEBUG
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      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);
      matrix by transitions matrix until convergence is reached */      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);
       /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   int i, ii,j,k;  #endif
   double min, max, maxmin, maxmax,sumnew=0.;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   double **matprod2();        *xmin=x; 
   double **out, cov[NCOVMAX], **pmij();        return fx; 
   double **newm;      } 
   double agefin, delaymax=50 ; /* Max number of years to converge */      ftemp=fu;
       if (fabs(e) > tol1) { 
   for (ii=1;ii<=nlstate+ndeath;ii++)        r=(x-w)*(fx-fv); 
     for (j=1;j<=nlstate+ndeath;j++){        q=(x-v)*(fx-fw); 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        p=(x-v)*q-(x-w)*r; 
     }        q=2.0*(q-r); 
         if (q > 0.0) p = -p; 
    cov[1]=1.;        q=fabs(q); 
          etemp=e; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        e=d; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     newm=savm;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     /* Covariates have to be included here again */        else { 
      cov[2]=agefin;          d=p/q; 
            u=x+d; 
       for (k=1; k<=cptcovn;k++) {          if (u-a < tol2 || b-u < tol2) 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];            d=SIGN(tol1,xm-x); 
         /*      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]]);*/        } 
       }      } else { 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       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]]];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       fu=(*f)(u); 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      if (fu <= fx) { 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        if (u >= x) a=x; else b=x; 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/        SHFT(v,w,x,u) 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);          SHFT(fv,fw,fx,fu) 
           } else { 
     savm=oldm;            if (u < x) a=u; else b=u; 
     oldm=newm;            if (fu <= fw || w == x) { 
     maxmax=0.;              v=w; 
     for(j=1;j<=nlstate;j++){              w=u; 
       min=1.;              fv=fw; 
       max=0.;              fw=fu; 
       for(i=1; i<=nlstate; i++) {            } else if (fu <= fv || v == x || v == w) { 
         sumnew=0;              v=u; 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];              fv=fu; 
         prlim[i][j]= newm[i][j]/(1-sumnew);            } 
         max=FMAX(max,prlim[i][j]);          } 
         min=FMIN(min,prlim[i][j]);    } 
       }    nrerror("Too many iterations in brent"); 
       maxmin=max-min;    *xmin=x; 
       maxmax=FMAX(maxmax,maxmin);    return fx; 
     }  } 
     if(maxmax < ftolpl){  
       return prlim;  /****************** mnbrak ***********************/
     }  
   }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
 }              double (*func)(double)) 
   { 
 /*************** transition probabilities ***************/    double ulim,u,r,q, dum;
     double fu; 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )   
 {    *fa=(*func)(*ax); 
   double s1, s2;    *fb=(*func)(*bx); 
   /*double t34;*/    if (*fb > *fa) { 
   int i,j,j1, nc, ii, jj;      SHFT(dum,*ax,*bx,dum) 
         SHFT(dum,*fb,*fa,dum) 
     for(i=1; i<= nlstate; i++){        } 
     for(j=1; j<i;j++){    *cx=(*bx)+GOLD*(*bx-*ax); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    *fc=(*func)(*cx); 
         /*s2 += param[i][j][nc]*cov[nc];*/    while (*fb > *fc) { 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      r=(*bx-*ax)*(*fb-*fc); 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      q=(*bx-*cx)*(*fb-*fa); 
       }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       ps[i][j]=s2;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     }      if ((*bx-u)*(u-*cx) > 0.0) { 
     for(j=i+1; j<=nlstate+ndeath;j++){        fu=(*func)(u); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        fu=(*func)(u); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        if (fu < *fc) { 
       }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       ps[i][j]=s2;            SHFT(*fb,*fc,fu,(*func)(u)) 
     }            } 
   }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     /*ps[3][2]=1;*/        u=ulim; 
         fu=(*func)(u); 
   for(i=1; i<= nlstate; i++){      } else { 
      s1=0;        u=(*cx)+GOLD*(*cx-*bx); 
     for(j=1; j<i; j++)        fu=(*func)(u); 
       s1+=exp(ps[i][j]);      } 
     for(j=i+1; j<=nlstate+ndeath; j++)      SHFT(*ax,*bx,*cx,u) 
       s1+=exp(ps[i][j]);        SHFT(*fa,*fb,*fc,fu) 
     ps[i][i]=1./(s1+1.);        } 
     for(j=1; j<i; j++)  } 
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     for(j=i+1; j<=nlstate+ndeath; j++)  /*************** linmin ************************/
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  int ncom; 
   } /* end i */  double *pcom,*xicom;
   double (*nrfunc)(double []); 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){   
     for(jj=1; jj<= nlstate+ndeath; jj++){  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       ps[ii][jj]=0;  { 
       ps[ii][ii]=1;    double brent(double ax, double bx, double cx, 
     }                 double (*f)(double), double tol, double *xmin); 
   }    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    int j; 
     for(jj=1; jj<= nlstate+ndeath; jj++){    double xx,xmin,bx,ax; 
      printf("%lf ",ps[ii][jj]);    double fx,fb,fa;
    }   
     printf("\n ");    ncom=n; 
     }    pcom=vector(1,n); 
     printf("\n ");printf("%lf ",cov[2]);*/    xicom=vector(1,n); 
 /*    nrfunc=func; 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    for (j=1;j<=n;j++) { 
   goto end;*/      pcom[j]=p[j]; 
     return ps;      xicom[j]=xi[j]; 
 }    } 
     ax=0.0; 
 /**************** Product of 2 matrices ******************/    xx=1.0; 
     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 {  #ifdef DEBUG
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   /* in, b, out are matrice of pointers which should have been initialized  #endif
      before: only the contents of out is modified. The function returns    for (j=1;j<=n;j++) { 
      a pointer to pointers identical to out */      xi[j] *= xmin; 
   long i, j, k;      p[j] += xi[j]; 
   for(i=nrl; i<= nrh; i++)    } 
     for(k=ncolol; k<=ncoloh; k++)    free_vector(xicom,1,n); 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    free_vector(pcom,1,n); 
         out[i][k] +=in[i][j]*b[j][k];  } 
   
   return out;  char *asc_diff_time(long time_sec, char ascdiff[])
 }  {
     long sec_left, days, hours, minutes;
     days = (time_sec) / (60*60*24);
 /************* Higher Matrix Product ***************/    sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    sec_left = (sec_left) %(60*60);
 {    minutes = (sec_left) /60;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    sec_left = (sec_left) % (60);
      duration (i.e. until    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    return ascdiff;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  }
      (typically every 2 years instead of every month which is too big).  
      Model is determined by parameters x and covariates have to be  /*************** powell ************************/
      included manually here.  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               double (*func)(double [])) 
      */  { 
     void linmin(double p[], double xi[], int n, double *fret, 
   int i, j, d, h, k;                double (*func)(double [])); 
   double **out, cov[NCOVMAX];    int i,ibig,j; 
   double **newm;    double del,t,*pt,*ptt,*xit;
     double fp,fptt;
   /* Hstepm could be zero and should return the unit matrix */    double *xits;
   for (i=1;i<=nlstate+ndeath;i++)    int niterf, itmp;
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);    pt=vector(1,n); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);    ptt=vector(1,n); 
     }    xit=vector(1,n); 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    xits=vector(1,n); 
   for(h=1; h <=nhstepm; h++){    *fret=(*func)(p); 
     for(d=1; d <=hstepm; d++){    for (j=1;j<=n;j++) pt[j]=p[j]; 
       newm=savm;    for (*iter=1;;++(*iter)) { 
       /* Covariates have to be included here again */      fp=(*fret); 
       cov[1]=1.;      ibig=0; 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      del=0.0; 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      last_time=curr_time;
       for (k=1; k<=cptcovage;k++)      (void) gettimeofday(&curr_time,&tzp);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      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);
       for (k=1; k<=cptcovprod;k++)      /*    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);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       */
      for (i=1;i<=n;i++) {
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        printf(" %d %.12f",i, p[i]);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        fprintf(ficlog," %d %.12lf",i, p[i]);
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        fprintf(ficrespow," %.12lf", p[i]);
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      }
       savm=oldm;      printf("\n");
       oldm=newm;      fprintf(ficlog,"\n");
     }      fprintf(ficrespow,"\n");fflush(ficrespow);
     for(i=1; i<=nlstate+ndeath; i++)      if(*iter <=3){
       for(j=1;j<=nlstate+ndeath;j++) {        tm = *localtime(&curr_time.tv_sec);
         po[i][j][h]=newm[i][j];        strcpy(strcurr,asctime(&tm));
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  /*       asctime_r(&tm,strcurr); */
          */        forecast_time=curr_time; 
       }        itmp = strlen(strcurr);
   } /* end h */        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   return po;          strcurr[itmp-1]='\0';
 }        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);
         for(niterf=10;niterf<=30;niterf+=10){
 /*************** log-likelihood *************/          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
 double func( double *x)          tmf = *localtime(&forecast_time.tv_sec);
 {  /*      asctime_r(&tmf,strfor); */
   int i, ii, j, k, mi, d, kk;          strcpy(strfor,asctime(&tmf));
   double l, ll[NLSTATEMAX], cov[NCOVMAX];          itmp = strlen(strfor);
   double **out;          if(strfor[itmp-1]=='\n')
   double sw; /* Sum of weights */          strfor[itmp-1]='\0';
   double lli; /* Individual log likelihood */          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);
   long ipmx;          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);
   /*extern weight */        }
   /* We are differentiating ll according to initial status */      }
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      for (i=1;i<=n;i++) { 
   /*for(i=1;i<imx;i++)        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     printf(" %d\n",s[4][i]);        fptt=(*fret); 
   */  #ifdef DEBUG
   cov[1]=1.;        printf("fret=%lf \n",*fret);
         fprintf(ficlog,"fret=%lf \n",*fret);
   for(k=1; k<=nlstate; k++) ll[k]=0.;  #endif
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        printf("%d",i);fflush(stdout);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        fprintf(ficlog,"%d",i);fflush(ficlog);
     for(mi=1; mi<= wav[i]-1; mi++){        linmin(p,xit,n,fret,func); 
       for (ii=1;ii<=nlstate+ndeath;ii++)        if (fabs(fptt-(*fret)) > del) { 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          del=fabs(fptt-(*fret)); 
       for(d=0; d<dh[mi][i]; d++){          ibig=i; 
         newm=savm;        } 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  #ifdef DEBUG
         for (kk=1; kk<=cptcovage;kk++) {        printf("%d %.12e",i,(*fret));
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        fprintf(ficlog,"%d %.12e",i,(*fret));
         }        for (j=1;j<=n;j++) {
                  xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,          printf(" x(%d)=%.12e",j,xit[j]);
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         savm=oldm;        }
         oldm=newm;        for(j=1;j<=n;j++) {
                  printf(" p=%.12e",p[j]);
                  fprintf(ficlog," p=%.12e",p[j]);
       } /* end mult */        }
              printf("\n");
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        fprintf(ficlog,"\n");
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  #endif
       ipmx +=1;      } 
       sw += weight[i];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  #ifdef DEBUG
     } /* end of wave */        int k[2],l;
   } /* end of individual */        k[0]=1;
         k[1]=-1;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        printf("Max: %.12e",(*func)(p));
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        fprintf(ficlog,"Max: %.12e",(*func)(p));
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        for (j=1;j<=n;j++) {
   return -l;          printf(" %.12e",p[j]);
 }          fprintf(ficlog," %.12e",p[j]);
         }
         printf("\n");
 /*********** Maximum Likelihood Estimation ***************/        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))          for (j=1;j<=n;j++) {
 {            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   int i,j, iter;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   double **xi,*delti;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   double fret;          }
   xi=matrix(1,npar,1,npar);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   for (i=1;i<=npar;i++)          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for (j=1;j<=npar;j++)        }
       xi[i][j]=(i==j ? 1.0 : 0.0);  #endif
   printf("Powell\n");  fprintf(ficlog,"Powell\n");  
   powell(p,xi,npar,ftol,&iter,&fret,func);  
         free_vector(xit,1,n); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        free_vector(xits,1,n); 
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        free_vector(ptt,1,n); 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        free_vector(pt,1,n); 
         return; 
 }      } 
       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 /**** Computes Hessian and covariance matrix ***/      for (j=1;j<=n;j++) { 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        ptt[j]=2.0*p[j]-pt[j]; 
 {        xit[j]=p[j]-pt[j]; 
   double  **a,**y,*x,pd;        pt[j]=p[j]; 
   double **hess;      } 
   int i, j,jk;      fptt=(*func)(ptt); 
   int *indx;      if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   double hessii(double p[], double delta, int theta, double delti[]);        if (t < 0.0) { 
   double hessij(double p[], double delti[], int i, int j);          linmin(p,xit,n,fret,func); 
   void lubksb(double **a, int npar, int *indx, double b[]) ;          for (j=1;j<=n;j++) { 
   void ludcmp(double **a, int npar, int *indx, double *d) ;            xi[j][ibig]=xi[j][n]; 
             xi[j][n]=xit[j]; 
   hess=matrix(1,npar,1,npar);          }
   #ifdef DEBUG
   printf("\nCalculation of the hessian matrix. Wait...\n");          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   for (i=1;i<=npar;i++){          for(j=1;j<=n;j++){
     printf("%d",i);fflush(stdout);            printf(" %.12e",xit[j]);
     fprintf(ficlog,"%d",i);fflush(ficlog);            fprintf(ficlog," %.12e",xit[j]);
     hess[i][i]=hessii(p,ftolhess,i,delti);          }
     /*printf(" %f ",p[i]);*/          printf("\n");
     /*printf(" %lf ",hess[i][i]);*/          fprintf(ficlog,"\n");
   }  #endif
          }
   for (i=1;i<=npar;i++) {      } 
     for (j=1;j<=npar;j++)  {    } 
       if (j>i) {  } 
         printf(".%d%d",i,j);fflush(stdout);  
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);  /**** Prevalence limit (stable prevalence)  ****************/
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];      double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         /*printf(" %lf ",hess[i][j]);*/  {
       }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     }       matrix by transitions matrix until convergence is reached */
   }  
   printf("\n");    int i, ii,j,k;
   fprintf(ficlog,"\n");    double min, max, maxmin, maxmax,sumnew=0.;
     double **matprod2();
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    double **out, cov[NCOVMAX], **pmij();
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");    double **newm;
      double agefin, delaymax=50 ; /* Max number of years to converge */
   a=matrix(1,npar,1,npar);  
   y=matrix(1,npar,1,npar);    for (ii=1;ii<=nlstate+ndeath;ii++)
   x=vector(1,npar);      for (j=1;j<=nlstate+ndeath;j++){
   indx=ivector(1,npar);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (i=1;i<=npar;i++)      }
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  
   ludcmp(a,npar,indx,&pd);     cov[1]=1.;
    
   for (j=1;j<=npar;j++) {   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for (i=1;i<=npar;i++) x[i]=0;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     x[j]=1;      newm=savm;
     lubksb(a,npar,indx,x);      /* Covariates have to be included here again */
     for (i=1;i<=npar;i++){       cov[2]=agefin;
       matcov[i][j]=x[i];    
     }        for (k=1; k<=cptcovn;k++) {
   }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
   printf("\n#Hessian matrix#\n");        }
   fprintf(ficlog,"\n#Hessian matrix#\n");        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   for (i=1;i<=npar;i++) {        for (k=1; k<=cptcovprod;k++)
     for (j=1;j<=npar;j++) {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       printf("%.3e ",hess[i][j]);  
       fprintf(ficlog,"%.3e ",hess[i][j]);        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     }        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     printf("\n");        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     fprintf(ficlog,"\n");      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   }  
       savm=oldm;
   /* Recompute Inverse */      oldm=newm;
   for (i=1;i<=npar;i++)      maxmax=0.;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      for(j=1;j<=nlstate;j++){
   ludcmp(a,npar,indx,&pd);        min=1.;
         max=0.;
   /*  printf("\n#Hessian matrix recomputed#\n");        for(i=1; i<=nlstate; i++) {
           sumnew=0;
   for (j=1;j<=npar;j++) {          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     for (i=1;i<=npar;i++) x[i]=0;          prlim[i][j]= newm[i][j]/(1-sumnew);
     x[j]=1;          max=FMAX(max,prlim[i][j]);
     lubksb(a,npar,indx,x);          min=FMIN(min,prlim[i][j]);
     for (i=1;i<=npar;i++){        }
       y[i][j]=x[i];        maxmin=max-min;
       printf("%.3e ",y[i][j]);        maxmax=FMAX(maxmax,maxmin);
       fprintf(ficlog,"%.3e ",y[i][j]);      }
     }      if(maxmax < ftolpl){
     printf("\n");        return prlim;
     fprintf(ficlog,"\n");      }
   }    }
   */  }
   
   free_matrix(a,1,npar,1,npar);  /*************** transition probabilities ***************/ 
   free_matrix(y,1,npar,1,npar);  
   free_vector(x,1,npar);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   free_ivector(indx,1,npar);  {
   free_matrix(hess,1,npar,1,npar);    double s1, s2;
     /*double t34;*/
     int i,j,j1, nc, ii, jj;
 }  
       for(i=1; i<= nlstate; i++){
 /*************** hessian matrix ****************/        for(j=1; j<i;j++){
 double hessii( double x[], double delta, int theta, double delti[])          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 {            /*s2 += param[i][j][nc]*cov[nc];*/
   int i;            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   int l=1, lmax=20;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
   double k1,k2;          }
   double p2[NPARMAX+1];          ps[i][j]=s2;
   double res;  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        }
   double fx;        for(j=i+1; j<=nlstate+ndeath;j++){
   int k=0,kmax=10;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   double l1;            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); */
   fx=func(x);          }
   for (i=1;i<=npar;i++) p2[i]=x[i];          ps[i][j]=s2;
   for(l=0 ; l <=lmax; l++){        }
     l1=pow(10,l);      }
     delts=delt;      /*ps[3][2]=1;*/
     for(k=1 ; k <kmax; k=k+1){      
       delt = delta*(l1*k);      for(i=1; i<= nlstate; i++){
       p2[theta]=x[theta] +delt;        s1=0;
       k1=func(p2)-fx;        for(j=1; j<i; j++)
       p2[theta]=x[theta]-delt;          s1+=exp(ps[i][j]);
       k2=func(p2)-fx;        for(j=i+1; j<=nlstate+ndeath; j++)
       /*res= (k1-2.0*fx+k2)/delt/delt; */          s1+=exp(ps[i][j]);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        ps[i][i]=1./(s1+1.);
              for(j=1; j<i; j++)
 #ifdef DEBUG          ps[i][j]= exp(ps[i][j])*ps[i][i];
       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(j=i+1; j<=nlstate+ndeath; 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);          ps[i][j]= exp(ps[i][j])*ps[i][i];
 #endif        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      } /* end i */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      
         k=kmax;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       }        for(jj=1; jj<= nlstate+ndeath; jj++){
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          ps[ii][jj]=0;
         k=kmax; l=lmax*10.;          ps[ii][ii]=1;
       }        }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      }
         delts=delt;      
       }  
     }  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   }  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   delti[theta]=delts;  /*         printf("ddd %lf ",ps[ii][jj]); */
   return res;  /*       } */
    /*       printf("\n "); */
 }  /*        } */
   /*        printf("\n ");printf("%lf ",cov[2]); */
 double hessij( double x[], double delti[], int thetai,int thetaj)         /*
 {        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   int i;        goto end;*/
   int l=1, l1, lmax=20;      return ps;
   double k1,k2,k3,k4,res,fx;  }
   double p2[NPARMAX+1];  
   int k;  /**************** Product of 2 matrices ******************/
   
   fx=func(x);  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   for (k=1; k<=2; k++) {  {
     for (i=1;i<=npar;i++) p2[i]=x[i];    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     p2[thetai]=x[thetai]+delti[thetai]/k;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    /* in, b, out are matrice of pointers which should have been initialized 
     k1=func(p2)-fx;       before: only the contents of out is modified. The function returns
         a pointer to pointers identical to out */
     p2[thetai]=x[thetai]+delti[thetai]/k;    long i, j, k;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    for(i=nrl; i<= nrh; i++)
     k2=func(p2)-fx;      for(k=ncolol; k<=ncoloh; k++)
          for(j=ncl,out[i][k]=0.; j<=nch; j++)
     p2[thetai]=x[thetai]-delti[thetai]/k;          out[i][k] +=in[i][j]*b[j][k];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k3=func(p2)-fx;    return out;
    }
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k4=func(p2)-fx;  /************* Higher Matrix Product ***************/
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  
 #ifdef DEBUG  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  {
     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);    /* Computes the transition matrix starting at age 'age' over 
 #endif       'nhstepm*hstepm*stepm' months (i.e. until
   }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   return res;       nhstepm*hstepm matrices. 
 }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        (typically every 2 years instead of every month which is too big 
 /************** Inverse of matrix **************/       for the memory).
 void ludcmp(double **a, int n, int *indx, double *d)       Model is determined by parameters x and covariates have to be 
 {       included manually here. 
   int i,imax,j,k;  
   double big,dum,sum,temp;       */
   double *vv;  
      int i, j, d, h, k;
   vv=vector(1,n);    double **out, cov[NCOVMAX];
   *d=1.0;    double **newm;
   for (i=1;i<=n;i++) {  
     big=0.0;    /* Hstepm could be zero and should return the unit matrix */
     for (j=1;j<=n;j++)    for (i=1;i<=nlstate+ndeath;i++)
       if ((temp=fabs(a[i][j])) > big) big=temp;      for (j=1;j<=nlstate+ndeath;j++){
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        oldm[i][j]=(i==j ? 1.0 : 0.0);
     vv[i]=1.0/big;        po[i][j][0]=(i==j ? 1.0 : 0.0);
   }      }
   for (j=1;j<=n;j++) {    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for (i=1;i<j;i++) {    for(h=1; h <=nhstepm; h++){
       sum=a[i][j];      for(d=1; d <=hstepm; d++){
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        newm=savm;
       a[i][j]=sum;        /* Covariates have to be included here again */
     }        cov[1]=1.;
     big=0.0;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     for (i=j;i<=n;i++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       sum=a[i][j];        for (k=1; k<=cptcovage;k++)
       for (k=1;k<j;k++)          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         sum -= a[i][k]*a[k][j];        for (k=1; k<=cptcovprod;k++)
       a[i][j]=sum;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       if ( (dum=vv[i]*fabs(sum)) >= big) {  
         big=dum;  
         imax=i;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     }        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     if (j != imax) {                     pmij(pmmij,cov,ncovmodel,x,nlstate));
       for (k=1;k<=n;k++) {        savm=oldm;
         dum=a[imax][k];        oldm=newm;
         a[imax][k]=a[j][k];      }
         a[j][k]=dum;      for(i=1; i<=nlstate+ndeath; i++)
       }        for(j=1;j<=nlstate+ndeath;j++) {
       *d = -(*d);          po[i][j][h]=newm[i][j];
       vv[imax]=vv[j];          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     }           */
     indx[j]=imax;        }
     if (a[j][j] == 0.0) a[j][j]=TINY;    } /* end h */
     if (j != n) {    return po;
       dum=1.0/(a[j][j]);  }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }  
   }  /*************** log-likelihood *************/
   free_vector(vv,1,n);  /* Doesn't work */  double func( double *x)
 ;  {
 }    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
 void lubksb(double **a, int n, int *indx, double b[])    double **out;
 {    double sw; /* Sum of weights */
   int i,ii=0,ip,j;    double lli; /* Individual log likelihood */
   double sum;    int s1, s2;
      double bbh, survp;
   for (i=1;i<=n;i++) {    long ipmx;
     ip=indx[i];    /*extern weight */
     sum=b[ip];    /* We are differentiating ll according to initial status */
     b[ip]=b[i];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     if (ii)    /*for(i=1;i<imx;i++) 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      printf(" %d\n",s[4][i]);
     else if (sum) ii=i;    */
     b[i]=sum;    cov[1]=1.;
   }  
   for (i=n;i>=1;i--) {    for(k=1; k<=nlstate; k++) ll[k]=0.;
     sum=b[i];  
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    if(mle==1){
     b[i]=sum/a[i][i];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 }        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
 /************ Frequencies ********************/            for (j=1;j<=nlstate+ndeath;j++){
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 {  /* Some frequencies */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          for(d=0; d<dh[mi][i]; d++){
   int first;            newm=savm;
   double ***freq; /* Frequencies */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double *pp;            for (kk=1; kk<=cptcovage;kk++) {
   double pos, k2, dateintsum=0,k2cpt=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   FILE *ficresp;            }
   char fileresp[FILENAMELENGTH];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   pp=vector(1,nlstate);            savm=oldm;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            oldm=newm;
   strcpy(fileresp,"p");          } /* end mult */
   strcat(fileresp,fileres);        
   if((ficresp=fopen(fileresp,"w"))==NULL) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     printf("Problem with prevalence resultfile: %s\n", fileresp);          /* But now since version 0.9 we anticipate for bias at large stepm.
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     exit(0);           * (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
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   j1=0;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
             * probability in order to take into account the bias as a fraction of the way
   j=cptcoveff;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   if (cptcovn<1) {j=1;ncodemax[1]=1;}           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
   first=1;           * For stepm > 1 the results are less biased than in previous versions. 
            */
   for(k1=1; k1<=j;k1++){          s1=s[mw[mi][i]][i];
     for(i1=1; i1<=ncodemax[k1];i1++){          s2=s[mw[mi+1][i]][i];
       j1++;          bbh=(double)bh[mi][i]/(double)stepm; 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          /* bias bh is positive if real duration
         scanf("%d", i);*/           * is higher than the multiple of stepm and negative otherwise.
       for (i=-1; i<=nlstate+ndeath; i++)             */
         for (jk=-1; jk<=nlstate+ndeath; jk++)            /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           for(m=agemin; m <= agemax+3; m++)          if( s2 > nlstate){ 
             freq[i][jk][m]=0;            /* i.e. if s2 is a death state and if the date of death is known 
                     then the contribution to the likelihood is the probability to 
       dateintsum=0;               die between last step unit time and current  step unit time, 
       k2cpt=0;               which is also equal to probability to die before dh 
       for (i=1; i<=imx; i++) {               minus probability to die before dh-stepm . 
         bool=1;               In version up to 0.92 likelihood was computed
         if  (cptcovn>0) {          as if date of death was unknown. Death was treated as any other
           for (z1=1; z1<=cptcoveff; z1++)          health state: the date of the interview describes the actual state
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          and not the date of a change in health state. The former idea was
               bool=0;          to consider that at each interview the state was recorded
         }          (healthy, disable or death) and IMaCh was corrected; but when we
         if (bool==1) {          introduced the exact date of death then we should have modified
           for(m=firstpass; m<=lastpass; m++){          the contribution of an exact death to the likelihood. This new
             k2=anint[m][i]+(mint[m][i]/12.);          contribution is smaller and very dependent of the step unit
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          stepm. It is no more the probability to die between last interview
               if(agev[m][i]==0) agev[m][i]=agemax+1;          and month of death but the probability to survive from last
               if(agev[m][i]==1) agev[m][i]=agemax+2;          interview up to one month before death multiplied by the
               if (m<lastpass) {          probability to die within a month. Thanks to Chris
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          Jackson for correcting this bug.  Former versions increased
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          mortality artificially. The bad side is that we add another loop
               }          which slows down the processing. The difference can be up to 10%
                        lower mortality.
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {            */
                 dateintsum=dateintsum+k2;            lli=log(out[s1][s2] - savm[s1][s2]);
                 k2cpt++;  
               }  
             }          } else if  (s2==-2) {
           }            for (j=1,survp=0. ; j<=nlstate; j++) 
         }              survp += out[s1][j];
       }            lli= survp;
                  }
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
   
       if  (cptcovn>0) {          else{
         fprintf(ficresp, "\n#********** Variable ");            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
         fprintf(ficresp, "**********\n#");          } 
       }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       for(i=1; i<=nlstate;i++)          /*if(lli ==000.0)*/
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          /*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); */
       fprintf(ficresp, "\n");          ipmx +=1;
                sw += weight[i];
       for(i=(int)agemin; i <= (int)agemax+3; i++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         if(i==(int)agemax+3){        } /* end of wave */
           fprintf(ficlog,"Total");      } /* end of individual */
         }else{    }  else if(mle==2){
           if(first==1){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             first=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             printf("See log file for details...\n");        for(mi=1; mi<= wav[i]-1; mi++){
           }          for (ii=1;ii<=nlstate+ndeath;ii++)
           fprintf(ficlog,"Age %d", i);            for (j=1;j<=nlstate+ndeath;j++){
         }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(jk=1; jk <=nlstate ; jk++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            }
             pp[jk] += freq[jk][m][i];          for(d=0; d<=dh[mi][i]; d++){
         }            newm=savm;
         for(jk=1; jk <=nlstate ; jk++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for(m=-1, pos=0; m <=0 ; m++)            for (kk=1; kk<=cptcovage;kk++) {
             pos += freq[jk][m][i];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           if(pp[jk]>=1.e-10){            }
             if(first==1){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             }            savm=oldm;
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            oldm=newm;
           }else{          } /* end mult */
             if(first==1)        
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          s1=s[mw[mi][i]][i];
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          s2=s[mw[mi+1][i]][i];
           }          bbh=(double)bh[mi][i]/(double)stepm; 
         }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           ipmx +=1;
         for(jk=1; jk <=nlstate ; jk++){          sw += weight[i];
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             pp[jk] += freq[jk][m][i];        } /* end of wave */
         }      } /* end of individual */
     }  else if(mle==3){  /* exponential inter-extrapolation */
         for(jk=1,pos=0; jk <=nlstate ; jk++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           pos += pp[jk];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(jk=1; jk <=nlstate ; jk++){        for(mi=1; mi<= wav[i]-1; mi++){
           if(pos>=1.e-5){          for (ii=1;ii<=nlstate+ndeath;ii++)
             if(first==1)            for (j=1;j<=nlstate+ndeath;j++){
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }else{            }
             if(first==1)          for(d=0; d<dh[mi][i]; d++){
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            newm=savm;
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           }            for (kk=1; kk<=cptcovage;kk++) {
           if( i <= (int) agemax){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             if(pos>=1.e-5){            }
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
               probs[i][jk][j1]= pp[jk]/pos;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/            savm=oldm;
             }            oldm=newm;
             else          } /* end mult */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        
           }          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+ndeath; jk++)          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 */
           for(m=-1; m <=nlstate+ndeath; m++)          ipmx +=1;
             if(freq[jk][m][i] !=0 ) {          sw += weight[i];
             if(first==1)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        } /* end of wave */
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);      } /* end of individual */
             }    }else if (mle==4){  /* ml=4 no inter-extrapolation */
         if(i <= (int) agemax)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           fprintf(ficresp,"\n");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         if(first==1)        for(mi=1; mi<= wav[i]-1; mi++){
           printf("Others in log...\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
         fprintf(ficlog,"\n");            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);
   }            }
   dateintmean=dateintsum/k2cpt;          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
   fclose(ficresp);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            for (kk=1; kk<=cptcovage;kk++) {
   free_vector(pp,1,nlstate);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
   /* End of Freq */          
 }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 /************ Prevalence ********************/            savm=oldm;
 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)            oldm=newm;
 {  /* Some frequencies */          } /* end mult */
          
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          s1=s[mw[mi][i]][i];
   double ***freq; /* Frequencies */          s2=s[mw[mi+1][i]][i];
   double *pp;          if( s2 > nlstate){ 
   double pos, k2;            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
   pp=vector(1,nlstate);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
            ipmx +=1;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          sw += weight[i];
   j1=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
    /*      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]); */
   j=cptcoveff;        } /* end of wave */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      } /* end of individual */
      }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   for(k1=1; k1<=j;k1++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(i1=1; i1<=ncodemax[k1];i1++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       j1++;        for(mi=1; mi<= wav[i]-1; mi++){
                for (ii=1;ii<=nlstate+ndeath;ii++)
       for (i=-1; i<=nlstate+ndeath; i++)              for (j=1;j<=nlstate+ndeath;j++){
         for (jk=-1; jk<=nlstate+ndeath; jk++)                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(m=agemin; m <= agemax+3; m++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             freq[i][jk][m]=0;            }
                for(d=0; d<dh[mi][i]; d++){
       for (i=1; i<=imx; i++) {            newm=savm;
         bool=1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         if  (cptcovn>0) {            for (kk=1; kk<=cptcovage;kk++) {
           for (z1=1; z1<=cptcoveff; z1++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            }
               bool=0;          
         }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         if (bool==1) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           for(m=firstpass; m<=lastpass; m++){            savm=oldm;
             k2=anint[m][i]+(mint[m][i]/12.);            oldm=newm;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          } /* end mult */
               if(agev[m][i]==0) agev[m][i]=agemax+1;        
               if(agev[m][i]==1) agev[m][i]=agemax+2;          s1=s[mw[mi][i]][i];
               if (m<lastpass) {          s2=s[mw[mi+1][i]][i];
                 if (calagedate>0)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          ipmx +=1;
                 else          sw += weight[i];
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
               }        } /* end of wave */
             }      } /* end of individual */
           }    } /* End of if */
         }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       for(i=(int)agemin; i <= (int)agemax+3; i++){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         for(jk=1; jk <=nlstate ; jk++){    return -l;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  }
             pp[jk] += freq[jk][m][i];  
         }  /*************** log-likelihood *************/
         for(jk=1; jk <=nlstate ; jk++){  double funcone( double *x)
           for(m=-1, pos=0; m <=0 ; m++)  {
             pos += freq[jk][m][i];    /* Same as likeli but slower because of a lot of printf and if */
         }    int i, ii, j, k, mi, d, kk;
            double l, ll[NLSTATEMAX], cov[NCOVMAX];
         for(jk=1; jk <=nlstate ; jk++){    double **out;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    double lli; /* Individual log likelihood */
             pp[jk] += freq[jk][m][i];    double llt;
         }    int s1, s2;
            double bbh, survp;
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    /*extern weight */
            /* We are differentiating ll according to initial status */
         for(jk=1; jk <=nlstate ; jk++){        /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           if( i <= (int) agemax){    /*for(i=1;i<imx;i++) 
             if(pos>=1.e-5){      printf(" %d\n",s[4][i]);
               probs[i][jk][j1]= pp[jk]/pos;    */
             }    cov[1]=1.;
           }  
         }/* end jk */    for(k=1; k<=nlstate; k++) ll[k]=0.;
       }/* end i */  
     } /* end i1 */    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   } /* end k1 */      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
          for (ii=1;ii<=nlstate+ndeath;ii++)
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          for (j=1;j<=nlstate+ndeath;j++){
   free_vector(pp,1,nlstate);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 }  /* End of Freq */          }
         for(d=0; d<dh[mi][i]; d++){
 /************* Waves Concatenation ***************/          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          for (kk=1; kk<=cptcovage;kk++) {
 {            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          }
      Death is a valid wave (if date is known).          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          savm=oldm;
      and mw[mi+1][i]. dh depends on stepm.          oldm=newm;
      */        } /* end mult */
         
   int i, mi, m;        s1=s[mw[mi][i]][i];
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        s2=s[mw[mi+1][i]][i];
      double sum=0., jmean=0.;*/        bbh=(double)bh[mi][i]/(double)stepm; 
   int first;        /* bias is positive if real duration
   int j, k=0,jk, ju, jl;         * is higher than the multiple of stepm and negative otherwise.
   double sum=0.;         */
   first=0;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   jmin=1e+5;          lli=log(out[s1][s2] - savm[s1][s2]);
   jmax=-1;        } else if (mle==1){
   jmean=0.;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   for(i=1; i<=imx; i++){        } else if(mle==2){
     mi=0;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     m=firstpass;        } else if(mle==3){  /* exponential inter-extrapolation */
     while(s[m][i] <= nlstate){          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 */
       if(s[m][i]>=1)        } else if (mle==4){  /* mle=4 no inter-extrapolation */
         mw[++mi][i]=m;          lli=log(out[s1][s2]); /* Original formula */
       if(m >=lastpass)        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
         break;          lli=log(out[s1][s2]); /* Original formula */
       else        } /* End of if */
         m++;        ipmx +=1;
     }/* end while */        sw += weight[i];
     if (s[m][i] > nlstate){        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       mi++;     /* Death is another wave */  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       /* if(mi==0)  never been interviewed correctly before death */        if(globpr){
          /* Only death is a correct wave */          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
       mw[mi][i]=m;   %10.6f %10.6f %10.6f ", \
     }                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                   2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     wav[i]=mi;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     if(mi==0){            llt +=ll[k]*gipmx/gsw;
       if(first==0){            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);          }
         first=1;          fprintf(ficresilk," %10.6f\n", -llt);
       }        }
       if(first==1){      } /* end of wave */
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);    } /* end of individual */
       }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     } /* end mi==0 */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if(globpr==0){ /* First time we count the contributions and weights */
   for(i=1; i<=imx; i++){      gipmx=ipmx;
     for(mi=1; mi<wav[i];mi++){      gsw=sw;
       if (stepm <=0)    }
         dh[mi][i]=1;    return -l;
       else{  }
         if (s[mw[mi+1][i]][i] > nlstate) {  
           if (agedc[i] < 2*AGESUP) {  
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  /*************** function likelione ***********/
           if(j==0) j=1;  /* Survives at least one month after exam */  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
           k=k+1;  {
           if (j >= jmax) jmax=j;    /* This routine should help understanding what is done with 
           if (j <= jmin) jmin=j;       the selection of individuals/waves and
           sum=sum+j;       to check the exact contribution to the likelihood.
           /*if (j<0) printf("j=%d num=%d \n",j,i); */       Plotting could be done.
           }     */
         }    int k;
         else{  
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    if(*globpri !=0){ /* Just counts and sums, no printings */
           k=k+1;      strcpy(fileresilk,"ilk"); 
           if (j >= jmax) jmax=j;      strcat(fileresilk,fileres);
           else if (j <= jmin)jmin=j;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        printf("Problem with resultfile: %s\n", fileresilk);
           sum=sum+j;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
         }      }
         jk= j/stepm;      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");
         jl= j -jk*stepm;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
         ju= j -(jk+1)*stepm;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
         if(jl <= -ju)      for(k=1; k<=nlstate; k++) 
           dh[mi][i]=jk;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
         else      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
           dh[mi][i]=jk+1;    }
         if(dh[mi][i]==0)  
           dh[mi][i]=1; /* At least one step */    *fretone=(*funcone)(p);
       }    if(*globpri !=0){
     }      fclose(ficresilk);
   }      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   jmean=sum/k;      fflush(fichtm); 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    } 
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    return;
  }  }
   
 /*********** Tricode ****************************/  
 void tricode(int *Tvar, int **nbcode, int imx)  /*********** Maximum Likelihood Estimation ***************/
 {  
   int Ndum[20],ij=1, k, j, i;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   int cptcode=0;  {
   cptcoveff=0;    int i,j, iter;
      double **xi;
   for (k=0; k<19; k++) Ndum[k]=0;    double fret;
   for (k=1; k<=7; k++) ncodemax[k]=0;    double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    xi=matrix(1,npar,1,npar);
     for (i=1; i<=imx; i++) {    for (i=1;i<=npar;i++)
       ij=(int)(covar[Tvar[j]][i]);      for (j=1;j<=npar;j++)
       Ndum[ij]++;        xi[i][j]=(i==j ? 1.0 : 0.0);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       if (ij > cptcode) cptcode=ij;    strcpy(filerespow,"pow"); 
     }    strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
     for (i=0; i<=cptcode; i++) {      printf("Problem with resultfile: %s\n", filerespow);
       if(Ndum[i]!=0) ncodemax[j]++;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }    }
     ij=1;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
     for (i=1; i<=ncodemax[j]; i++) {        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       for (k=0; k<=19; k++) {    fprintf(ficrespow,"\n");
         if (Ndum[k] != 0) {  
           nbcode[Tvar[j]][ij]=k;    powell(p,xi,npar,ftol,&iter,&fret,func);
            
           ij++;    fclose(ficrespow);
         }    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         if (ij > ncodemax[j]) break;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       }      fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     }  
   }    }
   
  for (k=0; k<19; k++) Ndum[k]=0;  /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
  for (i=1; i<=ncovmodel-2; i++) {  {
    ij=Tvar[i];    double  **a,**y,*x,pd;
    Ndum[ij]++;    double **hess;
  }    int i, j,jk;
     int *indx;
  ij=1;  
  for (i=1; i<=10; i++) {    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
    if((Ndum[i]!=0) && (i<=ncovcol)){    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
      Tvaraff[ij]=i;    void lubksb(double **a, int npar, int *indx, double b[]) ;
      ij++;    void ludcmp(double **a, int npar, int *indx, double *d) ;
    }    double gompertz(double p[]);
  }    hess=matrix(1,npar,1,npar);
    
  cptcoveff=ij-1;    printf("\nCalculation of the hessian matrix. Wait...\n");
 }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
 /*********** Health Expectancies ****************/      printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
 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 )     
        hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
 {      
   /* Health expectancies */      /*  printf(" %f ",p[i]);
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   double age, agelim, hf;    }
   double ***p3mat,***varhe;    
   double **dnewm,**doldm;    for (i=1;i<=npar;i++) {
   double *xp;      for (j=1;j<=npar;j++)  {
   double **gp, **gm;        if (j>i) { 
   double ***gradg, ***trgradg;          printf(".%d%d",i,j);fflush(stdout);
   int theta;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,delti,i,j,func,npar);
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);          
   xp=vector(1,npar);          hess[j][i]=hess[i][j];    
   dnewm=matrix(1,nlstate*2,1,npar);          /*printf(" %lf ",hess[i][j]);*/
   doldm=matrix(1,nlstate*2,1,nlstate*2);        }
        }
   fprintf(ficreseij,"# Health expectancies\n");    }
   fprintf(ficreseij,"# Age");    printf("\n");
   for(i=1; i<=nlstate;i++)    fprintf(ficlog,"\n");
     for(j=1; j<=nlstate;j++)  
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   fprintf(ficreseij,"\n");    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     
   if(estepm < stepm){    a=matrix(1,npar,1,npar);
     printf ("Problem %d lower than %d\n",estepm, stepm);    y=matrix(1,npar,1,npar);
   }    x=vector(1,npar);
   else  hstepm=estepm;      indx=ivector(1,npar);
   /* We compute the life expectancy from trapezoids spaced every estepm months    for (i=1;i<=npar;i++)
    * This is mainly to measure the difference between two models: for example      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
    * if stepm=24 months pijx are given only every 2 years and by summing them    ludcmp(a,npar,indx,&pd);
    * we are calculating an estimate of the Life Expectancy assuming a linear  
    * progression inbetween and thus overestimating or underestimating according    for (j=1;j<=npar;j++) {
    * to the curvature of the survival function. If, for the same date, we      for (i=1;i<=npar;i++) x[i]=0;
    * estimate the model with stepm=1 month, we can keep estepm to 24 months      x[j]=1;
    * to compare the new estimate of Life expectancy with the same linear      lubksb(a,npar,indx,x);
    * hypothesis. A more precise result, taking into account a more precise      for (i=1;i<=npar;i++){ 
    * curvature will be obtained if estepm is as small as stepm. */        matcov[i][j]=x[i];
       }
   /* For example we decided to compute the life expectancy with the smallest unit */    }
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.  
      nhstepm is the number of hstepm from age to agelim    printf("\n#Hessian matrix#\n");
      nstepm is the number of stepm from age to agelin.    fprintf(ficlog,"\n#Hessian matrix#\n");
      Look at hpijx to understand the reason of that which relies in memory size    for (i=1;i<=npar;i++) { 
      and note for a fixed period like estepm months */      for (j=1;j<=npar;j++) { 
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        printf("%.3e ",hess[i][j]);
      survival function given by stepm (the optimization length). Unfortunately it        fprintf(ficlog,"%.3e ",hess[i][j]);
      means that if the survival funtion is printed only each two years of age and if      }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      printf("\n");
      results. So we changed our mind and took the option of the best precision.      fprintf(ficlog,"\n");
   */    }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  
     /* Recompute Inverse */
   agelim=AGESUP;    for (i=1;i<=npar;i++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     /* nhstepm age range expressed in number of stepm */    ludcmp(a,npar,indx,&pd);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    /*  printf("\n#Hessian matrix recomputed#\n");
     /* if (stepm >= YEARM) hstepm=1;*/  
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    for (j=1;j<=npar;j++) {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (i=1;i<=npar;i++) x[i]=0;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);      x[j]=1;
     gp=matrix(0,nhstepm,1,nlstate*2);      lubksb(a,npar,indx,x);
     gm=matrix(0,nhstepm,1,nlstate*2);      for (i=1;i<=npar;i++){ 
         y[i][j]=x[i];
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        printf("%.3e ",y[i][j]);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        fprintf(ficlog,"%.3e ",y[i][j]);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        }
        printf("\n");
       fprintf(ficlog,"\n");
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    }
     */
     /* Computing Variances of health expectancies */  
     free_matrix(a,1,npar,1,npar);
      for(theta=1; theta <=npar; theta++){    free_matrix(y,1,npar,1,npar);
       for(i=1; i<=npar; i++){    free_vector(x,1,npar);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    free_ivector(indx,1,npar);
       }    free_matrix(hess,1,npar,1,npar);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
    
       cptj=0;  }
       for(j=1; j<= nlstate; j++){  
         for(i=1; i<=nlstate; i++){  /*************** hessian matrix ****************/
           cptj=cptj+1;  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){  {
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    int i;
           }    int l=1, lmax=20;
         }    double k1,k2;
       }    double p2[NPARMAX+1];
          double res;
          double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       for(i=1; i<=npar; i++)    double fx;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    int k=0,kmax=10;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      double l1;
        
       cptj=0;    fx=func(x);
       for(j=1; j<= nlstate; j++){    for (i=1;i<=npar;i++) p2[i]=x[i];
         for(i=1;i<=nlstate;i++){    for(l=0 ; l <=lmax; l++){
           cptj=cptj+1;      l1=pow(10,l);
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){      delts=delt;
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      for(k=1 ; k <kmax; k=k+1){
           }        delt = delta*(l1*k);
         }        p2[theta]=x[theta] +delt;
       }        k1=func(p2)-fx;
       for(j=1; j<= nlstate*2; j++)        p2[theta]=x[theta]-delt;
         for(h=0; h<=nhstepm-1; h++){        k2=func(p2)-fx;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        /*res= (k1-2.0*fx+k2)/delt/delt; */
         }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
      }        
      #ifdef DEBUG
 /* End 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);
         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);
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);  #endif
         /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
      for(h=0; h<=nhstepm-1; h++)        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       for(j=1; j<=nlstate*2;j++)          k=kmax;
         for(theta=1; theta <=npar; theta++)        }
           trgradg[h][j][theta]=gradg[h][theta][j];        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
                k=kmax; l=lmax*10.;
         }
      for(i=1;i<=nlstate*2;i++)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       for(j=1;j<=nlstate*2;j++)          delts=delt;
         varhe[i][j][(int)age] =0.;        }
       }
      printf("%d|",(int)age);fflush(stdout);    }
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);    delti[theta]=delts;
      for(h=0;h<=nhstepm-1;h++){    return res; 
       for(k=0;k<=nhstepm-1;k++){    
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);  }
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);  
         for(i=1;i<=nlstate*2;i++)  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
           for(j=1;j<=nlstate*2;j++)  {
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    int i;
       }    int l=1, l1, lmax=20;
     }    double k1,k2,k3,k4,res,fx;
     /* Computing expectancies */    double p2[NPARMAX+1];
     for(i=1; i<=nlstate;i++)    int k;
       for(j=1; j<=nlstate;j++)  
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    fx=func(x);
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    for (k=1; k<=2; k++) {
                for (i=1;i<=npar;i++) p2[i]=x[i];
 /* 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]);*/      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         }      k1=func(p2)-fx;
     
     fprintf(ficreseij,"%3.0f",age );      p2[thetai]=x[thetai]+delti[thetai]/k;
     cptj=0;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     for(i=1; i<=nlstate;i++)      k2=func(p2)-fx;
       for(j=1; j<=nlstate;j++){    
         cptj++;      p2[thetai]=x[thetai]-delti[thetai]/k;
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       }      k3=func(p2)-fx;
     fprintf(ficreseij,"\n");    
          p2[thetai]=x[thetai]-delti[thetai]/k;
     free_matrix(gm,0,nhstepm,1,nlstate*2);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     free_matrix(gp,0,nhstepm,1,nlstate*2);      k4=func(p2)-fx;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);  #ifdef DEBUG
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   }      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   printf("\n");  #endif
   fprintf(ficlog,"\n");    }
     return res;
   free_vector(xp,1,npar);  }
   free_matrix(dnewm,1,nlstate*2,1,npar);  
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);  /************** Inverse of matrix **************/
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);  void ludcmp(double **a, int n, int *indx, double *d) 
 }  { 
     int i,imax,j,k; 
 /************ Variance ******************/    double big,dum,sum,temp; 
 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)    double *vv; 
 {   
   /* Variance of health expectancies */    vv=vector(1,n); 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    *d=1.0; 
   /* double **newm;*/    for (i=1;i<=n;i++) { 
   double **dnewm,**doldm;      big=0.0; 
   double **dnewmp,**doldmp;      for (j=1;j<=n;j++) 
   int i, j, nhstepm, hstepm, h, nstepm ;        if ((temp=fabs(a[i][j])) > big) big=temp; 
   int k, cptcode;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   double *xp;      vv[i]=1.0/big; 
   double **gp, **gm;  /* for var eij */    } 
   double ***gradg, ***trgradg; /*for var eij */    for (j=1;j<=n;j++) { 
   double **gradgp, **trgradgp; /* for var p point j */      for (i=1;i<j;i++) { 
   double *gpp, *gmp; /* for var p point j */        sum=a[i][j]; 
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   double ***p3mat;        a[i][j]=sum; 
   double age,agelim, hf;      } 
   int theta;      big=0.0; 
   char digit[4];      for (i=j;i<=n;i++) { 
   char digitp[16];        sum=a[i][j]; 
         for (k=1;k<j;k++) 
   char fileresprobmorprev[FILENAMELENGTH];          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
   if(popbased==1)        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     strcpy(digitp,"-populbased-");          big=dum; 
   else          imax=i; 
     strcpy(digitp,"-stablbased-");        } 
       } 
   strcpy(fileresprobmorprev,"prmorprev");      if (j != imax) { 
   sprintf(digit,"%-d",ij);        for (k=1;k<=n;k++) { 
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/          dum=a[imax][k]; 
   strcat(fileresprobmorprev,digit); /* Tvar to be done */          a[imax][k]=a[j][k]; 
   strcat(fileresprobmorprev,digitp); /* Popbased or not */          a[j][k]=dum; 
   strcat(fileresprobmorprev,fileres);        } 
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {        *d = -(*d); 
     printf("Problem with resultfile: %s\n", fileresprobmorprev);        vv[imax]=vv[j]; 
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);      } 
   }      indx[j]=imax; 
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);      if (a[j][j] == 0.0) a[j][j]=TINY; 
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);      if (j != n) { 
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");        dum=1.0/(a[j][j]); 
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){      } 
     fprintf(ficresprobmorprev," p.%-d SE",j);    } 
     for(i=1; i<=nlstate;i++)    free_vector(vv,1,n);  /* Doesn't work */
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);  ;
   }    } 
   fprintf(ficresprobmorprev,"\n");  
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {  void lubksb(double **a, int n, int *indx, double b[]) 
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);  { 
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);    int i,ii=0,ip,j; 
     exit(0);    double sum; 
   }   
   else{    for (i=1;i<=n;i++) { 
     fprintf(ficgp,"\n# Routine varevsij");      ip=indx[i]; 
   }      sum=b[ip]; 
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {      b[ip]=b[i]; 
     printf("Problem with html file: %s\n", optionfilehtm);      if (ii) 
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     exit(0);      else if (sum) ii=i; 
   }      b[i]=sum; 
   else{    } 
     fprintf(fichtm,"\n<li><h4> Computing step probabilities of dying and weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");    for (i=n;i>=1;i--) { 
   }      sum=b[i]; 
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       b[i]=sum/a[i][i]; 
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");    } 
   fprintf(ficresvij,"# Age");  } 
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)  /************ Frequencies ********************/
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)
   fprintf(ficresvij,"\n");  {  /* Some frequencies */
     
   xp=vector(1,npar);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   dnewm=matrix(1,nlstate,1,npar);    int first;
   doldm=matrix(1,nlstate,1,nlstate);    double ***freq; /* Frequencies */
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);    double *pp, **prop;
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     FILE *ficresp;
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);    char fileresp[FILENAMELENGTH];
   gpp=vector(nlstate+1,nlstate+ndeath);    
   gmp=vector(nlstate+1,nlstate+ndeath);    pp=vector(1,nlstate);
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/    prop=matrix(1,nlstate,iagemin,iagemax+3);
      strcpy(fileresp,"p");
   if(estepm < stepm){    strcat(fileresp,fileres);
     printf ("Problem %d lower than %d\n",estepm, stepm);    if((ficresp=fopen(fileresp,"w"))==NULL) {
   }      printf("Problem with prevalence resultfile: %s\n", fileresp);
   else  hstepm=estepm;        fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   /* For example we decided to compute the life expectancy with the smallest unit */      exit(0);
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    }
      nhstepm is the number of hstepm from age to agelim    freq= ma3x(-2,nlstate+ndeath,-2,nlstate+ndeath,iagemin,iagemax+3);
      nstepm is the number of stepm from age to agelin.    j1=0;
      Look at hpijx to understand the reason of that which relies in memory size    
      and note for a fixed period like k years */    j=cptcoveff;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      survival function given by stepm (the optimization length). Unfortunately it  
      means that if the survival funtion is printed only each two years of age and if    first=1;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  
      results. So we changed our mind and took the option of the best precision.    for(k1=1; k1<=j;k1++){
   */      for(i1=1; i1<=ncodemax[k1];i1++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        j1++;
   agelim = AGESUP;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          scanf("%d", i);*/
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        for (i=-2; i<=nlstate+ndeath; i++)  
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          for (jk=-2; jk<=nlstate+ndeath; jk++)  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(m=iagemin; m <= iagemax+3; m++)
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);              freq[i][jk][m]=0;
     gp=matrix(0,nhstepm,1,nlstate);  
     gm=matrix(0,nhstepm,1,nlstate);      for (i=1; i<=nlstate; i++)  
         for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
     for(theta=1; theta <=npar; theta++){        
       for(i=1; i<=npar; i++){ /* Computes gradient */        dateintsum=0;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        k2cpt=0;
       }        for (i=1; i<=imx; i++) {
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            bool=1;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
       if (popbased==1) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         for(i=1; i<=nlstate;i++)                bool=0;
           prlim[i][i]=probs[(int)age][i][ij];          }
       }          if (bool==1){
              for(m=firstpass; m<=lastpass; m++){
       for(j=1; j<= nlstate; j++){              k2=anint[m][i]+(mint[m][i]/12.);
         for(h=0; h<=nhstepm; h++){              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)                if(agev[m][i]==0) agev[m][i]=iagemax+1;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         }                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
       }                if (m<lastpass) {
       /* This for computing forces of mortality (h=1)as a weighted average */                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
         for(i=1; i<= nlstate; i++)                }
           gpp[j] += prlim[i][i]*p3mat[i][j][1];                
       }                    if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
       /* end force of mortality */                  dateintsum=dateintsum+k2;
                   k2cpt++;
       for(i=1; i<=npar; i++) /* Computes gradient */                }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);                /*}*/
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          }
          }
       if (popbased==1) {         
         for(i=1; i<=nlstate;i++)        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
           prlim[i][i]=probs[(int)age][i][ij];  
       }        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
       for(j=1; j<= nlstate; j++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         for(h=0; h<=nhstepm; h++){          fprintf(ficresp, "**********\n#");
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        }
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        for(i=1; i<=nlstate;i++) 
         }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       }        fprintf(ficresp, "\n");
       /* This for computing force of mortality (h=1)as a weighted average */        
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){        for(i=iagemin; i <= iagemax+3; i++){
         for(i=1; i<= nlstate; i++)          if(i==iagemax+3){
           gmp[j] += prlim[i][i]*p3mat[i][j][1];            fprintf(ficlog,"Total");
       }              }else{
       /* end force of mortality */            if(first==1){
               first=0;
       for(j=1; j<= nlstate; j++) /* vareij */              printf("See log file for details...\n");
         for(h=0; h<=nhstepm; h++){            }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            fprintf(ficlog,"Age %d", i);
         }          }
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */          for(jk=1; jk <=nlstate ; jk++){
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       }              pp[jk] += freq[jk][m][i]; 
           }
     } /* End theta */          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
     for(h=0; h<=nhstepm; h++) /* veij */              if(first==1){
       for(j=1; j<=nlstate;j++)              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         for(theta=1; theta <=npar; theta++)              }
           trgradg[h][j][theta]=gradg[h][theta][j];              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */              if(first==1)
       for(theta=1; theta <=npar; theta++)                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         trgradgp[j][theta]=gradgp[theta][j];              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          }
     for(i=1;i<=nlstate;i++)  
       for(j=1;j<=nlstate;j++)          for(jk=1; jk <=nlstate ; jk++){
         vareij[i][j][(int)age] =0.;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
     for(h=0;h<=nhstepm;h++){          }       
       for(k=0;k<=nhstepm;k++){          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);            pos += pp[jk];
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            posprop += prop[jk][i];
         for(i=1;i<=nlstate;i++)          }
           for(j=1;j<=nlstate;j++)          for(jk=1; jk <=nlstate ; jk++){
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;            if(pos>=1.e-5){
       }              if(first==1)
     }                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);
     /* pptj */            }else{
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);              if(first==1)
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     for(j=nlstate+1;j<=nlstate+ndeath;j++)              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       for(i=nlstate+1;i<=nlstate+ndeath;i++)            }
         varppt[j][i]=doldmp[j][i];            if( i <= iagemax){
     /* end ppptj */              if(pos>=1.e-5){
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);                  fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);                /*probs[i][jk][j1]= pp[jk]/pos;*/
                  /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     if (popbased==1) {              }
       for(i=1; i<=nlstate;i++)              else
         prlim[i][i]=probs[(int)age][i][ij];                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     }            }
              }
     /* This for computing force of mortality (h=1)as a weighted average */          
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){          for(jk=-1; jk <=nlstate+ndeath; jk++)
       for(i=1; i<= nlstate; i++)            for(m=-1; m <=nlstate+ndeath; m++)
         gmp[j] += prlim[i][i]*p3mat[i][j][1];              if(freq[jk][m][i] !=0 ) {
     }                  if(first==1)
     /* end force of mortality */                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);              }
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){          if(i <= iagemax)
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));            fprintf(ficresp,"\n");
       for(i=1; i<=nlstate;i++){          if(first==1)
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);            printf("Others in log...\n");
       }          fprintf(ficlog,"\n");
     }        }
     fprintf(ficresprobmorprev,"\n");      }
     }
     fprintf(ficresvij,"%.0f ",age );    dateintmean=dateintsum/k2cpt; 
     for(i=1; i<=nlstate;i++)   
       for(j=1; j<=nlstate;j++){    fclose(ficresp);
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    free_ma3x(freq,-2,nlstate+ndeath,-2,nlstate+ndeath, iagemin, iagemax+3);
       }    free_vector(pp,1,nlstate);
     fprintf(ficresvij,"\n");    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     free_matrix(gp,0,nhstepm,1,nlstate);    /* End of Freq */
     free_matrix(gm,0,nhstepm,1,nlstate);  }
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  /************ Prevalence ********************/
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  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)
   } /* End age */  {  
   free_vector(gpp,nlstate+1,nlstate+ndeath);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   free_vector(gmp,nlstate+1,nlstate+ndeath);       in each health status at the date of interview (if between dateprev1 and dateprev2).
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);       We still use firstpass and lastpass as another selection.
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/    */
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");   
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");    double ***freq; /* Frequencies */
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);    double *pp, **prop;
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);    double pos,posprop; 
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);    double  y2; /* in fractional years */
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);    int iagemin, iagemax;
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);  
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);    iagemin= (int) agemin;
     iagemax= (int) agemax;
   free_vector(xp,1,npar);    /*pp=vector(1,nlstate);*/
   free_matrix(doldm,1,nlstate,1,nlstate);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   free_matrix(dnewm,1,nlstate,1,npar);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    j1=0;
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);    
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    j=cptcoveff;
   fclose(ficresprobmorprev);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   fclose(ficgp);    
   fclose(fichtm);    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
 }        j1++;
         
 /************ Variance of prevlim ******************/        for (i=1; i<=nlstate; 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(m=iagemin; m <= iagemax+3; m++)
 {            prop[i][m]=0.0;
   /* Variance of prevalence limit */       
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        for (i=1; i<=imx; i++) { /* Each individual */
   double **newm;          bool=1;
   double **dnewm,**doldm;          if  (cptcovn>0) {
   int i, j, nhstepm, hstepm;            for (z1=1; z1<=cptcoveff; z1++) 
   int k, cptcode;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   double *xp;                bool=0;
   double *gp, *gm;          } 
   double **gradg, **trgradg;          if (bool==1) { 
   double age,agelim;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   int theta;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                  if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   fprintf(ficresvpl,"# Age");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   for(i=1; i<=nlstate;i++)                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); 
       fprintf(ficresvpl," %1d-%1d",i,i);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   fprintf(ficresvpl,"\n");                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];
   xp=vector(1,npar);                  prop[s[m][i]][iagemax+3] += weight[i]; 
   dnewm=matrix(1,nlstate,1,npar);                } 
   doldm=matrix(1,nlstate,1,nlstate);              }
              } /* end selection of waves */
   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(i=iagemin; i <= iagemax+3; i++){  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     if (stepm >= YEARM) hstepm=1;            posprop += prop[jk][i]; 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          } 
     gradg=matrix(1,npar,1,nlstate);  
     gp=vector(1,nlstate);          for(jk=1; jk <=nlstate ; jk++){     
     gm=vector(1,nlstate);            if( i <=  iagemax){ 
               if(posprop>=1.e-5){ 
     for(theta=1; theta <=npar; theta++){                probs[i][jk][j1]= prop[jk][i]/posprop;
       for(i=1; i<=npar; i++){ /* Computes gradient */              } 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            } 
       }          }/* end jk */ 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        }/* end i */ 
       for(i=1;i<=nlstate;i++)      } /* end i1 */
         gp[i] = prlim[i][i];    } /* end k1 */
        
       for(i=1; i<=npar; i++) /* Computes gradient */    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    /*free_vector(pp,1,nlstate);*/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       for(i=1;i<=nlstate;i++)  }  /* End of prevalence */
         gm[i] = prlim[i][i];  
   /************* Waves Concatenation ***************/
       for(i=1;i<=nlstate;i++)  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  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)
     } /* End theta */  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     trgradg =matrix(1,nlstate,1,npar);       Death is a valid wave (if date is known).
        mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     for(j=1; j<=nlstate;j++)       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       for(theta=1; theta <=npar; theta++)       and mw[mi+1][i]. dh depends on stepm.
         trgradg[j][theta]=gradg[theta][j];       */
   
     for(i=1;i<=nlstate;i++)    int i, mi, m;
       varpl[i][(int)age] =0.;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);       double sum=0., jmean=0.;*/
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    int first;
     for(i=1;i<=nlstate;i++)    int j, k=0,jk, ju, jl;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    double sum=0.;
     first=0;
     fprintf(ficresvpl,"%.0f ",age );    jmin=1e+5;
     for(i=1; i<=nlstate;i++)    jmax=-1;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    jmean=0.;
     fprintf(ficresvpl,"\n");    for(i=1; i<=imx; i++){
     free_vector(gp,1,nlstate);      mi=0;
     free_vector(gm,1,nlstate);      m=firstpass;
     free_matrix(gradg,1,npar,1,nlstate);      while(s[m][i] <= nlstate){
     free_matrix(trgradg,1,nlstate,1,npar);        if(s[m][i]>=1 || s[m][i]==-2)
   } /* End age */          mw[++mi][i]=m;
         if(m >=lastpass)
   free_vector(xp,1,npar);          break;
   free_matrix(doldm,1,nlstate,1,npar);        else
   free_matrix(dnewm,1,nlstate,1,nlstate);          m++;
       }/* end while */
 }      if (s[m][i] > nlstate){
         mi++;     /* Death is another wave */
 /************ Variance of one-step probabilities  ******************/        /* if(mi==0)  never been interviewed correctly before death */
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)           /* Only death is a correct wave */
 {        mw[mi][i]=m;
   int i, j=0,  i1, k1, l1, t, tj;      }
   int k2, l2, j1,  z1;  
   int k=0,l, cptcode;      wav[i]=mi;
   int first=1, first1;      if(mi==0){
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;        nbwarn++;
   double **dnewm,**doldm;        if(first==0){
   double *xp;          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   double *gp, *gm;          first=1;
   double **gradg, **trgradg;        }
   double **mu;        if(first==1){
   double age,agelim, cov[NCOVMAX];          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */        }
   int theta;      } /* end mi==0 */
   char fileresprob[FILENAMELENGTH];    } /* End individuals */
   char fileresprobcov[FILENAMELENGTH];  
   char fileresprobcor[FILENAMELENGTH];    for(i=1; i<=imx; i++){
       for(mi=1; mi<wav[i];mi++){
   double ***varpij;        if (stepm <=0)
           dh[mi][i]=1;
   strcpy(fileresprob,"prob");        else{
   strcat(fileresprob,fileres);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {            if (agedc[i] < 2*AGESUP) {
     printf("Problem with resultfile: %s\n", fileresprob);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);              if(j==0) j=1;  /* Survives at least one month after exam */
   }              else if(j<0){
   strcpy(fileresprobcov,"probcov");                nberr++;
   strcat(fileresprobcov,fileres);                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]);
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {                j=1; /* Temporary Dangerous patch */
     printf("Problem with resultfile: %s\n", fileresprobcov);                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   }                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
   strcpy(fileresprobcor,"probcor");              }
   strcat(fileresprobcor,fileres);              k=k+1;
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {              if (j >= jmax) jmax=j;
     printf("Problem with resultfile: %s\n", fileresprobcor);              if (j <= jmin) jmin=j;
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);              sum=sum+j;
   }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);            }
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);          }
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);          else{
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);  /*        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(ficresprob,"#One-step probabilities and stand. devi in ()\n");            k=k+1;
   fprintf(ficresprob,"# Age");            if (j >= jmax) jmax=j;
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");            else if (j <= jmin)jmin=j;
   fprintf(ficresprobcov,"# Age");            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\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(ficresprobcov,"# Age");            if(j<0){
               nberr++;
               printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   for(i=1; i<=nlstate;i++)              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     for(j=1; j<=(nlstate+ndeath);j++){            }
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);            sum=sum+j;
       fprintf(ficresprobcov," p%1d-%1d ",i,j);          }
       fprintf(ficresprobcor," p%1d-%1d ",i,j);          jk= j/stepm;
     }            jl= j -jk*stepm;
   fprintf(ficresprob,"\n");          ju= j -(jk+1)*stepm;
   fprintf(ficresprobcov,"\n");          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   fprintf(ficresprobcor,"\n");            if(jl==0){
   xp=vector(1,npar);              dh[mi][i]=jk;
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);              bh[mi][i]=0;
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));            }else{ /* We want a negative bias in order to only have interpolation ie
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);                    * at the price of an extra matrix product in likelihood */
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);              dh[mi][i]=jk+1;
   first=1;              bh[mi][i]=ju;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {            }
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);          }else{
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);            if(jl <= -ju){
     exit(0);              dh[mi][i]=jk;
   }              bh[mi][i]=jl;       /* bias is positive if real duration
   else{                                   * is higher than the multiple of stepm and negative otherwise.
     fprintf(ficgp,"\n# Routine varprob");                                   */
   }            }
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {            else{
     printf("Problem with html file: %s\n", optionfilehtm);              dh[mi][i]=jk+1;
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);              bh[mi][i]=ju;
     exit(0);            }
   }            if(dh[mi][i]==0){
   else{              dh[mi][i]=1; /* At least one step */
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");              bh[mi][i]=ju; /* At least one step */
     fprintf(fichtm,"\n");              /*  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);*/
             }
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");          } /* end if mle */
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");        }
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");      } /* end wave */
     }
   }    jmean=sum/k;
     printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
      fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   cov[1]=1;   }
   tj=cptcoveff;  
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}  /*********** Tricode ****************************/
   j1=0;  void tricode(int *Tvar, int **nbcode, int imx)
   for(t=1; t<=tj;t++){  {
     for(i1=1; i1<=ncodemax[t];i1++){    
       j1++;    int Ndum[20],ij=1, k, j, i, maxncov=19;
          int cptcode=0;
       if  (cptcovn>0) {    cptcoveff=0; 
         fprintf(ficresprob, "\n#********** Variable ");   
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    for (k=0; k<maxncov; k++) Ndum[k]=0;
         fprintf(ficresprob, "**********\n#");    for (k=1; k<=7; k++) ncodemax[k]=0;
         fprintf(ficresprobcov, "\n#********** Variable ");  
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
         fprintf(ficresprobcov, "**********\n#");      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                         modality*/ 
         fprintf(ficgp, "\n#********** Variable ");        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        Ndum[ij]++; /*store the modality */
         fprintf(ficgp, "**********\n#");        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
                if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                                                 Tvar[j]. If V=sex and male is 0 and 
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");                                         female is 1, then  cptcode=1.*/
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      }
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");  
              for (i=0; i<=cptcode; i++) {
         fprintf(ficresprobcor, "\n#********** Variable ");            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 */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      }
         fprintf(ficgp, "**********\n#");      
       }      ij=1; 
            for (i=1; i<=ncodemax[j]; i++) {
       for (age=bage; age<=fage; age ++){        for (k=0; k<= maxncov; k++) {
         cov[2]=age;          if (Ndum[k] != 0) {
         for (k=1; k<=cptcovn;k++) {            nbcode[Tvar[j]][ij]=k; 
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
         }            
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];            ij++;
         for (k=1; k<=cptcovprod;k++)          }
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          if (ij > ncodemax[j]) break; 
                }  
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));      } 
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    }  
         gp=vector(1,(nlstate)*(nlstate+ndeath));  
         gm=vector(1,(nlstate)*(nlstate+ndeath));   for (k=0; k< maxncov; k++) Ndum[k]=0;
      
         for(theta=1; theta <=npar; theta++){   for (i=1; i<=ncovmodel-2; i++) { 
           for(i=1; i<=npar; i++)     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
             xp[i] = x[i] + (i==theta ?delti[theta]:0);     ij=Tvar[i];
               Ndum[ij]++;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);   }
            
           k=0;   ij=1;
           for(i=1; i<= (nlstate); i++){   for (i=1; i<= maxncov; i++) {
             for(j=1; j<=(nlstate+ndeath);j++){     if((Ndum[i]!=0) && (i<=ncovcol)){
               k=k+1;       Tvaraff[ij]=i; /*For printing */
               gp[k]=pmmij[i][j];       ij++;
             }     }
           }   }
             
           for(i=1; i<=npar; i++)   cptcoveff=ij-1; /*Number of simple covariates*/
             xp[i] = x[i] - (i==theta ?delti[theta]:0);  }
      
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  /*********** Health Expectancies ****************/
           k=0;  
           for(i=1; i<=(nlstate); i++){  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
             for(j=1; j<=(nlstate+ndeath);j++){  
               k=k+1;  {
               gm[k]=pmmij[i][j];    /* Health expectancies */
             }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
           }    double age, agelim, hf;
          double ***p3mat,***varhe;
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)    double **dnewm,**doldm;
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      double *xp;
         }    double **gp, **gm;
     double ***gradg, ***trgradg;
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)    int theta;
           for(theta=1; theta <=npar; theta++)  
             trgradg[j][theta]=gradg[theta][j];    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
            xp=vector(1,npar);
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);    dnewm=matrix(1,nlstate*nlstate,1,npar);
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
            
         pmij(pmmij,cov,ncovmodel,x,nlstate);    fprintf(ficreseij,"# Health expectancies\n");
            fprintf(ficreseij,"# Age");
         k=0;    for(i=1; i<=nlstate;i++)
         for(i=1; i<=(nlstate); i++){      for(j=1; j<=nlstate;j++)
           for(j=1; j<=(nlstate+ndeath);j++){        fprintf(ficreseij," %1d-%1d (SE)",i,j);
             k=k+1;    fprintf(ficreseij,"\n");
             mu[k][(int) age]=pmmij[i][j];  
           }    if(estepm < stepm){
         }      printf ("Problem %d lower than %d\n",estepm, stepm);
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)    }
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)    else  hstepm=estepm;   
             varpij[i][j][(int)age] = doldm[i][j];    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
         /*printf("\n%d ",(int)age);     * if stepm=24 months pijx are given only every 2 years and by summing them
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){     * we are calculating an estimate of the Life Expectancy assuming a linear 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));     * progression in between and thus overestimating or underestimating according
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));     * 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
      * to compare the new estimate of Life expectancy with the same linear 
         fprintf(ficresprob,"\n%d ",(int)age);     * hypothesis. A more precise result, taking into account a more precise
         fprintf(ficresprobcov,"\n%d ",(int)age);     * curvature will be obtained if estepm is as small as stepm. */
         fprintf(ficresprobcor,"\n%d ",(int)age);  
     /* For example we decided to compute the life expectancy with the smallest unit */
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));       nhstepm is the number of hstepm from age to agelim 
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){       nstepm is the number of stepm from age to agelin. 
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);       Look at hpijx to understand the reason of that which relies in memory size
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);       and note for a fixed period like estepm months */
         }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         i=0;       survival function given by stepm (the optimization length). Unfortunately it
         for (k=1; k<=(nlstate);k++){       means that if the survival funtion is printed only each two years of age and if
           for (l=1; l<=(nlstate+ndeath);l++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
             i=i++;       results. So we changed our mind and took the option of the best precision.
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);    */
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
             for (j=1; j<=i;j++){  
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);    agelim=AGESUP;
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
             }      /* nhstepm age range expressed in number of stepm */
           }      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
         }/* end of loop for state */      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       } /* end of loop for age */      /* if (stepm >= YEARM) hstepm=1;*/
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       /* Confidence intervalle of pij  */      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       /*      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       fprintf(ficgp,"\nset noparametric;unset label");      gp=matrix(0,nhstepm,1,nlstate*nlstate);
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");      gm=matrix(0,nhstepm,1,nlstate*nlstate);
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");  
       fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);   
       */  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/  
       first1=1;      /* Computing  Variances of health expectancies */
       for (k2=1; k2<=(nlstate);k2++){  
         for (l2=1; l2<=(nlstate+ndeath);l2++){       for(theta=1; theta <=npar; theta++){
           if(l2==k2) continue;        for(i=1; i<=npar; i++){ 
           j=(k2-1)*(nlstate+ndeath)+l2;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           for (k1=1; k1<=(nlstate);k1++){        }
             for (l1=1; l1<=(nlstate+ndeath);l1++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
               if(l1==k1) continue;    
               i=(k1-1)*(nlstate+ndeath)+l1;        cptj=0;
               if(i<=j) continue;        for(j=1; j<= nlstate; j++){
               for (age=bage; age<=fage; age ++){          for(i=1; i<=nlstate; i++){
                 if ((int)age %5==0){            cptj=cptj+1;
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;            }
                   mu1=mu[i][(int) age]/stepm*YEARM ;          }
                   mu2=mu[j][(int) age]/stepm*YEARM;        }
                   c12=cv12/sqrt(v1*v2);       
                   /* Computing eigen value of matrix of covariance */       
                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;        for(i=1; i<=npar; i++) 
                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
                   /* Eigen vectors */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));        
                   /*v21=sqrt(1.-v11*v11); *//* error */        cptj=0;
                   v21=(lc1-v1)/cv12*v11;        for(j=1; j<= nlstate; j++){
                   v12=-v21;          for(i=1;i<=nlstate;i++){
                   v22=v11;            cptj=cptj+1;
                   tnalp=v21/v11;            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
                   if(first1==1){  
                     first1=0;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);            }
                   }          }
                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);        }
                   /*printf(fignu*/        for(j=1; j<= nlstate*nlstate; j++)
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */          for(h=0; h<=nhstepm-1; h++){
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                   if(first==1){          }
                     first=0;       } 
                     fprintf(ficgp,"\nset parametric;unset label");     
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);  /* End theta */
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");  
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);  
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);       for(h=0; h<=nhstepm-1; h++)
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);        for(j=1; j<=nlstate*nlstate;j++)
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);          for(theta=1; theta <=npar; theta++)
                     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",\            trgradg[h][j][theta]=gradg[h][theta][j];
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\       
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));  
                   }else{       for(i=1;i<=nlstate*nlstate;i++)
                     first=0;        for(j=1;j<=nlstate*nlstate;j++)
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);          varhe[i][j][(int)age] =0.;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);  
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\       printf("%d|",(int)age);fflush(stdout);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));       for(h=0;h<=nhstepm-1;h++){
                   }/* if first */        for(k=0;k<=nhstepm-1;k++){
                 } /* age mod 5 */          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
               } /* end loop age */          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);          for(i=1;i<=nlstate*nlstate;i++)
               first=1;            for(j=1;j<=nlstate*nlstate;j++)
             } /*l12 */              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
           } /* k12 */        }
         } /*l1 */      }
       }/* k1 */      /* Computing expectancies */
     } /* loop covariates */      for(i=1; i<=nlstate;i++)
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);        for(j=1; j<=nlstate;j++)
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);            
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  /* 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]);*/
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   }          }
   free_vector(xp,1,npar);  
   fclose(ficresprob);      fprintf(ficreseij,"%3.0f",age );
   fclose(ficresprobcov);      cptj=0;
   fclose(ficresprobcor);      for(i=1; i<=nlstate;i++)
   fclose(ficgp);        for(j=1; j<=nlstate;j++){
   fclose(fichtm);          cptj++;
 }          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
         }
       fprintf(ficreseij,"\n");
 /******************* Printing html file ***********/     
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
                   int lastpass, int stepm, int weightopt, char model[],\      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
                   int popforecast, int estepm ,\      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
                   double jprev1, double mprev1,double anprev1, \      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   double jprev2, double mprev2,double anprev2){    }
   int jj1, k1, i1, cpt;    printf("\n");
   /*char optionfilehtm[FILENAMELENGTH];*/    fprintf(ficlog,"\n");
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm), exit(0);    free_vector(xp,1,npar);
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n  }
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n  
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n  /************ Variance ******************/
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n  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)
  - Life expectancies by age and initial health status (estepm=%2d months):  {
    <a href=\"e%s\">e%s</a> <br>\n</li>", \    /* Variance of health expectancies */
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");    double **dnewm,**doldm;
     double **dnewmp,**doldmp;
  m=cptcoveff;    int i, j, nhstepm, hstepm, h, nstepm ;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    int k, cptcode;
     double *xp;
  jj1=0;    double **gp, **gm;  /* for var eij */
  for(k1=1; k1<=m;k1++){    double ***gradg, ***trgradg; /*for var eij */
    for(i1=1; i1<=ncodemax[k1];i1++){    double **gradgp, **trgradgp; /* for var p point j */
      jj1++;    double *gpp, *gmp; /* for var p point j */
      if (cptcovn > 0) {    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    double ***p3mat;
        for (cpt=1; cpt<=cptcoveff;cpt++)    double age,agelim, hf;
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    double ***mobaverage;
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    int theta;
      }    char digit[4];
      /* Pij */    char digitp[25];
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>  
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        char fileresprobmorprev[FILENAMELENGTH];
      /* Quasi-incidences */  
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>    if(popbased==1){
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      if(mobilav!=0)
        /* Stable prevalence in each health state */        strcpy(digitp,"-populbased-mobilav-");
        for(cpt=1; cpt<nlstate;cpt++){      else strcpy(digitp,"-populbased-nomobil-");
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    }
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    else 
        }      strcpy(digitp,"-stablbased-");
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    if (mobilav!=0) {
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      }      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
 health expectancies in states (1) and (2): e%s%d.png<br>        printf(" Error in movingaverage mobilav=%d\n",mobilav);
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      }
    } /* end i1 */    }
  }/* End k1 */  
  fprintf(fichtm,"</ul>");    strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n    strcat(fileresprobmorprev,digit); /* Tvar to be done */
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    strcat(fileresprobmorprev,fileres);
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n      printf("Problem with resultfile: %s\n", fileresprobmorprev);
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n    }
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
  if(popforecast==1) fprintf(fichtm,"\n    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);
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         <br>",fileres,fileres,fileres,fileres);      fprintf(ficresprobmorprev," p.%-d SE",j);
  else      for(i=1; i<=nlstate;i++)
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");    }  
     fprintf(ficresprobmorprev,"\n");
  m=cptcoveff;    fprintf(ficgp,"\n# Routine varevsij");
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
  jj1=0;  /*   } */
  for(k1=1; k1<=m;k1++){    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    for(i1=1; i1<=ncodemax[k1];i1++){  
      jj1++;    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");
      if (cptcovn > 0) {    fprintf(ficresvij,"# Age");
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    for(i=1; i<=nlstate;i++)
        for (cpt=1; cpt<=cptcoveff;cpt++)      for(j=1; j<=nlstate;j++)
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    fprintf(ficresvij,"\n");
      }  
      for(cpt=1; cpt<=nlstate;cpt++) {    xp=vector(1,npar);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    dnewm=matrix(1,nlstate,1,npar);
 interval) in state (%d): v%s%d%d.png <br>    doldm=matrix(1,nlstate,1,nlstate);
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
      }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    } /* end i1 */  
  }/* End k1 */    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
  fprintf(fichtm,"</ul>");    gpp=vector(nlstate+1,nlstate+ndeath);
 fclose(fichtm);    gmp=vector(nlstate+1,nlstate+ndeath);
 }    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
 /******************* Gnuplot file **************/    if(estepm < stepm){
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    else  hstepm=estepm;   
   int ng;    /* For example we decided to compute the life expectancy with the smallest unit */
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     printf("Problem with file %s",optionfilegnuplot);       nhstepm is the number of hstepm from age to agelim 
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);       nstepm is the number of stepm from age to agelin. 
   }       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
 #ifdef windows    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     fprintf(ficgp,"cd \"%s\" \n",pathc);       survival function given by stepm (the optimization length). Unfortunately it
 #endif       means that if the survival funtion is printed every two years of age and if
 m=pow(2,cptcoveff);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         results. So we changed our mind and took the option of the best precision.
  /* 1eme*/    */
   for (cpt=1; cpt<= nlstate ; cpt ++) {    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
    for (k1=1; k1<= m ; k1 ++) {    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 #ifdef windows      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 #endif      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
 #ifdef unix      gp=matrix(0,nhstepm,1,nlstate);
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      gm=matrix(0,nhstepm,1,nlstate);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);  
 #endif  
       for(theta=1; theta <=npar; theta++){
 for (i=1; i<= nlstate ; i ++) {        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        if (popbased==1) {
   else fprintf(ficgp," \%%*lf (\%%*lf)");          if(mobilav ==0){
 }            for(i=1; i<=nlstate;i++)
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);              prlim[i][i]=probs[(int)age][i][ij];
      for (i=1; i<= nlstate ; i ++) {          }else{ /* mobilav */ 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            for(i=1; i<=nlstate;i++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");              prlim[i][i]=mobaverage[(int)age][i][ij];
 }            }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        }
 #ifdef unix    
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");        for(j=1; j<= nlstate; j++){
 #endif          for(h=0; h<=nhstepm; h++){
    }            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   }              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   /*2 eme*/          }
         }
   for (k1=1; k1<= m ; k1 ++) {        /* This for computing probability of death (h=1 means
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);           computed over hstepm matrices product = hstepm*stepm months) 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);           as a weighted average of prlim.
            */
     for (i=1; i<= nlstate+1 ; i ++) {        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       k=2*i;          for(i=1,gpp[j]=0.; i<= nlstate; i++)
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
       for (j=1; j<= nlstate+1 ; j ++) {        }    
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        /* end probability of death */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }          for(i=1; i<=npar; i++) /* Computes gradient x - delta */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       for (j=1; j<= nlstate+1 ; j ++) {   
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        if (popbased==1) {
         else fprintf(ficgp," \%%*lf (\%%*lf)");          if(mobilav ==0){
 }              for(i=1; i<=nlstate;i++)
       fprintf(ficgp,"\" t\"\" w l 0,");              prlim[i][i]=probs[(int)age][i][ij];
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          }else{ /* mobilav */ 
       for (j=1; j<= nlstate+1 ; j ++) {            for(i=1; i<=nlstate;i++)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              prlim[i][i]=mobaverage[(int)age][i][ij];
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }          }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  
       else fprintf(ficgp,"\" t\"\" w l 0,");        for(j=1; j<= nlstate; j++){
     }          for(h=0; h<=nhstepm; h++){
   }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   /*3eme*/          }
         }
   for (k1=1; k1<= m ; k1 ++) {        /* This for computing probability of death (h=1 means
     for (cpt=1; cpt<= nlstate ; cpt ++) {           computed over hstepm matrices product = hstepm*stepm months) 
       k=2+nlstate*(2*cpt-2);           as a weighted average of prlim.
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        */
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");           gmp[j] += prlim[i][i]*p3mat[i][j][1];
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        }    
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        /* end probability of death */
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");  
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
 */            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       for (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+2*i,cpt,i+1);  
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       }          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     }        }
   }  
        } /* End theta */
   /* CV preval stat */  
     for (k1=1; k1<= m ; k1 ++) {      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     for (cpt=1; cpt<nlstate ; cpt ++) {  
       k=3;      for(h=0; h<=nhstepm; h++) /* veij */
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        for(j=1; j<=nlstate;j++)
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
       for (i=1; i< nlstate ; i ++)  
         fprintf(ficgp,"+$%d",k+i+1);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        for(theta=1; theta <=npar; theta++)
                trgradgp[j][theta]=gradgp[theta][j];
       l=3+(nlstate+ndeath)*cpt;    
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  
       for (i=1; i< nlstate ; i ++) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         l=3+(nlstate+ndeath)*cpt;      for(i=1;i<=nlstate;i++)
         fprintf(ficgp,"+$%d",l+i+1);        for(j=1;j<=nlstate;j++)
       }          vareij[i][j][(int)age] =0.;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    
     }      for(h=0;h<=nhstepm;h++){
   }          for(k=0;k<=nhstepm;k++){
            matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   /* proba elementaires */          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
    for(i=1,jk=1; i <=nlstate; i++){          for(i=1;i<=nlstate;i++)
     for(k=1; k <=(nlstate+ndeath); k++){            for(j=1;j<=nlstate;j++)
       if (k != i) {              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         for(j=1; j <=ncovmodel; j++){        }
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      }
           jk++;    
           fprintf(ficgp,"\n");      /* pptj */
         }      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       }      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
     }      for(j=nlstate+1;j<=nlstate+ndeath;j++)
    }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/      /* end ppptj */
      for(jk=1; jk <=m; jk++) {      /*  x centered again */
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
        if (ng==2)      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");   
        else      if (popbased==1) {
          fprintf(ficgp,"\nset title \"Probability\"\n");        if(mobilav ==0){
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          for(i=1; i<=nlstate;i++)
        i=1;            prlim[i][i]=probs[(int)age][i][ij];
        for(k2=1; k2<=nlstate; k2++) {        }else{ /* mobilav */ 
          k3=i;          for(i=1; i<=nlstate;i++)
          for(k=1; k<=(nlstate+ndeath); k++) {            prlim[i][i]=mobaverage[(int)age][i][ij];
            if (k != k2){        }
              if(ng==2)      }
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);               
              else      /* This for computing probability of death (h=1 means
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
              ij=1;         as a weighted average of prlim.
              for(j=3; j <=ncovmodel; j++) {      */
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      for(j=nlstate+1;j<=nlstate+ndeath;j++){
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
                  ij++;          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
                }      }    
                else      /* end probability of death */
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
              }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
              fprintf(ficgp,")/(1");      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                      fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
              for(k1=1; k1 <=nlstate; k1++){          for(i=1; i<=nlstate;i++){
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
                ij=1;        }
                for(j=3; j <=ncovmodel; j++){      } 
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      fprintf(ficresprobmorprev,"\n");
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
                    ij++;      fprintf(ficresvij,"%.0f ",age );
                  }      for(i=1; i<=nlstate;i++)
                  else        for(j=1; j<=nlstate;j++){
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
                }        }
                fprintf(ficgp,")");      fprintf(ficresvij,"\n");
              }      free_matrix(gp,0,nhstepm,1,nlstate);
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);      free_matrix(gm,0,nhstepm,1,nlstate);
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
              i=i+ncovmodel;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
            }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          } /* end k */    } /* End age */
        } /* end k2 */    free_vector(gpp,nlstate+1,nlstate+ndeath);
      } /* end jk */    free_vector(gmp,nlstate+1,nlstate+ndeath);
    } /* end ng */    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
    fclose(ficgp);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
 }  /* end gnuplot */    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
 /*************** Moving average **************/  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   int i, cpt, cptcod;    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
       for (i=1; i<=nlstate;i++)    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
           mobaverage[(int)agedeb][i][cptcod]=0.;    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
        /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){  */
       for (i=1; i<=nlstate;i++){  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
           for (cpt=0;cpt<=4;cpt++){  
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    free_vector(xp,1,npar);
           }    free_matrix(doldm,1,nlstate,1,nlstate);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    free_matrix(dnewm,1,nlstate,1,npar);
         }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       }    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 }    fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
 /************** Forecasting ******************/  }  /* end varevsij */
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){  
    /************ Variance of prevlim ******************/
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
   int *popage;  {
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    /* Variance of prevalence limit */
   double *popeffectif,*popcount;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   double ***p3mat;    double **newm;
   char fileresf[FILENAMELENGTH];    double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
  agelim=AGESUP;    int k, cptcode;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    double *xp;
     double *gp, *gm;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    double **gradg, **trgradg;
      double age,agelim;
      int theta;
   strcpy(fileresf,"f");     
   strcat(fileresf,fileres);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   if((ficresf=fopen(fileresf,"w"))==NULL) {    fprintf(ficresvpl,"# Age");
     printf("Problem with forecast resultfile: %s\n", fileresf);    for(i=1; i<=nlstate;i++)
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);        fprintf(ficresvpl," %1d-%1d",i,i);
   }    fprintf(ficresvpl,"\n");
   printf("Computing forecasting: result on file '%s' \n", fileresf);  
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);    xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    doldm=matrix(1,nlstate,1,nlstate);
     
   if (mobilav==1) {    hstepm=1*YEARM; /* Every year of age */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     movingaverage(agedeb, fage, ageminpar, mobaverage);    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 */ 
   stepsize=(int) (stepm+YEARM-1)/YEARM;      if (stepm >= YEARM) hstepm=1;
   if (stepm<=12) stepsize=1;      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
        gradg=matrix(1,npar,1,nlstate);
   agelim=AGESUP;      gp=vector(1,nlstate);
        gm=vector(1,nlstate);
   hstepm=1;  
   hstepm=hstepm/stepm;      for(theta=1; theta <=npar; theta++){
   yp1=modf(dateintmean,&yp);        for(i=1; i<=npar; i++){ /* Computes gradient */
   anprojmean=yp;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   yp2=modf((yp1*12),&yp);        }
   mprojmean=yp;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   yp1=modf((yp2*30.5),&yp);        for(i=1;i<=nlstate;i++)
   jprojmean=yp;          gp[i] = prlim[i][i];
   if(jprojmean==0) jprojmean=1;      
   if(mprojmean==0) jprojmean=1;        for(i=1; i<=npar; i++) /* Computes gradient */
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
          for(i=1;i<=nlstate;i++)
   for(cptcov=1;cptcov<=i2;cptcov++){          gm[i] = prlim[i][i];
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;        for(i=1;i<=nlstate;i++)
       fprintf(ficresf,"\n#******");          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       for(j=1;j<=cptcoveff;j++) {      } /* End theta */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }      trgradg =matrix(1,nlstate,1,npar);
       fprintf(ficresf,"******\n");  
       fprintf(ficresf,"# StartingAge FinalAge");      for(j=1; j<=nlstate;j++)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        for(theta=1; theta <=npar; theta++)
                trgradg[j][theta]=gradg[theta][j];
        
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      for(i=1;i<=nlstate;i++)
         fprintf(ficresf,"\n");        varpl[i][(int)age] =0.;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      for(i=1;i<=nlstate;i++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
           nhstepm = nhstepm/hstepm;  
                fprintf(ficresvpl,"%.0f ",age );
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(i=1; i<=nlstate;i++)
           oldm=oldms;savm=savms;        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        fprintf(ficresvpl,"\n");
              free_vector(gp,1,nlstate);
           for (h=0; h<=nhstepm; h++){      free_vector(gm,1,nlstate);
             if (h==(int) (calagedate+YEARM*cpt)) {      free_matrix(gradg,1,npar,1,nlstate);
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);      free_matrix(trgradg,1,nlstate,1,npar);
             }    } /* End age */
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;    free_vector(xp,1,npar);
               for(i=1; i<=nlstate;i++) {                  free_matrix(doldm,1,nlstate,1,npar);
                 if (mobilav==1)    free_matrix(dnewm,1,nlstate,1,nlstate);
                   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];  
                 }  /************ Variance of one-step probabilities  ******************/
                  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
               }  {
               if (h==(int)(calagedate+12*cpt)){    int i, j=0,  i1, k1, l1, t, tj;
                 fprintf(ficresf," %.3f", kk1);    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;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double *xp;
         }    double *gp, *gm;
       }    double **gradg, **trgradg;
     }    double **mu;
   }    double age,agelim, cov[NCOVMAX];
            double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int theta;
     char fileresprob[FILENAMELENGTH];
   fclose(ficresf);    char fileresprobcov[FILENAMELENGTH];
 }    char fileresprobcor[FILENAMELENGTH];
 /************** Forecasting ******************/  
 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){    double ***varpij;
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    strcpy(fileresprob,"prob"); 
   int *popage;    strcat(fileresprob,fileres);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   double *popeffectif,*popcount;      printf("Problem with resultfile: %s\n", fileresprob);
   double ***p3mat,***tabpop,***tabpopprev;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   char filerespop[FILENAMELENGTH];    }
     strcpy(fileresprobcov,"probcov"); 
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    strcat(fileresprobcov,fileres);
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   agelim=AGESUP;      printf("Problem with resultfile: %s\n", fileresprobcov);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
      }
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    strcpy(fileresprobcor,"probcor"); 
      strcat(fileresprobcor,fileres);
      if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   strcpy(filerespop,"pop");      printf("Problem with resultfile: %s\n", fileresprobcor);
   strcat(filerespop,fileres);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    }
     printf("Problem with forecast resultfile: %s\n", filerespop);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   }    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   printf("Computing forecasting: result on file '%s' \n", filerespop);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   if (mobilav==1) {    fprintf(ficresprob,"# Age");
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     movingaverage(agedeb, fage, ageminpar, mobaverage);    fprintf(ficresprobcov,"# Age");
   }    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# Age");
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   if (stepm<=12) stepsize=1;  
      for(i=1; i<=nlstate;i++)
   agelim=AGESUP;      for(j=1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   hstepm=1;        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   hstepm=hstepm/stepm;        fprintf(ficresprobcor," p%1d-%1d ",i,j);
        }  
   if (popforecast==1) {   /* fprintf(ficresprob,"\n");
     if((ficpop=fopen(popfile,"r"))==NULL) {    fprintf(ficresprobcov,"\n");
       printf("Problem with population file : %s\n",popfile);exit(0);    fprintf(ficresprobcor,"\n");
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);   */
     }   xp=vector(1,npar);
     popage=ivector(0,AGESUP);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     popeffectif=vector(0,AGESUP);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     popcount=vector(0,AGESUP);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
        varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     i=1;      first=1;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    fprintf(ficgp,"\n# Routine varprob");
        fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     imx=i;    fprintf(fichtm,"\n");
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];  
   }    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\
   for(cptcov=1;cptcov<=i2;cptcov++){    file %s<br>\n",optionfilehtmcov);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
       k=k+1;  and drawn. It helps understanding how is the covariance between two incidences.\
       fprintf(ficrespop,"\n#******");   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
       for(j=1;j<=cptcoveff;j++) {    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. \
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
       }  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
       fprintf(ficrespop,"******\n");  standard deviations wide on each axis. <br>\
       fprintf(ficrespop,"# Age");   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
       if (popforecast==1)  fprintf(ficrespop," [Population]");  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
        
       for (cpt=0; cpt<=0;cpt++) {    cov[1]=1;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      tj=cptcoveff;
            if (cptcovn<1) {tj=1;ncodemax[1]=1;}
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    j1=0;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    for(t=1; t<=tj;t++){
           nhstepm = nhstepm/hstepm;      for(i1=1; i1<=ncodemax[t];i1++){ 
                  j1++;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if  (cptcovn>0) {
           oldm=oldms;savm=savms;          fprintf(ficresprob, "\n#********** Variable "); 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                  fprintf(ficresprob, "**********\n#\n");
           for (h=0; h<=nhstepm; h++){          fprintf(ficresprobcov, "\n#********** Variable "); 
             if (h==(int) (calagedate+YEARM*cpt)) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          fprintf(ficresprobcov, "**********\n#\n");
             }          
             for(j=1; j<=nlstate+ndeath;j++) {          fprintf(ficgp, "\n#********** Variable "); 
               kk1=0.;kk2=0;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
               for(i=1; i<=nlstate;i++) {                        fprintf(ficgp, "**********\n#\n");
                 if (mobilav==1)          
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          
                 else {          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                 }          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
               }          
               if (h==(int)(calagedate+12*cpt)){          fprintf(ficresprobcor, "\n#********** Variable ");    
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   /*fprintf(ficrespop," %.3f", kk1);          fprintf(ficresprobcor, "**********\n#");    
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        }
               }        
             }        for (age=bage; age<=fage; age ++){ 
             for(i=1; i<=nlstate;i++){          cov[2]=age;
               kk1=0.;          for (k=1; k<=cptcovn;k++) {
                 for(j=1; j<=nlstate;j++){            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          }
                 }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];          for (k=1; k<=cptcovprod;k++)
             }            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           }          gp=vector(1,(nlstate)*(nlstate+ndeath));
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          gm=vector(1,(nlstate)*(nlstate+ndeath));
         }      
       }          for(theta=1; theta <=npar; theta++){
              for(i=1; i<=npar; i++)
   /******/              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);              
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){            k=0;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            for(i=1; i<= (nlstate); i++){
           nhstepm = nhstepm/hstepm;              for(j=1; j<=(nlstate+ndeath);j++){
                          k=k+1;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                gp[k]=pmmij[i][j];
           oldm=oldms;savm=savms;              }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              }
           for (h=0; h<=nhstepm; h++){            
             if (h==(int) (calagedate+YEARM*cpt)) {            for(i=1; i<=npar; i++)
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
             }      
             for(j=1; j<=nlstate+ndeath;j++) {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
               kk1=0.;kk2=0;            k=0;
               for(i=1; i<=nlstate;i++) {                          for(i=1; i<=(nlstate); i++){
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                  for(j=1; j<=(nlstate+ndeath);j++){
               }                k=k+1;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);                gm[k]=pmmij[i][j];
             }              }
           }            }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       
         }            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       }              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
    }          }
   }  
            for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
   if (popforecast==1) {          
     free_ivector(popage,0,AGESUP);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     free_vector(popeffectif,0,AGESUP);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     free_vector(popcount,0,AGESUP);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   }          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   fclose(ficrespop);  
 }          pmij(pmmij,cov,ncovmodel,x,nlstate);
           
 /***********************************************/          k=0;
 /**************** Main Program *****************/          for(i=1; i<=(nlstate); i++){
 /***********************************************/            for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
 int main(int argc, char *argv[])              mu[k][(int) age]=pmmij[i][j];
 {            }
           }
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   double agedeb, agefin,hf;            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;              varpij[i][j][(int)age] = doldm[i][j];
   
   double fret;          /*printf("\n%d ",(int)age);
   double **xi,tmp,delta;            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   double dum; /* Dummy variable */            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   double ***p3mat;            }*/
   int *indx;  
   char line[MAXLINE], linepar[MAXLINE];          fprintf(ficresprob,"\n%d ",(int)age);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];          fprintf(ficresprobcov,"\n%d ",(int)age);
   int firstobs=1, lastobs=10;          fprintf(ficresprobcor,"\n%d ",(int)age);
   int sdeb, sfin; /* Status at beginning and end */  
   int c,  h , cpt,l;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   int ju,jl, mi;            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   int mobilav=0,popforecast=0;            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   int hstepm, nhstepm;          }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;          i=0;
           for (k=1; k<=(nlstate);k++){
   double bage, fage, age, agelim, agebase;            for (l=1; l<=(nlstate+ndeath);l++){ 
   double ftolpl=FTOL;              i=i++;
   double **prlim;              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   double *severity;              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   double ***param; /* Matrix of parameters */              for (j=1; j<=i;j++){
   double  *p;                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   double **matcov; /* Matrix of covariance */                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   double ***delti3; /* Scale */              }
   double *delti; /* Scale */            }
   double ***eij, ***vareij;          }/* end of loop for state */
   double **varpl; /* Variances of prevalence limits by age */        } /* end of loop for age */
   double *epj, vepp;  
   double kk1, kk2;        /* Confidence intervalle of pij  */
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;        /*
            fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   char *alph[]={"a","a","b","c","d","e"}, str[4];          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   char z[1]="c", occ;          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
 #include <sys/time.h>          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
 #include <time.h>        */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  
          /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   /* long total_usecs;        first1=1;
   struct timeval start_time, end_time;        for (k2=1; k2<=(nlstate);k2++){
            for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */            if(l2==k2) continue;
   getcwd(pathcd, size);            j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
   printf("\n%s",version);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   if(argc <=1){                if(l1==k1) continue;
     printf("\nEnter the parameter file name: ");                i=(k1-1)*(nlstate+ndeath)+l1;
     scanf("%s",pathtot);                if(i<=j) continue;
   }                for (age=bage; age<=fage; age ++){ 
   else{                  if ((int)age %5==0){
     strcpy(pathtot,argv[1]);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   }                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   /*cygwin_split_path(pathtot,path,optionfile);                    mu1=mu[i][(int) age]/stepm*YEARM ;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/                    mu2=mu[j][(int) age]/stepm*YEARM;
   /* cutv(path,optionfile,pathtot,'\\');*/                    c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   chdir(path);                    /* Eigen vectors */
   replace(pathc,path);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
 /*-------- arguments in the command line --------*/                    v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
   /* Log file */                    v22=v11;
   strcat(filelog, optionfilefiname);                    tnalp=v21/v11;
   strcat(filelog,".log");    /* */                    if(first1==1){
   if((ficlog=fopen(filelog,"w"))==NULL)    {                      first1=0;
     printf("Problem with logfile %s\n",filelog);                      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);
     goto end;                    }
   }                    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(ficlog,"Log filename:%s\n",filelog);                    /*printf(fignu*/
   fprintf(ficlog,"\n%s",version);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   fprintf(ficlog,"\nEnter the parameter file name: ");                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);                    if(first==1){
   fflush(ficlog);                      first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
   /* */                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
   strcpy(fileres,"r");                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   strcat(fileres, optionfilefiname);                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   strcat(fileres,".txt");    /* Other files have txt extension */   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
   /*---------arguments file --------*/                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     printf("Problem with optionfile %s\n",optionfile);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     goto end;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   strcpy(filereso,"o");                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   strcat(filereso,fileres);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   if((ficparo=fopen(filereso,"w"))==NULL) {                    }else{
     printf("Problem with Output resultfile: %s\n", filereso);                      first=0;
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
     goto end;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   /* Reads comments: lines beginning with '#' */                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   while((c=getc(ficpar))=='#' && c!= EOF){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     ungetc(c,ficpar);                    }/* if first */
     fgets(line, MAXLINE, ficpar);                  } /* age mod 5 */
     puts(line);                } /* end loop age */
     fputs(line,ficparo);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   }                first=1;
   ungetc(c,ficpar);              } /*l12 */
             } /* k12 */
   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);          } /*l1 */
   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);        }/* k1 */
   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);      } /* loop covariates */
 while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     fgets(line, MAXLINE, ficpar);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     puts(line);    free_vector(xp,1,npar);
     fputs(line,ficparo);    fclose(ficresprob);
   }    fclose(ficresprobcov);
   ungetc(c,ficpar);    fclose(ficresprobcor);
      fflush(ficgp);
        fflush(fichtmcov);
   covar=matrix(0,NCOVMAX,1,n);  }
   cptcovn=0;  
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  
   /******************* Printing html file ***********/
   ncovmodel=2+cptcovn;  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */                    int lastpass, int stepm, int weightopt, char model[],\
                      int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   /* Read guess parameters */                    int popforecast, int estepm ,\
   /* Reads comments: lines beginning with '#' */                    double jprev1, double mprev1,double anprev1, \
   while((c=getc(ficpar))=='#' && c!= EOF){                    double jprev2, double mprev2,double anprev2){
     ungetc(c,ficpar);    int jj1, k1, i1, cpt;
     fgets(line, MAXLINE, ficpar);  
     puts(line);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
     fputs(line,ficparo);   - 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"));
   ungetc(c,ficpar);     fprintf(fichtm,"\
     - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
     for(i=1; i <=nlstate; i++)     fprintf(fichtm,"\
     for(j=1; j <=nlstate+ndeath-1; j++){   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
       fscanf(ficpar,"%1d%1d",&i1,&j1);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
       fprintf(ficparo,"%1d%1d",i1,j1);     fprintf(fichtm,"\
       if(mle==1)   - Life expectancies by age and initial health status (estepm=%2d months): \
         printf("%1d%1d",i,j);     <a href=\"%s\">%s</a> <br>\n</li>",
       fprintf(ficlog,"%1d%1d",i,j);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
         if(mle==1){  
           printf(" %lf",param[i][j][k]);   m=cptcoveff;
           fprintf(ficlog," %lf",param[i][j][k]);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
         }  
         else   jj1=0;
           fprintf(ficlog," %lf",param[i][j][k]);   for(k1=1; k1<=m;k1++){
         fprintf(ficparo," %lf",param[i][j][k]);     for(i1=1; i1<=ncodemax[k1];i1++){
       }       jj1++;
       fscanf(ficpar,"\n");       if (cptcovn > 0) {
       if(mle==1)         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
         printf("\n");         for (cpt=1; cpt<=cptcoveff;cpt++) 
       fprintf(ficlog,"\n");           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
       fprintf(ficparo,"\n");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     }       }
         /* Pij */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;       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);     
   p=param[1][1];       /* Quasi-incidences */
         fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   /* Reads comments: lines beginning with '#' */   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   while((c=getc(ficpar))=='#' && c!= EOF){  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
     ungetc(c,ficpar);         /* Stable prevalence in each health state */
     fgets(line, MAXLINE, ficpar);         for(cpt=1; cpt<nlstate;cpt++){
     puts(line);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
     fputs(line,ficparo);  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
   }         }
   ungetc(c,ficpar);       for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */       }
   for(i=1; i <=nlstate; i++){     } /* end i1 */
     for(j=1; j <=nlstate+ndeath-1; j++){   }/* End k1 */
       fscanf(ficpar,"%1d%1d",&i1,&j1);   fprintf(fichtm,"</ul>");
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);  
       for(k=1; k<=ncovmodel;k++){   fprintf(fichtm,"\
         fscanf(ficpar,"%le",&delti3[i][j][k]);  \n<br><li><h4> Result files (second order: variances)</h4>\n\
         printf(" %le",delti3[i][j][k]);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
         fprintf(ficparo," %le",delti3[i][j][k]);  
       }   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
       fscanf(ficpar,"\n");           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
       printf("\n");   fprintf(fichtm,"\
       fprintf(ficparo,"\n");   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
     }           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   }  
   delti=delti3[1][1];   fprintf(fichtm,"\
     - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   /* Reads comments: lines beginning with '#' */           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
   while((c=getc(ficpar))=='#' && c!= EOF){   fprintf(fichtm,"\
     ungetc(c,ficpar);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
     fgets(line, MAXLINE, ficpar);           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
     puts(line);   fprintf(fichtm,"\
     fputs(line,ficparo);   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
   }           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
   ungetc(c,ficpar);   fprintf(fichtm,"\
     - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
   matcov=matrix(1,npar,1,npar);           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   for(i=1; i <=npar; i++){  
     fscanf(ficpar,"%s",&str);  /*  if(popforecast==1) fprintf(fichtm,"\n */
     if(mle==1)  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
       printf("%s",str);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
     fprintf(ficlog,"%s",str);  /*      <br>",fileres,fileres,fileres,fileres); */
     fprintf(ficparo,"%s",str);  /*  else  */
     for(j=1; j <=i; j++){  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
       fscanf(ficpar," %le",&matcov[i][j]);   fflush(fichtm);
       if(mle==1){   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
         printf(" %.5le",matcov[i][j]);  
         fprintf(ficlog," %.5le",matcov[i][j]);   m=cptcoveff;
       }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       else  
         fprintf(ficlog," %.5le",matcov[i][j]);   jj1=0;
       fprintf(ficparo," %.5le",matcov[i][j]);   for(k1=1; k1<=m;k1++){
     }     for(i1=1; i1<=ncodemax[k1];i1++){
     fscanf(ficpar,"\n");       jj1++;
     if(mle==1)       if (cptcovn > 0) {
       printf("\n");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     fprintf(ficlog,"\n");         for (cpt=1; cpt<=cptcoveff;cpt++) 
     fprintf(ficparo,"\n");           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   for(i=1; i <=npar; i++)       }
     for(j=i+1;j<=npar;j++)       for(cpt=1; cpt<=nlstate;cpt++) {
       matcov[i][j]=matcov[j][i];         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
      prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   if(mle==1)  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
     printf("\n");       }
   fprintf(ficlog,"\n");       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
     /*-------- Rewriting paramater file ----------*/     } /* end i1 */
      strcpy(rfileres,"r");    /* "Rparameterfile */   }/* End k1 */
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/   fprintf(fichtm,"</ul>");
      strcat(rfileres,".");    /* */   fflush(fichtm);
      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;  /******************* Gnuplot file **************/
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
     }  
     fprintf(ficres,"#%s\n",version);    char dirfileres[132],optfileres[132];
        int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     /*-------- data file ----------*/    int ng;
     if((fic=fopen(datafile,"r"))==NULL)    {  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
       printf("Problem with datafile: %s\n", datafile);goto end;  /*     printf("Problem with file %s",optionfilegnuplot); */
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
     }  /*   } */
   
     n= lastobs;    /*#ifdef windows */
     severity = vector(1,maxwav);    fprintf(ficgp,"cd \"%s\" \n",pathc);
     outcome=imatrix(1,maxwav+1,1,n);      /*#endif */
     num=ivector(1,n);    m=pow(2,cptcoveff);
     moisnais=vector(1,n);  
     annais=vector(1,n);    strcpy(dirfileres,optionfilefiname);
     moisdc=vector(1,n);    strcpy(optfileres,"vpl");
     andc=vector(1,n);   /* 1eme*/
     agedc=vector(1,n);    for (cpt=1; cpt<= nlstate ; cpt ++) {
     cod=ivector(1,n);     for (k1=1; k1<= m ; k1 ++) {
     weight=vector(1,n);       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
     mint=matrix(1,maxwav,1,n);       fprintf(ficgp,"set xlabel \"Age\" \n\
     anint=matrix(1,maxwav,1,n);  set ylabel \"Probability\" \n\
     s=imatrix(1,maxwav+1,1,n);  set ter png small\n\
     adl=imatrix(1,maxwav+1,1,n);      set size 0.65,0.65\n\
     tab=ivector(1,NCOVMAX);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
     ncodemax=ivector(1,8);  
        for (i=1; i<= nlstate ; i ++) {
     i=1;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     while (fgets(line, MAXLINE, fic) != NULL)    {         else fprintf(ficgp," \%%*lf (\%%*lf)");
       if ((i >= firstobs) && (i <=lastobs)) {       }
               fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
         for (j=maxwav;j>=1;j--){       for (i=1; i<= nlstate ; i ++) {
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           strcpy(line,stra);         else fprintf(ficgp," \%%*lf (\%%*lf)");
           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);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
         }       for (i=1; i<= nlstate ; i ++) {
                 if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);         else fprintf(ficgp," \%%*lf (\%%*lf)");
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);       }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);     }
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    }
     /*2 eme*/
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    
         for (j=ncovcol;j>=1;j--){    for (k1=1; k1<= m ; k1 ++) { 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      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);
         num[i]=atol(stra);      
              for (i=1; i<= nlstate+1 ; i ++) {
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        k=2*i;
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
         i=i+1;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       }          else fprintf(ficgp," \%%*lf (\%%*lf)");
     }        }   
     /* printf("ii=%d", ij);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
        scanf("%d",i);*/        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   imx=i-1; /* Number of individuals */        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 ++) {
   /* for (i=1; i<=imx; i++){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          else fprintf(ficgp," \%%*lf (\%%*lf)");
     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;        fprintf(ficgp,"\" t\"\" w l 0,");
     }*/        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
    /*  for (i=1; i<=imx; i++){        for (j=1; j<= nlstate+1 ; j ++) {
      if (s[4][i]==9)  s[4][i]=-1;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/          else fprintf(ficgp," \%%*lf (\%%*lf)");
          }   
          if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
   /* Calculation of the number of parameter from char model*/        else fprintf(ficgp,"\" t\"\" w l 0,");
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */      }
   Tprod=ivector(1,15);    }
   Tvaraff=ivector(1,15);    
   Tvard=imatrix(1,15,1,2);    /*3eme*/
   Tage=ivector(1,15);          
        for (k1=1; k1<= m ; k1 ++) { 
   if (strlen(model) >1){      for (cpt=1; cpt<= nlstate ; cpt ++) {
     j=0, j1=0, k1=1, k2=1;        k=2+nlstate*(2*cpt-2);
     j=nbocc(model,'+');        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
     j1=nbocc(model,'*');        fprintf(ficgp,"set ter png small\n\
     cptcovn=j+1;  set size 0.65,0.65\n\
     cptcovprod=j1;  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
            /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     strcpy(modelsav,model);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       printf("Error. Non available option model=%s ",model);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
       fprintf(ficlog,"Error. Non available option model=%s ",model);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       goto end;          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     }          
            */
     for(i=(j+1); i>=1;i--){        for (i=1; i< nlstate ; i ++) {
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */          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);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze 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 */    /* CV preval stable (period) */
           cptcovprod--;    for (k1=1; k1<= m ; k1 ++) { 
           cutv(strb,stre,strd,'V');      for (cpt=1; cpt<=nlstate ; cpt ++) {
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/        k=3;
           cptcovage++;        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
             Tage[cptcovage]=i;        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
             /*printf("stre=%s ", stre);*/  set ter png small\nset size 0.65,0.65\n\
         }  unset log y\n\
         else if (strcmp(strd,"age")==0) { /* or age*Vn */  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
           cptcovprod--;        
           cutv(strb,stre,strc,'V');        for (i=1; i< nlstate ; i ++)
           Tvar[i]=atoi(stre);          fprintf(ficgp,"+$%d",k+i+1);
           cptcovage++;        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
           Tage[cptcovage]=i;        
         }        l=3+(nlstate+ndeath)*cpt;
         else {  /* Age is not in the model */        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/        for (i=1; i< nlstate ; i ++) {
           Tvar[i]=ncovcol+k1;          l=3+(nlstate+ndeath)*cpt;
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */          fprintf(ficgp,"+$%d",l+i+1);
           Tprod[k1]=i;        }
           Tvard[k1][1]=atoi(strc); /* m*/        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
           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++)    /* proba elementaires */
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    for(i=1,jk=1; i <=nlstate; i++){
           k1++;      for(k=1; k <=(nlstate+ndeath); k++){
           k2=k2+2;        if (k != i) {
         }          for(j=1; j <=ncovmodel; j++){
       }            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
       else { /* no more sum */            jk++; 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/            fprintf(ficgp,"\n");
        /*  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);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
         scanf("%d",i);*/       for(jk=1; jk <=m; jk++) {
     } /* end of loop + */         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
   } /* end model */         if (ng==2)
             fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);         else
   printf("cptcovprod=%d ", cptcovprod);           fprintf(ficgp,"\nset title \"Probability\"\n");
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
   scanf("%d ",i);*/         i=1;
     fclose(fic);         for(k2=1; k2<=nlstate; k2++) {
            k3=i;
     /*  if(mle==1){*/           for(k=1; k<=(nlstate+ndeath); k++) {
     if (weightopt != 1) { /* Maximisation without weights*/             if (k != k2){
       for(i=1;i<=n;i++) weight[i]=1.0;               if(ng==2)
     }                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
     /*-calculation of age at interview from date of interview and age at death -*/               else
     agev=matrix(1,maxwav,1,imx);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
     for (i=1; i<=imx; i++) {               for(j=3; j <=ncovmodel; j++) {
       for(m=2; (m<= maxwav); m++) {                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
          anint[m][i]=9999;                   ij++;
          s[m][i]=-1;                 }
        }                 else
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       }               }
     }               fprintf(ficgp,")/(1");
                
     for (i=1; i<=imx; i++)  {               for(k1=1; k1 <=nlstate; k1++){   
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
       for(m=1; (m<= maxwav); m++){                 ij=1;
         if(s[m][i] >0){                 for(j=3; j <=ncovmodel; j++){
           if (s[m][i] >= nlstate+1) {                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
             if(agedc[i]>0)                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
               if(moisdc[i]!=99 && andc[i]!=9999)                     ij++;
                 agev[m][i]=agedc[i];                   }
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/                   else
            else {                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
               if (andc[i]!=9999){                 }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                 fprintf(ficgp,")");
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);               }
               agev[m][i]=-1;               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
               }               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
             }               i=i+ncovmodel;
           }             }
           else if(s[m][i] !=9){ /* Should no more exist */           } /* end k */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);         } /* end k2 */
             if(mint[m][i]==99 || anint[m][i]==9999)       } /* end jk */
               agev[m][i]=1;     } /* end ng */
             else if(agev[m][i] <agemin){     fflush(ficgp); 
               agemin=agev[m][i];  }  /* end gnuplot */
               /*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){  /*************** Moving average **************/
               agemax=agev[m][i];  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  
             }    int i, cpt, cptcod;
             /*agev[m][i]=anint[m][i]-annais[i];*/    int modcovmax =1;
             /*   agev[m][i] = age[i]+2*m;*/    int mobilavrange, mob;
           }    double age;
           else { /* =9 */  
             agev[m][i]=1;    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
             s[m][i]=-1;                             a covariate has 2 modalities */
           }    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
         }  
         else /*= 0 Unknown */    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
           agev[m][i]=1;      if(mobilav==1) mobilavrange=5; /* default */
       }      else mobilavrange=mobilav;
          for (age=bage; age<=fage; age++)
     }        for (i=1; i<=nlstate;i++)
     for (i=1; i<=imx; i++)  {          for (cptcod=1;cptcod<=modcovmax;cptcod++)
       for(m=1; (m<= maxwav); m++){            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
         if (s[m][i] > (nlstate+ndeath)) {      /* We keep the original values on the extreme ages bage, fage and for 
           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);           fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
           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);           we use a 5 terms etc. until the borders are no more concerned. 
           goto end;      */ 
         }      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++){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
     free_vector(severity,1,maxwav);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
     free_imatrix(outcome,1,maxwav+1,1,n);                }
     free_vector(moisnais,1,n);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
     free_vector(annais,1,n);            }
     /* free_matrix(mint,1,maxwav,1,n);          }
        free_matrix(anint,1,maxwav,1,n);*/        }/* end age */
     free_vector(moisdc,1,n);      }/* end mob */
     free_vector(andc,1,n);    }else return -1;
     return 0;
      }/* End movingaverage */
     wav=ivector(1,imx);  
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  /************** 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){
     /* Concatenates waves */    /* proj1, year, month, day of starting projection 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);       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).
       Tcode=ivector(1,100);    */
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
       ncodemax[1]=1;    int *popage;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    double agec; /* generic age */
          double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
    codtab=imatrix(1,100,1,10);    double *popeffectif,*popcount;
    h=0;    double ***p3mat;
    m=pow(2,cptcoveff);    double ***mobaverage;
      char fileresf[FILENAMELENGTH];
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){    agelim=AGESUP;
        for(j=1; j <= ncodemax[k]; j++){    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){   
            h++;    strcpy(fileresf,"f"); 
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    strcat(fileresf,fileres);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/    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);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
       codtab[1][2]=1;codtab[2][2]=2; */  
    /* for(i=1; i <=m ;i++){    if (cptcoveff==0) ncodemax[cptcoveff]=1;
       for(k=1; k <=cptcovn; k++){  
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    if (mobilav!=0) {
       }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       printf("\n");      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
       }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       scanf("%d",i);*/        printf(" Error in movingaverage mobilav=%d\n",mobilav);
          }
    /* Calculates basic frequencies. Computes observed prevalence at single age    }
        and prints on file fileres'p'. */  
     stepsize=(int) (stepm+YEARM-1)/YEARM;
        if (stepm<=12) stepsize=1;
        if(estepm < stepm){
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      printf ("Problem %d lower than %d\n",estepm, stepm);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    else  hstepm=estepm;   
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    hstepm=hstepm/stepm; 
          yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
     /* For Powell, parameters are in a vector p[] starting at p[1]                                 fractional in yp1 */
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    anprojmean=yp;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     if(mle==1){    yp1=modf((yp2*30.5),&yp);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    jprojmean=yp;
     }    if(jprojmean==0) jprojmean=1;
        if(mprojmean==0) jprojmean=1;
     /*--------- 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);    i1=cptcoveff;
      if (cptcovn < 1){i1=1;}
     
    jk=1;    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    fprintf(ficresf,"#****** Routine prevforecast **\n");
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  
    for(i=1,jk=1; i <=nlstate; i++){  /*            if (h==(int)(YEARM*yearp)){ */
      for(k=1; k <=(nlstate+ndeath); k++){    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
        if (k != i)      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
          {        k=k+1;
            printf("%d%d ",i,k);        fprintf(ficresf,"\n#******");
            fprintf(ficlog,"%d%d ",i,k);        for(j=1;j<=cptcoveff;j++) {
            fprintf(ficres,"%1d%1d ",i,k);          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]]);
            for(j=1; j <=ncovmodel; j++){        }
              printf("%f ",p[jk]);        fprintf(ficresf,"******\n");
              fprintf(ficlog,"%f ",p[jk]);        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
              fprintf(ficres,"%f ",p[jk]);        for(j=1; j<=nlstate+ndeath;j++){ 
              jk++;          for(i=1; i<=nlstate;i++)              
            }            fprintf(ficresf," p%d%d",i,j);
            printf("\n");          fprintf(ficresf," p.%d",j);
            fprintf(ficlog,"\n");        }
            fprintf(ficres,"\n");        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
          }          fprintf(ficresf,"\n");
      }          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
    }  
    if(mle==1){          for (agec=fage; agec>=(ageminpar-1); agec--){ 
      /* Computing hessian and covariance matrix */            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
      ftolhess=ftol; /* Usually correct */            nhstepm = nhstepm/hstepm; 
      hesscov(matcov, p, npar, delti, ftolhess, func);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    }            oldm=oldms;savm=savms;
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
    printf("# Scales (for hessian or gradient estimation)\n");          
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");            for (h=0; h<=nhstepm; h++){
    for(i=1,jk=1; i <=nlstate; i++){              if (h*hstepm/YEARM*stepm ==yearp) {
      for(j=1; j <=nlstate+ndeath; j++){                fprintf(ficresf,"\n");
        if (j!=i) {                for(j=1;j<=cptcoveff;j++) 
          fprintf(ficres,"%1d%1d",i,j);                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
          printf("%1d%1d",i,j);                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
          fprintf(ficlog,"%1d%1d",i,j);              } 
          for(k=1; k<=ncovmodel;k++){              for(j=1; j<=nlstate+ndeath;j++) {
            printf(" %.5e",delti[jk]);                ppij=0.;
            fprintf(ficlog," %.5e",delti[jk]);                for(i=1; i<=nlstate;i++) {
            fprintf(ficres," %.5e",delti[jk]);                  if (mobilav==1) 
            jk++;                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
          }                  else {
          printf("\n");                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
          fprintf(ficlog,"\n");                  }
          fprintf(ficres,"\n");                  if (h*hstepm/YEARM*stepm== yearp) {
        }                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
      }                  }
    }                } /* end i */
                    if (h*hstepm/YEARM*stepm==yearp) {
    k=1;                  fprintf(ficresf," %.3f", ppij);
    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)              }/* end j */
      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");            } /* end h */
    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");            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    for(i=1;i<=npar;i++){          } /* end agec */
      /*  if (k>nlstate) k=1;        } /* end yearp */
          i1=(i-1)/(ncovmodel*nlstate)+1;      } /* end cptcod */
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    } /* end  cptcov */
          printf("%s%d%d",alph[k],i1,tab[i]);*/         
      fprintf(ficres,"%3d",i);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      if(mle==1)  
        printf("%3d",i);    fclose(ficresf);
      fprintf(ficlog,"%3d",i);  }
      for(j=1; j<=i;j++){  
        fprintf(ficres," %.5e",matcov[i][j]);  /************** Forecasting *****not tested NB*************/
        if(mle==1)  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){
          printf(" %.5e",matcov[i][j]);    
        fprintf(ficlog," %.5e",matcov[i][j]);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
      }    int *popage;
      fprintf(ficres,"\n");    double calagedatem, agelim, kk1, kk2;
      if(mle==1)    double *popeffectif,*popcount;
        printf("\n");    double ***p3mat,***tabpop,***tabpopprev;
      fprintf(ficlog,"\n");    double ***mobaverage;
      k++;    char filerespop[FILENAMELENGTH];
    }  
        tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    while((c=getc(ficpar))=='#' && c!= EOF){    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      ungetc(c,ficpar);    agelim=AGESUP;
      fgets(line, MAXLINE, ficpar);    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
      puts(line);    
      fputs(line,ficparo);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    }    
    ungetc(c,ficpar);    
    estepm=0;    strcpy(filerespop,"pop"); 
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);    strcat(filerespop,fileres);
    if (estepm==0 || estepm < stepm) estepm=stepm;    if((ficrespop=fopen(filerespop,"w"))==NULL) {
    if (fage <= 2) {      printf("Problem with forecast resultfile: %s\n", filerespop);
      bage = ageminpar;      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
      fage = agemaxpar;    }
    }    printf("Computing forecasting: result on file '%s' \n", filerespop);
        fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
    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);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);  
        if (mobilav!=0) {
    while((c=getc(ficpar))=='#' && c!= EOF){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      ungetc(c,ficpar);      if (movingaverage(probs, ageminpar, 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);  
      stepsize=(int) (stepm+YEARM-1)/YEARM;
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    if (stepm<=12) stepsize=1;
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    agelim=AGESUP;
        
    while((c=getc(ficpar))=='#' && c!= EOF){    hstepm=1;
      ungetc(c,ficpar);    hstepm=hstepm/stepm; 
      fgets(line, MAXLINE, ficpar);    
      puts(line);    if (popforecast==1) {
      fputs(line,ficparo);      if((ficpop=fopen(popfile,"r"))==NULL) {
    }        printf("Problem with population file : %s\n",popfile);exit(0);
    ungetc(c,ficpar);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
        } 
       popage=ivector(0,AGESUP);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;      popeffectif=vector(0,AGESUP);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      popcount=vector(0,AGESUP);
       
   fscanf(ficpar,"pop_based=%d\n",&popbased);      i=1;   
   fprintf(ficparo,"pop_based=%d\n",popbased);        while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
   fprintf(ficres,"pop_based=%d\n",popbased);       
        imx=i;
   while((c=getc(ficpar))=='#' && c!= EOF){      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);  
     puts(line);    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
     fputs(line,ficparo);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   }        k=k+1;
   ungetc(c,ficpar);        fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
   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);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][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);        fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
 while((c=getc(ficpar))=='#' && c!= EOF){        if (popforecast==1)  fprintf(ficrespop," [Population]");
     ungetc(c,ficpar);        
     fgets(line, MAXLINE, ficpar);        for (cpt=0; cpt<=0;cpt++) { 
     puts(line);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
     fputs(line,ficparo);          
   }          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   ungetc(c,ficpar);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);            
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);            oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          
             for (h=0; h<=nhstepm; h++){
 /*------------ gnuplot -------------*/              if (h==(int) (calagedatem+YEARM*cpt)) {
   strcpy(optionfilegnuplot,optionfilefiname);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   strcat(optionfilegnuplot,".gp");              } 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {              for(j=1; j<=nlstate+ndeath;j++) {
     printf("Problem with file %s",optionfilegnuplot);                kk1=0.;kk2=0;
   }                for(i=1; i<=nlstate;i++) {              
   fclose(ficgp);                  if (mobilav==1) 
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
 /*--------- index.htm --------*/                  else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
   strcpy(optionfilehtm,optionfile);                  }
   strcat(optionfilehtm,".htm");                }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {                if (h==(int)(calagedatem+12*cpt)){
     printf("Problem with %s \n",optionfilehtm), exit(0);                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
   }                    /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
   fprintf(fichtm,"<body> <font size=\"2\">%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              for(i=1; i<=nlstate;i++){
 Total number of observations=%d <br>\n                kk1=0.;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n                  for(j=1; j<=nlstate;j++){
 <hr  size=\"2\" color=\"#EC5E5E\">                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
  <ul><li><h4>Parameter files</h4>\n                  }
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
  - Log file of the run: <a href=\"%s\">%s</a><br>\n              }
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);  
   fclose(fichtm);              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);            }
              free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 /*------------ free_vector  -------------*/          }
  chdir(path);        }
     
  free_ivector(wav,1,imx);    /******/
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
  free_ivector(num,1,n);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
  free_vector(agedc,1,n);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
  /*free_matrix(covar,1,NCOVMAX,1,n);*/            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
  fclose(ficparo);            nhstepm = nhstepm/hstepm; 
  fclose(ficres);            
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
   /*--------------- Prevalence limit --------------*/            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
              for (h=0; h<=nhstepm; h++){
   strcpy(filerespl,"pl");              if (h==(int) (calagedatem+YEARM*cpt)) {
   strcat(filerespl,fileres);                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {              } 
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;              for(j=1; j<=nlstate+ndeath;j++) {
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;                kk1=0.;kk2=0;
   }                for(i=1; i<=nlstate;i++) {              
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);                }
   fprintf(ficrespl,"#Prevalence limit\n");                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
   fprintf(ficrespl,"#Age ");              }
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);            }
   fprintf(ficrespl,"\n");            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            }
   prlim=matrix(1,nlstate,1,nlstate);        }
   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 */    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
   k=0;    if (popforecast==1) {
   agebase=ageminpar;      free_ivector(popage,0,AGESUP);
   agelim=agemaxpar;      free_vector(popeffectif,0,AGESUP);
   ftolpl=1.e-10;      free_vector(popcount,0,AGESUP);
   i1=cptcoveff;    }
   if (cptcovn < 1){i1=1;}    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   for(cptcov=1;cptcov<=i1;cptcov++){    fclose(ficrespop);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  } /* End of popforecast */
         k=k+1;  
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  int fileappend(FILE *fichier, char *optionfich)
         fprintf(ficrespl,"\n#******");  {
         printf("\n#******");    if((fichier=fopen(optionfich,"a"))==NULL) {
         fprintf(ficlog,"\n#******");      printf("Problem with file: %s\n", optionfich);
         for(j=1;j<=cptcoveff;j++) {      fprintf(ficlog,"Problem with file: %s\n", optionfich);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      return (0);
           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]]);    fflush(fichier);
         }    return (1);
         fprintf(ficrespl,"******\n");  }
         printf("******\n");  
         fprintf(ficlog,"******\n");  
          /**************** function prwizard **********************/
         for (age=agebase; age<=agelim; age++){  void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  {
           fprintf(ficrespl,"%.0f",age );  
           for(i=1; i<=nlstate;i++)    /* Wizard to print covariance matrix template */
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");    char ca[32], cb[32], cc[32];
         }    int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
       }    int numlinepar;
     }  
   fclose(ficrespl);    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   /*------------- h Pij x at various ages ------------*/    for(i=1; i <=nlstate; i++){
        jj=0;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      for(j=1; j <=nlstate+ndeath; j++){
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        if(j==i) continue;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        jj++;
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;        /*ca[0]= k+'a'-1;ca[1]='\0';*/
   }        printf("%1d%1d",i,j);
   printf("Computing pij: result on file '%s' \n", filerespij);        fprintf(ficparo,"%1d%1d",i,j);
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);        for(k=1; k<=ncovmodel;k++){
            /*        printf(" %lf",param[i][j][k]); */
   stepsize=(int) (stepm+YEARM-1)/YEARM;          /*        fprintf(ficparo," %lf",param[i][j][k]); */
   /*if (stepm<=24) stepsize=2;*/          printf(" 0.");
           fprintf(ficparo," 0.");
   agelim=AGESUP;        }
   hstepm=stepsize*YEARM; /* Every year of age */        printf("\n");
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */        fprintf(ficparo,"\n");
       }
   /* hstepm=1;   aff par mois*/    }
     printf("# Scales (for hessian or gradient estimation)\n");
   k=0;    fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
   for(cptcov=1;cptcov<=i1;cptcov++){    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    for(i=1; i <=nlstate; i++){
       k=k+1;      jj=0;
         fprintf(ficrespij,"\n#****** ");      for(j=1; j <=nlstate+ndeath; j++){
         for(j=1;j<=cptcoveff;j++)        if(j==i) continue;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        jj++;
         fprintf(ficrespij,"******\n");        fprintf(ficparo,"%1d%1d",i,j);
                printf("%1d%1d",i,j);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        fflush(stdout);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        for(k=1; k<=ncovmodel;k++){
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           /*      nhstepm=nhstepm*YEARM; aff par mois*/          printf(" 0.");
           fprintf(ficparo," 0.");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
           oldm=oldms;savm=savms;        numlinepar++;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          printf("\n");
           fprintf(ficrespij,"# Age");        fprintf(ficparo,"\n");
           for(i=1; i<=nlstate;i++)      }
             for(j=1; j<=nlstate+ndeath;j++)    }
               fprintf(ficrespij," %1d-%1d",i,j);    printf("# Covariance matrix\n");
           fprintf(ficrespij,"\n");  /* # 121 Var(a12)\n\ */
            for (h=0; h<=nhstepm; h++){  /* # 122 Cov(b12,a12) Var(b12)\n\ */
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
             for(i=1; i<=nlstate;i++)  /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
               for(j=1; j<=nlstate+ndeath;j++)  /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
             fprintf(ficrespij,"\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" */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fflush(stdout);
           fprintf(ficrespij,"\n");    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" */
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    
     for(itimes=1;itimes<=2;itimes++){
   fclose(ficrespij);      jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
   /*---------- Forecasting ------------------*/          if(j==i) continue;
   if((stepm == 1) && (strcmp(model,".")==0)){          for(k=1; k<=ncovmodel;k++){
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);            jj++;
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);            ca[0]= k+'a'-1;ca[1]='\0';
   }            if(itimes==1){
   else{              printf("#%1d%1d%d",i,j,k);
     erreur=108;              fprintf(ficparo,"#%1d%1d%d",i,j,k);
     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);            }else{
     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);              printf("%1d%1d%d",i,j,k);
   }              fprintf(ficparo,"%1d%1d%d",i,j,k);
                /*  printf(" %.5le",matcov[i][j]); */
             }
   /*---------- Health expectancies and variances ------------*/            ll=0;
             for(li=1;li <=nlstate; li++){
   strcpy(filerest,"t");              for(lj=1;lj <=nlstate+ndeath; lj++){
   strcat(filerest,fileres);                if(lj==li) continue;
   if((ficrest=fopen(filerest,"w"))==NULL) {                for(lk=1;lk<=ncovmodel;lk++){
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                  ll++;
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;                  if(ll<=jj){
   }                    cb[0]= lk +'a'-1;cb[1]='\0';
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                    if(ll<jj){
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);                      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);
   strcpy(filerese,"e");                      }else{
   strcat(filerese,fileres);                        printf(" 0.");
   if((ficreseij=fopen(filerese,"w"))==NULL) {                        fprintf(ficparo," 0.");
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                      }
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                    }else{
   }                      if(itimes==1){
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);                        printf(" Var(%s%1d%1d)",ca,i,j);
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);                        fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
   strcpy(fileresv,"v");                        printf(" 0.");
   strcat(fileresv,fileres);                        fprintf(ficparo," 0.");
   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);                  }
   }                } /* end lk */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);              } /* end lj */
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);            } /* end li */
   calagedate=-1;            printf("\n");
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            fprintf(ficparo,"\n");
             numlinepar++;
   k=0;          } /* end k*/
   for(cptcov=1;cptcov<=i1;cptcov++){        } /*end j */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      } /* end i */
       k=k+1;    } /* end itimes */
       fprintf(ficrest,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)  } /* end of prwizard */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /******************* Gompertz Likelihood ******************************/
       fprintf(ficrest,"******\n");  double gompertz(double x[])
   { 
       fprintf(ficreseij,"\n#****** ");    double A,B,L=0.0,sump=0.,num=0.;
       for(j=1;j<=cptcoveff;j++)    int i,n=0; /* n is the size of the sample */
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for (i=0;i<=imx-1 ; i++) {
       fprintf(ficreseij,"******\n");      sump=sump+weight[i];
       /*    sump=sump+1;*/
       fprintf(ficresvij,"\n#****** ");      num=num+1;
       for(j=1;j<=cptcoveff;j++)    }
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   
       fprintf(ficresvij,"******\n");   
     /* for (i=0; i<=imx; i++) 
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);       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]);*/
       oldm=oldms;savm=savms;  
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      for (i=1;i<=imx ; i++)
        {
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        if (cens[i]==1 & wav[i]>1)
       oldm=oldms;savm=savms;          A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);        
       if(popbased==1){        if (cens[i]==0 & wav[i]>1)
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);          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) {
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          L=L+A*weight[i];
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",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]);*/
       fprintf(ficrest,"\n");        }
       }
       epj=vector(1,nlstate+1);  
       for(age=bage; age <=fage ;age++){   /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   
         if (popbased==1) {    return -2*L*num/sump;
           for(i=1; i<=nlstate;i++)  }
             prlim[i][i]=probs[(int)age][i][k];  
         }  /******************* Printing html file ***********/
          void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
         fprintf(ficrest," %4.0f",age);                    int lastpass, int stepm, int weightopt, char model[],\
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                    int imx,  double p[],double **matcov){
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    int i;
             epj[j] += prlim[i][i]*eij[i][j][(int)age];  
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    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);
           epj[nlstate+1] +=epj[j];    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\">");
         for(i=1, vepp=0.;i <=nlstate;i++)    fprintf(fichtm,"</ul>");
           for(j=1;j <=nlstate;j++)    fflush(fichtm);
             vepp += vareij[i][j][(int)age];  }
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));  
         for(j=1;j <=nlstate;j++){  /******************* Gnuplot file **************/
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));  void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
         }  
         fprintf(ficrest,"\n");    char dirfileres[132],optfileres[132];
       }    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     }    int ng;
   }  
 free_matrix(mint,1,maxwav,1,n);  
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    /*#ifdef windows */
     free_vector(weight,1,n);    fprintf(ficgp,"cd \"%s\" \n",pathc);
   fclose(ficreseij);      /*#endif */
   fclose(ficresvij);  
   fclose(ficrest);  
   fclose(ficpar);    strcpy(dirfileres,optionfilefiname);
   free_vector(epj,1,nlstate+1);    strcpy(optfileres,"vpl");
      fprintf(ficgp,"set out \"graphmort.png\"\n "); 
   /*------- Variance limit prevalence------*/      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"); 
   strcpy(fileresvpl,"vpl");    fprintf(ficgp, "set size 0.65,0.65\n");
   strcat(fileresvpl,fileres);    fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  } 
     exit(0);  
   }  
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  
   
   k=0;  /***********************************************/
   for(cptcov=1;cptcov<=i1;cptcov++){  /**************** Main Program *****************/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  /***********************************************/
       k=k+1;  
       fprintf(ficresvpl,"\n#****** ");  int main(int argc, char *argv[])
       for(j=1;j<=cptcoveff;j++)  {
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
       fprintf(ficresvpl,"******\n");    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
          int jj, ll, li, lj, lk, imk;
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    int numlinepar=0; /* Current linenumber of parameter file */
       oldm=oldms;savm=savms;    int itimes;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    int NDIM=2;
     }  
  }    char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
   fclose(ficresvpl);    /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
   /*---------- End : free ----------------*/    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
      double fret;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    double **xi,tmp,delta;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
      double dum; /* Dummy variable */
      double ***p3mat;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    double ***mobaverage;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    int *indx;
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    char line[MAXLINE], linepar[MAXLINE];
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
      char pathr[MAXLINE], pathimach[MAXLINE]; 
   free_matrix(matcov,1,npar,1,npar);    int firstobs=1, lastobs=10;
   free_vector(delti,1,npar);    int sdeb, sfin; /* Status at beginning and end */
   free_matrix(agev,1,maxwav,1,imx);    int c,  h , cpt,l;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
   fprintf(fichtm,"\n</body>");    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
   fclose(fichtm);    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
   fclose(ficgp);    int mobilav=0,popforecast=0;
      int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
   if(erreur >0){    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
     printf("End of Imach with error or warning %d\n",erreur);  
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);    double bage, fage, age, agelim, agebase;
   }else{    double ftolpl=FTOL;
    printf("End of Imach\n");    double **prlim;
    fprintf(ficlog,"End of Imach\n");    double *severity;
   }    double ***param; /* Matrix of parameters */
   printf("See log file on %s\n",filelog);    double  *p;
   fclose(ficlog);    double **matcov; /* Matrix of covariance */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    double ***delti3; /* Scale */
      double *delti; /* Scale */
   /* 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);*/    double ***eij, ***vareij;
   /*printf("Total time was %d uSec.\n", total_usecs);*/    double **varpl; /* Variances of prevalence limits by age */
   /*------ End -----------*/    double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
  end:    double **ximort;
 #ifdef windows    char *alph[]={"a","a","b","c","d","e"}, str[4];
   /* chdir(pathcd);*/    int *dcwave;
 #endif  
  /*system("wgnuplot graph.plt");*/    char z[1]="c", occ;
  /*system("../gp37mgw/wgnuplot graph.plt");*/  
  /*system("cd ../gp37mgw");*/    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    char strstart[80], *strt, strtend[80];
  strcpy(plotcmd,GNUPLOTPROGRAM);    char *stratrunc;
  strcat(plotcmd," ");    int lstra;
  strcat(plotcmd,optionfilegnuplot);  
  system(plotcmd);    long total_usecs;
    
 #ifdef windows  /*   setlocale (LC_ALL, ""); */
   while (z[0] != 'q') {  /*   bindtextdomain (PACKAGE, LOCALEDIR); */
     /* chdir(path); */  /*   textdomain (PACKAGE); */
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");  /*   setlocale (LC_CTYPE, ""); */
     scanf("%s",z);  /*   setlocale (LC_MESSAGES, ""); */
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') system(optionfilehtm);    /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     else if (z[0] == 'g') system(plotcmd);    (void) gettimeofday(&start_time,&tzp);
     else if (z[0] == 'q') exit(0);    curr_time=start_time;
   }    tm = *localtime(&start_time.tv_sec);
 #endif    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 parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (j=1; j<=lastpass; j++)
           if (s[j][i]>nlstate) {
             dcwave[i]=j;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];agecens[i]=1.; 
           if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
           cens[i]=1;
           
           if (ageexmed[i]<1) cens[i]=-1;
           if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
   
       p[1]=0.1; p[2]=0.1;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow-mort"); 
     strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
     /*  for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     */
     fprintf(ficrespow,"\n");
   
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM,delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov);
     } /* Endof if mle==-3 */
   
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficrespl,"#Stable prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
   
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /*---------- Health expectancies and variances ------------*/
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total LEs with variances: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficreseij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
           }
   
    
           fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficreseij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of stable prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocaltime at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
     strcpy(plotcmd,"\"");
     strcat(plotcmd,pathimach);
     strcat(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd,"\"");
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     if((outcmd=system(plotcmd)) != 0){
       printf(" Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.51  
changed lines
  Added in v.1.104


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