Diff for /imach/src/imach.c between versions 1.47 and 1.104

version 1.47, 2002/06/10 13:12:01 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
 #else    concerning matrix of covariance. It has extension -cov.htm.
 #define DIRSEPARATOR '/'  
 #endif    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
 char version[80]="Imach version 0.8g, May 2002, INED-EUROREVES ";    mle=-1 a template is output in file "or"mypar.txt with the design
 int erreur; /* Error number */    of the covariance matrix to be input.
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.89  2003/06/24 12:30:52  brouard
 int npar=NPARMAX;    (Module): Some bugs corrected for windows. Also, when
 int nlstate=2; /* Number of live states */    mle=-1 a template is output in file "or"mypar.txt with the design
 int ndeath=1; /* Number of dead states */    of the covariance matrix to be input.
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.88  2003/06/23 17:54:56  brouard
     * 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 *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.87  2003/06/18 12:26:01  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    Version 0.96
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.86  2003/06/17 20:04:08  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    (Module): Change position of html and gnuplot routines and added
 double jmean; /* Mean space between 2 waves */    routine fileappend.
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.85  2003/06/17 13:12:43  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    * imach.c (Repository): Check when date of death was earlier that
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    current date of interview. It may happen when the death was just
 FILE *fichtm; /* Html File */    prior to the death. In this case, dh was negative and likelihood
 FILE *ficreseij;    was wrong (infinity). We still send an "Error" but patch by
 char filerese[FILENAMELENGTH];    assuming that the date of death was just one stepm after the
 FILE  *ficresvij;    interview.
 char fileresv[FILENAMELENGTH];    (Repository): Because some people have very long ID (first column)
 FILE  *ficresvpl;    we changed int to long in num[] and we added a new lvector for
 char fileresvpl[FILENAMELENGTH];    memory allocation. But we also truncated to 8 characters (left
 char title[MAXLINE];    truncation)
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    (Repository): No more line truncation errors.
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  
     Revision 1.84  2003/06/13 21:44:43  brouard
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    * imach.c (Repository): Replace "freqsummary" at a correct
     place. It differs from routine "prevalence" which may be called
 char filerest[FILENAMELENGTH];    many times. Probs is memory consuming and must be used with
 char fileregp[FILENAMELENGTH];    parcimony.
 char popfile[FILENAMELENGTH];    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.82  2003/06/05 15:57:20  brouard
 #define FTOL 1.0e-10    Add log in  imach.c and  fullversion number is now printed.
   
 #define NRANSI  */
 #define ITMAX 200  /*
      Interpolated Markov Chain
 #define TOL 2.0e-4  
     Short summary of the programme:
 #define CGOLD 0.3819660    
 #define ZEPS 1.0e-10    This program computes Healthy Life Expectancies from
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     first survey ("cross") where individuals from different ages are
 #define GOLD 1.618034    interviewed on their health status or degree of disability (in the
 #define GLIMIT 100.0    case of a health survey which is our main interest) -2- at least a
 #define TINY 1.0e-20    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
 static double maxarg1,maxarg2;    computed from the time spent in each health state according to a
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    model. More health states you consider, more time is necessary to reach the
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Maximum Likelihood of the parameters involved in the model.  The
      simplest model is the multinomial logistic model where pij is the
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    probability to be observed in state j at the second wave
 #define rint(a) floor(a+0.5)    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
 static double sqrarg;    'age' is age and 'sex' is a covariate. If you want to have a more
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    complex model than "constant and age", you should modify the program
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
 int imx;    convergence.
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    The advantage of this computer programme, compared to a simple
     multinomial logistic model, is clear when the delay between waves is not
 int estepm;    identical for each individual. Also, if a individual missed an
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    intermediate interview, the information is lost, but taken into
     account using an interpolation or extrapolation.  
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    hPijx is the probability to be observed in state i at age x+h
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    conditional to the observed state i at age x. The delay 'h' can be
 double **pmmij, ***probs, ***mobaverage;    split into an exact number (nh*stepm) of unobserved intermediate
 double dateintmean=0;    states. This elementary transition (by month, quarter,
     semester or year) is modelled as a multinomial logistic.  The hPx
 double *weight;    matrix is simply the matrix product of nh*stepm elementary matrices
 int **s; /* Status */    and the contribution of each individual to the likelihood is simply
 double *agedc, **covar, idx;    hPijx.
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Also this programme outputs the covariance matrix of the parameters but also
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    of the life expectancies. It also computes the stable prevalence. 
 double ftolhess; /* Tolerance for computing hessian */    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 /**************** split *************************/             Institut national d'études démographiques, Paris.
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    This software have been partly granted by Euro-REVES, a concerted action
 {    from the European Union.
    char *s;                             /* pointer */    It is copyrighted identically to a GNU software product, ie programme and
    int  l1, l2;                         /* length counters */    software can be distributed freely for non commercial use. Latest version
     can be accessed at http://euroreves.ined.fr/imach .
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
    s = strrchr( path,  DIRSEPARATOR );          /* find last / */    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
    if ( s == NULL ) {                   /* no directory, so use current */    
 #if     defined(__bsd__)                /* get current working directory */    **********************************************************************/
       extern char       *getwd( );  /*
     main
       if ( getwd( dirc ) == NULL ) {    read parameterfile
 #else    read datafile
       extern char       *getcwd( );    concatwav
     freqsummary
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    if (mle >= 1)
 #endif      mlikeli
          return( GLOCK_ERROR_GETCWD );    print results files
       }    if mle==1 
       strcpy( name, path );             /* we've got it */       computes hessian
    } else {                             /* strip direcotry from path */    read end of parameter file: agemin, agemax, bage, fage, estepm
       s++;                              /* after this, the filename */        begin-prev-date,...
       l2 = strlen( s );                 /* length of filename */    open gnuplot file
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    open html file
       strcpy( name, s );                /* save file name */    stable prevalence
       strncpy( dirc, path, l1 - l2 );   /* now the directory */     for age prevalim()
       dirc[l1-l2] = 0;                  /* add zero */    h Pij x
    }    variance of p varprob
    l1 = strlen( dirc );                 /* length of directory */    forecasting if prevfcast==1 prevforecast call prevalence()
 #ifdef windows    health expectancies
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Variance-covariance of DFLE
 #else    prevalence()
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }     movingaverage()
 #endif    varevsij() 
    s = strrchr( name, '.' );            /* find last / */    if popbased==1 varevsij(,popbased)
    s++;    total life expectancies
    strcpy(ext,s);                       /* save extension */    Variance of stable prevalence
    l1= strlen( name);   end
    l2= strlen( s)+1;  */
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;  
    return( 0 );                         /* we're done */  
 }   
   #include <math.h>
   #include <stdio.h>
 /******************************************/  #include <stdlib.h>
   #include <unistd.h>
 void replace(char *s, char*t)  
 {  /* #include <sys/time.h> */
   int i;  #include <time.h>
   int lg=20;  #include "timeval.h"
   i=0;  
   lg=strlen(t);  /* #include <libintl.h> */
   for(i=0; i<= lg; i++) {  /* #define _(String) gettext (String) */
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';  #define MAXLINE 256
   }  #define GNUPLOTPROGRAM "gnuplot"
 }  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
 int nbocc(char *s, char occ)  /*#define DEBUG*/
 {  /*#define windows*/
   int i,j=0;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   int lg=20;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   i=0;  
   lg=strlen(s);  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   for(i=0; i<= lg; i++) {  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   if  (s[i] == occ ) j++;  
   }  #define NINTERVMAX 8
   return j;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 }  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 8 /* Maximum number of covariates */
 void cutv(char *u,char *v, char*t, char occ)  #define MAXN 20000
 {  #define YEARM 12. /* Number of months per year */
   int i,lg,j,p=0;  #define AGESUP 130
   i=0;  #define AGEBASE 40
   for(j=0; j<=strlen(t)-1; j++) {  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  #ifdef UNIX
   }  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
   lg=strlen(t);  #else
   for(j=0; j<p; j++) {  #define DIRSEPARATOR '\\'
     (u[j] = t[j]);  #define ODIRSEPARATOR '/'
   }  #endif
      u[p]='\0';  
   /* $Id$ */
    for(j=0; j<= lg; j++) {  /* $State$ */
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }  char version[]="Imach version 0.98, September 2005, INED-EUROREVES ";
 }  char fullversion[]="$Revision$ $Date$"; 
   int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 /********************** nrerror ********************/  int nvar;
   int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 void nrerror(char error_text[])  int npar=NPARMAX;
 {  int nlstate=2; /* Number of live states */
   fprintf(stderr,"ERREUR ...\n");  int ndeath=1; /* Number of dead states */
   fprintf(stderr,"%s\n",error_text);  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   exit(1);  int popbased=0;
 }  
 /*********************** vector *******************/  int *wav; /* Number of waves for this individuual 0 is possible */
 double *vector(int nl, int nh)  int maxwav; /* Maxim number of waves */
 {  int jmin, jmax; /* min, max spacing between 2 waves */
   double *v;  int gipmx, gsw; /* Global variables on the number of contributions 
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));                     to the likelihood and the sum of weights (done by funcone)*/
   if (!v) nrerror("allocation failure in vector");  int mle, weightopt;
   return v-nl+NR_END;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 }  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 /************************ free vector ******************/             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 void free_vector(double*v, int nl, int nh)  double jmean; /* Mean space between 2 waves */
 {  double **oldm, **newm, **savm; /* Working pointers to matrices */
   free((FREE_ARG)(v+nl-NR_END));  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 }  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog, *ficrespow;
 /************************ivector *******************************/  int globpr; /* Global variable for printing or not */
 int *ivector(long nl,long nh)  double fretone; /* Only one call to likelihood */
 {  long ipmx; /* Number of contributions */
   int *v;  double sw; /* Sum of weights */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  char filerespow[FILENAMELENGTH];
   if (!v) nrerror("allocation failure in ivector");  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   return v-nl+NR_END;  FILE *ficresilk;
 }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 /******************free ivector **************************/  FILE *fichtm, *fichtmcov; /* Html File */
 void free_ivector(int *v, long nl, long nh)  FILE *ficreseij;
 {  char filerese[FILENAMELENGTH];
   free((FREE_ARG)(v+nl-NR_END));  FILE  *ficresvij;
 }  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
 /******************* imatrix *******************************/  char fileresvpl[FILENAMELENGTH];
 int **imatrix(long nrl, long nrh, long ncl, long nch)  char title[MAXLINE];
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 {  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   int **m;  char command[FILENAMELENGTH];
    int  outcmd=0;
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  char filelog[FILENAMELENGTH]; /* Log file */
   m -= nrl;  char filerest[FILENAMELENGTH];
    char fileregp[FILENAMELENGTH];
    char popfile[FILENAMELENGTH];
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   m[nrl] -= ncl;  struct timezone tzp;
    extern int gettimeofday();
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
    long time_value;
   /* return pointer to array of pointers to rows */  extern long time();
   return m;  char strcurr[80], strfor[80];
 }  
   #define NR_END 1
 /****************** free_imatrix *************************/  #define FREE_ARG char*
 void free_imatrix(m,nrl,nrh,ncl,nch)  #define FTOL 1.0e-10
       int **m;  
       long nch,ncl,nrh,nrl;  #define NRANSI 
      /* free an int matrix allocated by imatrix() */  #define ITMAX 200 
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #define TOL 2.0e-4 
   free((FREE_ARG) (m+nrl-NR_END));  
 }  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 /******************* matrix *******************************/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {  #define GOLD 1.618034 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  #define GLIMIT 100.0 
   double **m;  #define TINY 1.0e-20 
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  static double maxarg1,maxarg2;
   if (!m) nrerror("allocation failure 1 in matrix()");  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   m += NR_END;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   m -= nrl;    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define rint(a) floor(a+0.5)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  static double sqrarg;
   m[nrl] -= ncl;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int agegomp= AGEGOMP;
   return m;  
 }  int imx; 
   int stepm=1;
 /*************************free matrix ************************/  /* Stepm, step in month: minimum step interpolation*/
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {  int estepm;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   free((FREE_ARG)(m+nrl-NR_END));  
 }  int m,nb;
   long *num;
 /******************* ma3x *******************************/  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 {  double **pmmij, ***probs;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  double *ageexmed,*agecens;
   double ***m;  double dateintmean=0;
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  double *weight;
   if (!m) nrerror("allocation failure 1 in matrix()");  int **s; /* Status */
   m += NR_END;  double *agedc, **covar, idx;
   m -= nrl;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  double ftolhess; /* Tolerance for computing hessian */
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  {
     /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    */ 
   m[nrl][ncl] += NR_END;    char  *ss;                            /* pointer */
   m[nrl][ncl] -= nll;    int   l1, l2;                         /* length counters */
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;    l1 = strlen(path );                   /* length of path */
      if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   for (i=nrl+1; i<=nrh; i++) {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    if ( ss == NULL ) {                   /* no directory, so use current */
     for (j=ncl+1; j<=nch; j++)      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       m[i][j]=m[i][j-1]+nlay;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   }      /* get current working directory */
   return m;      /*    extern  char* getcwd ( char *buf , int len);*/
 }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         return( GLOCK_ERROR_GETCWD );
 /*************************free ma3x ************************/      }
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)      strcpy( name, path );               /* we've got it */
 {    } else {                              /* strip direcotry from path */
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));      ss++;                               /* after this, the filename */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));      l2 = strlen( ss );                  /* length of filename */
   free((FREE_ARG)(m+nrl-NR_END));      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 }      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );     /* now the directory */
 /***************** f1dim *************************/      dirc[l1-l2] = 0;                    /* add zero */
 extern int ncom;    }
 extern double *pcom,*xicom;    l1 = strlen( dirc );                  /* length of directory */
 extern double (*nrfunc)(double []);    /*#ifdef windows
      if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 double f1dim(double x)  #else
 {    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   int j;  #endif
   double f;    */
   double *xt;    ss = strrchr( name, '.' );            /* find last / */
      if (ss >0){
   xt=vector(1,ncom);      ss++;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];      strcpy(ext,ss);                     /* save extension */
   f=(*nrfunc)(xt);      l1= strlen( name);
   free_vector(xt,1,ncom);      l2= strlen(ss)+1;
   return f;      strncpy( finame, name, l1-l2);
 }      finame[l1-l2]= 0;
     }
 /*****************brent *************************/    return( 0 );                          /* we're done */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  }
 {  
   int iter;  
   double a,b,d,etemp;  /******************************************/
   double fu,fv,fw,fx;  
   double ftemp;  void replace_back_to_slash(char *s, char*t)
   double p,q,r,tol1,tol2,u,v,w,x,xm;  {
   double e=0.0;    int i;
      int lg=0;
   a=(ax < cx ? ax : cx);    i=0;
   b=(ax > cx ? ax : cx);    lg=strlen(t);
   x=w=v=bx;    for(i=0; i<= lg; i++) {
   fw=fv=fx=(*f)(x);      (s[i] = t[i]);
   for (iter=1;iter<=ITMAX;iter++) {      if (t[i]== '\\') s[i]='/';
     xm=0.5*(a+b);    }
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  }
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  int nbocc(char *s, char occ)
 #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);    int i,j=0;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    int lg=20;
 #endif    i=0;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    lg=strlen(s);
       *xmin=x;    for(i=0; i<= lg; i++) {
       return fx;    if  (s[i] == occ ) j++;
     }    }
     ftemp=fu;    return j;
     if (fabs(e) > tol1) {  }
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);  void cutv(char *u,char *v, char*t, char occ)
       p=(x-v)*q-(x-w)*r;  {
       q=2.0*(q-r);    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
       if (q > 0.0) p = -p;       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       q=fabs(q);       gives u="abcedf" and v="ghi2j" */
       etemp=e;    int i,lg,j,p=0;
       e=d;    i=0;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    for(j=0; j<=strlen(t)-1; j++) {
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
       else {    }
         d=p/q;  
         u=x+d;    lg=strlen(t);
         if (u-a < tol2 || b-u < tol2)    for(j=0; j<p; j++) {
           d=SIGN(tol1,xm-x);      (u[j] = t[j]);
       }    }
     } else {       u[p]='\0';
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }     for(j=0; j<= lg; j++) {
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));      if (j>=(p+1))(v[j-p-1] = t[j]);
     fu=(*f)(u);    }
     if (fu <= fx) {  }
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)  /********************** nrerror ********************/
         SHFT(fv,fw,fx,fu)  
         } else {  void nrerror(char error_text[])
           if (u < x) a=u; else b=u;  {
           if (fu <= fw || w == x) {    fprintf(stderr,"ERREUR ...\n");
             v=w;    fprintf(stderr,"%s\n",error_text);
             w=u;    exit(EXIT_FAILURE);
             fv=fw;  }
             fw=fu;  /*********************** vector *******************/
           } else if (fu <= fv || v == x || v == w) {  double *vector(int nl, int nh)
             v=u;  {
             fv=fu;    double *v;
           }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
         }    if (!v) nrerror("allocation failure in vector");
   }    return v-nl+NR_END;
   nrerror("Too many iterations in brent");  }
   *xmin=x;  
   return fx;  /************************ free vector ******************/
 }  void free_vector(double*v, int nl, int nh)
   {
 /****************** mnbrak ***********************/    free((FREE_ARG)(v+nl-NR_END));
   }
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))  /************************ivector *******************************/
 {  int *ivector(long nl,long nh)
   double ulim,u,r,q, dum;  {
   double fu;    int *v;
      v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   *fa=(*func)(*ax);    if (!v) nrerror("allocation failure in ivector");
   *fb=(*func)(*bx);    return v-nl+NR_END;
   if (*fb > *fa) {  }
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  /******************free ivector **************************/
       }  void free_ivector(int *v, long nl, long nh)
   *cx=(*bx)+GOLD*(*bx-*ax);  {
   *fc=(*func)(*cx);    free((FREE_ARG)(v+nl-NR_END));
   while (*fb > *fc) {  }
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);  /************************lvector *******************************/
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  long *lvector(long nl,long nh)
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  {
     ulim=(*bx)+GLIMIT*(*cx-*bx);    long *v;
     if ((*bx-u)*(u-*cx) > 0.0) {    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       fu=(*func)(u);    if (!v) nrerror("allocation failure in ivector");
     } else if ((*cx-u)*(u-ulim) > 0.0) {    return v-nl+NR_END;
       fu=(*func)(u);  }
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  /******************free lvector **************************/
           SHFT(*fb,*fc,fu,(*func)(u))  void free_lvector(long *v, long nl, long nh)
           }  {
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    free((FREE_ARG)(v+nl-NR_END));
       u=ulim;  }
       fu=(*func)(u);  
     } else {  /******************* imatrix *******************************/
       u=(*cx)+GOLD*(*cx-*bx);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       fu=(*func)(u);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     }  { 
     SHFT(*ax,*bx,*cx,u)    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       SHFT(*fa,*fb,*fc,fu)    int **m; 
       }    
 }    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 /*************** linmin ************************/    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
 int ncom;    m -= nrl; 
 double *pcom,*xicom;    
 double (*nrfunc)(double []);    
      /* allocate rows and set pointers to them */ 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   double brent(double ax, double bx, double cx,    m[nrl] += NR_END; 
                double (*f)(double), double tol, double *xmin);    m[nrl] -= ncl; 
   double f1dim(double x);    
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
               double *fc, double (*func)(double));    
   int j;    /* return pointer to array of pointers to rows */ 
   double xx,xmin,bx,ax;    return m; 
   double fx,fb,fa;  } 
    
   ncom=n;  /****************** free_imatrix *************************/
   pcom=vector(1,n);  void free_imatrix(m,nrl,nrh,ncl,nch)
   xicom=vector(1,n);        int **m;
   nrfunc=func;        long nch,ncl,nrh,nrl; 
   for (j=1;j<=n;j++) {       /* free an int matrix allocated by imatrix() */ 
     pcom[j]=p[j];  { 
     xicom[j]=xi[j];    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   }    free((FREE_ARG) (m+nrl-NR_END)); 
   ax=0.0;  } 
   xx=1.0;  
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /******************* matrix *******************************/
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  double **matrix(long nrl, long nrh, long ncl, long nch)
 #ifdef DEBUG  {
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 #endif    double **m;
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     p[j] += xi[j];    if (!m) nrerror("allocation failure 1 in matrix()");
   }    m += NR_END;
   free_vector(xicom,1,n);    m -= nrl;
   free_vector(pcom,1,n);  
 }    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 /*************** powell ************************/    m[nrl] += NR_END;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    m[nrl] -= ncl;
             double (*func)(double []))  
 {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   void linmin(double p[], double xi[], int n, double *fret,    return m;
               double (*func)(double []));    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   int i,ibig,j;     */
   double del,t,*pt,*ptt,*xit;  }
   double fp,fptt;  
   double *xits;  /*************************free matrix ************************/
   pt=vector(1,n);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   ptt=vector(1,n);  {
   xit=vector(1,n);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   xits=vector(1,n);    free((FREE_ARG)(m+nrl-NR_END));
   *fret=(*func)(p);  }
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  /******************* ma3x *******************************/
     fp=(*fret);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     ibig=0;  {
     del=0.0;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    double ***m;
     for (i=1;i<=n;i++)  
       printf(" %d %.12f",i, p[i]);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     printf("\n");    if (!m) nrerror("allocation failure 1 in matrix()");
     for (i=1;i<=n;i++) {    m += NR_END;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    m -= nrl;
       fptt=(*fret);  
 #ifdef DEBUG    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       printf("fret=%lf \n",*fret);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 #endif    m[nrl] += NR_END;
       printf("%d",i);fflush(stdout);    m[nrl] -= ncl;
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         del=fabs(fptt-(*fret));  
         ibig=i;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       }    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 #ifdef DEBUG    m[nrl][ncl] += NR_END;
       printf("%d %.12e",i,(*fret));    m[nrl][ncl] -= nll;
       for (j=1;j<=n;j++) {    for (j=ncl+1; j<=nch; j++) 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      m[nrl][j]=m[nrl][j-1]+nlay;
         printf(" x(%d)=%.12e",j,xit[j]);    
       }    for (i=nrl+1; i<=nrh; i++) {
       for(j=1;j<=n;j++)      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         printf(" p=%.12e",p[j]);      for (j=ncl+1; j<=nch; j++) 
       printf("\n");        m[i][j]=m[i][j-1]+nlay;
 #endif    }
     }    return m; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 #ifdef DEBUG             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       int k[2],l;    */
       k[0]=1;  }
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  /*************************free ma3x ************************/
       for (j=1;j<=n;j++)  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
         printf(" %.12e",p[j]);  {
       printf("\n");    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       for(l=0;l<=1;l++) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         for (j=1;j<=n;j++) {    free((FREE_ARG)(m+nrl-NR_END));
           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]);  
         }  /*************** function subdirf ***********/
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  char *subdirf(char fileres[])
       }  {
 #endif    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
       free_vector(xit,1,n);    strcat(tmpout,fileres);
       free_vector(xits,1,n);    return tmpout;
       free_vector(ptt,1,n);  }
       free_vector(pt,1,n);  
       return;  /*************** function subdirf2 ***********/
     }  char *subdirf2(char fileres[], char *preop)
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  {
     for (j=1;j<=n;j++) {    
       ptt[j]=2.0*p[j]-pt[j];    /* Caution optionfilefiname is hidden */
       xit[j]=p[j]-pt[j];    strcpy(tmpout,optionfilefiname);
       pt[j]=p[j];    strcat(tmpout,"/");
     }    strcat(tmpout,preop);
     fptt=(*func)(ptt);    strcat(tmpout,fileres);
     if (fptt < fp) {    return tmpout;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  }
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);  /*************** function subdirf3 ***********/
         for (j=1;j<=n;j++) {  char *subdirf3(char fileres[], char *preop, char *preop2)
           xi[j][ibig]=xi[j][n];  {
           xi[j][n]=xit[j];    
         }    /* Caution optionfilefiname is hidden */
 #ifdef DEBUG    strcpy(tmpout,optionfilefiname);
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    strcat(tmpout,"/");
         for(j=1;j<=n;j++)    strcat(tmpout,preop);
           printf(" %.12e",xit[j]);    strcat(tmpout,preop2);
         printf("\n");    strcat(tmpout,fileres);
 #endif    return tmpout;
       }  }
     }  
   }  /***************** f1dim *************************/
 }  extern int ncom; 
   extern double *pcom,*xicom;
 /**** Prevalence limit ****************/  extern double (*nrfunc)(double []); 
    
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  double f1dim(double x) 
 {  { 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    int j; 
      matrix by transitions matrix until convergence is reached */    double f;
     double *xt; 
   int i, ii,j,k;   
   double min, max, maxmin, maxmax,sumnew=0.;    xt=vector(1,ncom); 
   double **matprod2();    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   double **out, cov[NCOVMAX], **pmij();    f=(*nrfunc)(xt); 
   double **newm;    free_vector(xt,1,ncom); 
   double agefin, delaymax=50 ; /* Max number of years to converge */    return f; 
   } 
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){  /*****************brent *************************/
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     }  { 
     int iter; 
    cov[1]=1.;    double a,b,d,etemp;
      double fu,fv,fw,fx;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    double ftemp;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     newm=savm;    double e=0.0; 
     /* Covariates have to be included here again */   
      cov[2]=agefin;    a=(ax < cx ? ax : cx); 
      b=(ax > cx ? ax : cx); 
       for (k=1; k<=cptcovn;k++) {    x=w=v=bx; 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    fw=fv=fx=(*f)(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]]);*/    for (iter=1;iter<=ITMAX;iter++) { 
       }      xm=0.5*(a+b); 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       for (k=1; k<=cptcovprod;k++)      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  #ifdef DEBUG
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      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);
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      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);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   #endif
     savm=oldm;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     oldm=newm;        *xmin=x; 
     maxmax=0.;        return fx; 
     for(j=1;j<=nlstate;j++){      } 
       min=1.;      ftemp=fu;
       max=0.;      if (fabs(e) > tol1) { 
       for(i=1; i<=nlstate; i++) {        r=(x-w)*(fx-fv); 
         sumnew=0;        q=(x-v)*(fx-fw); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        p=(x-v)*q-(x-w)*r; 
         prlim[i][j]= newm[i][j]/(1-sumnew);        q=2.0*(q-r); 
         max=FMAX(max,prlim[i][j]);        if (q > 0.0) p = -p; 
         min=FMIN(min,prlim[i][j]);        q=fabs(q); 
       }        etemp=e; 
       maxmin=max-min;        e=d; 
       maxmax=FMAX(maxmax,maxmin);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     }          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     if(maxmax < ftolpl){        else { 
       return prlim;          d=p/q; 
     }          u=x+d; 
   }          if (u-a < tol2 || b-u < tol2) 
 }            d=SIGN(tol1,xm-x); 
         } 
 /*************** transition probabilities ***************/      } else { 
         d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      } 
 {      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   double s1, s2;      fu=(*f)(u); 
   /*double t34;*/      if (fu <= fx) { 
   int i,j,j1, nc, ii, jj;        if (u >= x) a=x; else b=x; 
         SHFT(v,w,x,u) 
     for(i=1; i<= nlstate; i++){          SHFT(fv,fw,fx,fu) 
     for(j=1; j<i;j++){          } else { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){            if (u < x) a=u; else b=u; 
         /*s2 += param[i][j][nc]*cov[nc];*/            if (fu <= fw || w == x) { 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];              v=w; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/              w=u; 
       }              fv=fw; 
       ps[i][j]=s2;              fw=fu; 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/            } else if (fu <= fv || v == x || v == w) { 
     }              v=u; 
     for(j=i+1; j<=nlstate+ndeath;j++){              fv=fu; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){            } 
         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);*/    } 
       }    nrerror("Too many iterations in brent"); 
       ps[i][j]=s2;    *xmin=x; 
     }    return fx; 
   }  } 
     /*ps[3][2]=1;*/  
   /****************** mnbrak ***********************/
   for(i=1; i<= nlstate; i++){  
      s1=0;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     for(j=1; j<i; j++)              double (*func)(double)) 
       s1+=exp(ps[i][j]);  { 
     for(j=i+1; j<=nlstate+ndeath; j++)    double ulim,u,r,q, dum;
       s1+=exp(ps[i][j]);    double fu; 
     ps[i][i]=1./(s1+1.);   
     for(j=1; j<i; j++)    *fa=(*func)(*ax); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    *fb=(*func)(*bx); 
     for(j=i+1; j<=nlstate+ndeath; j++)    if (*fb > *fa) { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];      SHFT(dum,*ax,*bx,dum) 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        SHFT(dum,*fb,*fa,dum) 
   } /* end i */        } 
     *cx=(*bx)+GOLD*(*bx-*ax); 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    *fc=(*func)(*cx); 
     for(jj=1; jj<= nlstate+ndeath; jj++){    while (*fb > *fc) { 
       ps[ii][jj]=0;      r=(*bx-*ax)*(*fb-*fc); 
       ps[ii][ii]=1;      q=(*bx-*cx)*(*fb-*fa); 
     }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if ((*bx-u)*(u-*cx) > 0.0) { 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        fu=(*func)(u); 
     for(jj=1; jj<= nlstate+ndeath; jj++){      } else if ((*cx-u)*(u-ulim) > 0.0) { 
      printf("%lf ",ps[ii][jj]);        fu=(*func)(u); 
    }        if (fu < *fc) { 
     printf("\n ");          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     }            SHFT(*fb,*fc,fu,(*func)(u)) 
     printf("\n ");printf("%lf ",cov[2]);*/            } 
 /*      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        u=ulim; 
   goto end;*/        fu=(*func)(u); 
     return ps;      } else { 
 }        u=(*cx)+GOLD*(*cx-*bx); 
         fu=(*func)(u); 
 /**************** Product of 2 matrices ******************/      } 
       SHFT(*ax,*bx,*cx,u) 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        SHFT(*fa,*fb,*fc,fu) 
 {        } 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  } 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized  /*************** linmin ************************/
      before: only the contents of out is modified. The function returns  
      a pointer to pointers identical to out */  int ncom; 
   long i, j, k;  double *pcom,*xicom;
   for(i=nrl; i<= nrh; i++)  double (*nrfunc)(double []); 
     for(k=ncolol; k<=ncoloh; k++)   
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         out[i][k] +=in[i][j]*b[j][k];  { 
     double brent(double ax, double bx, double cx, 
   return out;                 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)); 
 /************* Higher Matrix Product ***************/    int j; 
     double xx,xmin,bx,ax; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    double fx,fb,fa;
 {   
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    ncom=n; 
      duration (i.e. until    pcom=vector(1,n); 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    xicom=vector(1,n); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    nrfunc=func; 
      (typically every 2 years instead of every month which is too big).    for (j=1;j<=n;j++) { 
      Model is determined by parameters x and covariates have to be      pcom[j]=p[j]; 
      included manually here.      xicom[j]=xi[j]; 
     } 
      */    ax=0.0; 
     xx=1.0; 
   int i, j, d, h, k;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   double **out, cov[NCOVMAX];    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   double **newm;  #ifdef DEBUG
     printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   /* Hstepm could be zero and should return the unit matrix */    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   for (i=1;i<=nlstate+ndeath;i++)  #endif
     for (j=1;j<=nlstate+ndeath;j++){    for (j=1;j<=n;j++) { 
       oldm[i][j]=(i==j ? 1.0 : 0.0);      xi[j] *= xmin; 
       po[i][j][0]=(i==j ? 1.0 : 0.0);      p[j] += xi[j]; 
     }    } 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    free_vector(xicom,1,n); 
   for(h=1; h <=nhstepm; h++){    free_vector(pcom,1,n); 
     for(d=1; d <=hstepm; d++){  } 
       newm=savm;  
       /* Covariates have to be included here again */  char *asc_diff_time(long time_sec, char ascdiff[])
       cov[1]=1.;  {
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    long sec_left, days, hours, minutes;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    days = (time_sec) / (60*60*24);
       for (k=1; k<=cptcovage;k++)    sec_left = (time_sec) % (60*60*24);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    hours = (sec_left) / (60*60) ;
       for (k=1; k<=cptcovprod;k++)    sec_left = (sec_left) %(60*60);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    minutes = (sec_left) /60;
     sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    return ascdiff;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  }
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  /*************** powell ************************/
       savm=oldm;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       oldm=newm;              double (*func)(double [])) 
     }  { 
     for(i=1; i<=nlstate+ndeath; i++)    void linmin(double p[], double xi[], int n, double *fret, 
       for(j=1;j<=nlstate+ndeath;j++) {                double (*func)(double [])); 
         po[i][j][h]=newm[i][j];    int i,ibig,j; 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    double del,t,*pt,*ptt,*xit;
          */    double fp,fptt;
       }    double *xits;
   } /* end h */    int niterf, itmp;
   return po;  
 }    pt=vector(1,n); 
     ptt=vector(1,n); 
     xit=vector(1,n); 
 /*************** log-likelihood *************/    xits=vector(1,n); 
 double func( double *x)    *fret=(*func)(p); 
 {    for (j=1;j<=n;j++) pt[j]=p[j]; 
   int i, ii, j, k, mi, d, kk;    for (*iter=1;;++(*iter)) { 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      fp=(*fret); 
   double **out;      ibig=0; 
   double sw; /* Sum of weights */      del=0.0; 
   double lli; /* Individual log likelihood */      last_time=curr_time;
   long ipmx;      (void) gettimeofday(&curr_time,&tzp);
   /*extern weight */      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);
   /* We are differentiating ll according to initial status */      /*    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);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   /*for(i=1;i<imx;i++)      */
     printf(" %d\n",s[4][i]);     for (i=1;i<=n;i++) {
   */        printf(" %d %.12f",i, p[i]);
   cov[1]=1.;        fprintf(ficlog," %d %.12lf",i, p[i]);
         fprintf(ficrespow," %.12lf", p[i]);
   for(k=1; k<=nlstate; k++) ll[k]=0.;      }
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      printf("\n");
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      fprintf(ficlog,"\n");
     for(mi=1; mi<= wav[i]-1; mi++){      fprintf(ficrespow,"\n");fflush(ficrespow);
       for (ii=1;ii<=nlstate+ndeath;ii++)      if(*iter <=3){
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        tm = *localtime(&curr_time.tv_sec);
       for(d=0; d<dh[mi][i]; d++){        strcpy(strcurr,asctime(&tm));
         newm=savm;  /*       asctime_r(&tm,strcurr); */
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        forecast_time=curr_time; 
         for (kk=1; kk<=cptcovage;kk++) {        itmp = strlen(strcurr);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         }          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);
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        for(niterf=10;niterf<=30;niterf+=10){
         savm=oldm;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
         oldm=newm;          tmf = *localtime(&forecast_time.tv_sec);
          /*      asctime_r(&tmf,strfor); */
                  strcpy(strfor,asctime(&tmf));
       } /* end mult */          itmp = strlen(strfor);
                if(strfor[itmp-1]=='\n')
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);          strfor[itmp-1]='\0';
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/          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);
       ipmx +=1;          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);
       sw += weight[i];        }
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      }
     } /* end of wave */      for (i=1;i<=n;i++) { 
   } /* end of individual */        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         fptt=(*fret); 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  #ifdef DEBUG
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        printf("fret=%lf \n",*fret);
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        fprintf(ficlog,"fret=%lf \n",*fret);
   return -l;  #endif
 }        printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
         linmin(p,xit,n,fret,func); 
 /*********** Maximum Likelihood Estimation ***************/        if (fabs(fptt-(*fret)) > del) { 
           del=fabs(fptt-(*fret)); 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))          ibig=i; 
 {        } 
   int i,j, iter;  #ifdef DEBUG
   double **xi,*delti;        printf("%d %.12e",i,(*fret));
   double fret;        fprintf(ficlog,"%d %.12e",i,(*fret));
   xi=matrix(1,npar,1,npar);        for (j=1;j<=n;j++) {
   for (i=1;i<=npar;i++)          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     for (j=1;j<=npar;j++)          printf(" x(%d)=%.12e",j,xit[j]);
       xi[i][j]=(i==j ? 1.0 : 0.0);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   printf("Powell\n");        }
   powell(p,xi,npar,ftol,&iter,&fret,func);        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          fprintf(ficlog," p=%.12e",p[j]);
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        }
         printf("\n");
 }        fprintf(ficlog,"\n");
   #endif
 /**** Computes Hessian and covariance matrix ***/      } 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
 {  #ifdef DEBUG
   double  **a,**y,*x,pd;        int k[2],l;
   double **hess;        k[0]=1;
   int i, j,jk;        k[1]=-1;
   int *indx;        printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
   double hessii(double p[], double delta, int theta, double delti[]);        for (j=1;j<=n;j++) {
   double hessij(double p[], double delti[], int i, int j);          printf(" %.12e",p[j]);
   void lubksb(double **a, int npar, int *indx, double b[]) ;          fprintf(ficlog," %.12e",p[j]);
   void ludcmp(double **a, int npar, int *indx, double *d) ;        }
         printf("\n");
   hess=matrix(1,npar,1,npar);        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
   printf("\nCalculation of the hessian matrix. Wait...\n");          for (j=1;j<=n;j++) {
   for (i=1;i<=npar;i++){            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     printf("%d",i);fflush(stdout);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     hess[i][i]=hessii(p,ftolhess,i,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]);
     /*printf(" %f ",p[i]);*/          }
     /*printf(" %lf ",hess[i][i]);*/          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
          }
   for (i=1;i<=npar;i++) {  #endif
     for (j=1;j<=npar;j++)  {  
       if (j>i) {  
         printf(".%d%d",i,j);fflush(stdout);        free_vector(xit,1,n); 
         hess[i][j]=hessij(p,delti,i,j);        free_vector(xits,1,n); 
         hess[j][i]=hess[i][j];            free_vector(ptt,1,n); 
         /*printf(" %lf ",hess[i][j]);*/        free_vector(pt,1,n); 
       }        return; 
     }      } 
   }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   printf("\n");      for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        xit[j]=p[j]-pt[j]; 
          pt[j]=p[j]; 
   a=matrix(1,npar,1,npar);      } 
   y=matrix(1,npar,1,npar);      fptt=(*func)(ptt); 
   x=vector(1,npar);      if (fptt < fp) { 
   indx=ivector(1,npar);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   for (i=1;i<=npar;i++)        if (t < 0.0) { 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          linmin(p,xit,n,fret,func); 
   ludcmp(a,npar,indx,&pd);          for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; 
   for (j=1;j<=npar;j++) {            xi[j][n]=xit[j]; 
     for (i=1;i<=npar;i++) x[i]=0;          }
     x[j]=1;  #ifdef DEBUG
     lubksb(a,npar,indx,x);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for (i=1;i<=npar;i++){          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       matcov[i][j]=x[i];          for(j=1;j<=n;j++){
     }            printf(" %.12e",xit[j]);
   }            fprintf(ficlog," %.12e",xit[j]);
           }
   printf("\n#Hessian matrix#\n");          printf("\n");
   for (i=1;i<=npar;i++) {          fprintf(ficlog,"\n");
     for (j=1;j<=npar;j++) {  #endif
       printf("%.3e ",hess[i][j]);        }
     }      } 
     printf("\n");    } 
   }  } 
   
   /* Recompute Inverse */  /**** Prevalence limit (stable prevalence)  ****************/
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   ludcmp(a,npar,indx,&pd);  {
     /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   /*  printf("\n#Hessian matrix recomputed#\n");       matrix by transitions matrix until convergence is reached */
   
   for (j=1;j<=npar;j++) {    int i, ii,j,k;
     for (i=1;i<=npar;i++) x[i]=0;    double min, max, maxmin, maxmax,sumnew=0.;
     x[j]=1;    double **matprod2();
     lubksb(a,npar,indx,x);    double **out, cov[NCOVMAX], **pmij();
     for (i=1;i<=npar;i++){    double **newm;
       y[i][j]=x[i];    double agefin, delaymax=50 ; /* Max number of years to converge */
       printf("%.3e ",y[i][j]);  
     }    for (ii=1;ii<=nlstate+ndeath;ii++)
     printf("\n");      for (j=1;j<=nlstate+ndeath;j++){
   }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   */      }
   
   free_matrix(a,1,npar,1,npar);     cov[1]=1.;
   free_matrix(y,1,npar,1,npar);   
   free_vector(x,1,npar);   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   free_ivector(indx,1,npar);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   free_matrix(hess,1,npar,1,npar);      newm=savm;
       /* Covariates have to be included here again */
        cov[2]=agefin;
 }    
         for (k=1; k<=cptcovn;k++) {
 /*************** hessian matrix ****************/          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 double hessii( double x[], double delta, int theta, double delti[])          /*      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]]);*/
 {        }
   int i;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   int l=1, lmax=20;        for (k=1; k<=cptcovprod;k++)
   double k1,k2;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   double p2[NPARMAX+1];  
   double res;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   double fx;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   int k=0,kmax=10;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   double l1;  
       savm=oldm;
   fx=func(x);      oldm=newm;
   for (i=1;i<=npar;i++) p2[i]=x[i];      maxmax=0.;
   for(l=0 ; l <=lmax; l++){      for(j=1;j<=nlstate;j++){
     l1=pow(10,l);        min=1.;
     delts=delt;        max=0.;
     for(k=1 ; k <kmax; k=k+1){        for(i=1; i<=nlstate; i++) {
       delt = delta*(l1*k);          sumnew=0;
       p2[theta]=x[theta] +delt;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       k1=func(p2)-fx;          prlim[i][j]= newm[i][j]/(1-sumnew);
       p2[theta]=x[theta]-delt;          max=FMAX(max,prlim[i][j]);
       k2=func(p2)-fx;          min=FMIN(min,prlim[i][j]);
       /*res= (k1-2.0*fx+k2)/delt/delt; */        }
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        maxmin=max-min;
              maxmax=FMAX(maxmax,maxmin);
 #ifdef DEBUG      }
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);      if(maxmax < ftolpl){
 #endif        return prlim;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      }
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    }
         k=kmax;  }
       }  
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  /*************** transition probabilities ***************/ 
         k=kmax; l=lmax*10.;  
       }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  {
         delts=delt;    double s1, s2;
       }    /*double t34;*/
     }    int i,j,j1, nc, ii, jj;
   }  
   delti[theta]=delts;      for(i=1; i<= nlstate; i++){
   return res;        for(j=1; j<i;j++){
            for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 }            /*s2 += param[i][j][nc]*cov[nc];*/
             s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 double hessij( double x[], double delti[], int thetai,int thetaj)  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
 {          }
   int i;          ps[i][j]=s2;
   int l=1, l1, lmax=20;  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
   double k1,k2,k3,k4,res,fx;        }
   double p2[NPARMAX+1];        for(j=i+1; j<=nlstate+ndeath;j++){
   int k;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
             s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   fx=func(x);  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
   for (k=1; k<=2; k++) {          }
     for (i=1;i<=npar;i++) p2[i]=x[i];          ps[i][j]=s2;
     p2[thetai]=x[thetai]+delti[thetai]/k;        }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      }
     k1=func(p2)-fx;      /*ps[3][2]=1;*/
        
     p2[thetai]=x[thetai]+delti[thetai]/k;      for(i=1; i<= nlstate; i++){
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        s1=0;
     k2=func(p2)-fx;        for(j=1; j<i; j++)
            s1+=exp(ps[i][j]);
     p2[thetai]=x[thetai]-delti[thetai]/k;        for(j=i+1; j<=nlstate+ndeath; j++)
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          s1+=exp(ps[i][j]);
     k3=func(p2)-fx;        ps[i][i]=1./(s1+1.);
          for(j=1; j<i; j++)
     p2[thetai]=x[thetai]-delti[thetai]/k;          ps[i][j]= exp(ps[i][j])*ps[i][i];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        for(j=i+1; j<=nlstate+ndeath; j++)
     k4=func(p2)-fx;          ps[i][j]= exp(ps[i][j])*ps[i][i];
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
 #ifdef DEBUG      } /* end i */
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);      
 #endif      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   }        for(jj=1; jj<= nlstate+ndeath; jj++){
   return res;          ps[ii][jj]=0;
 }          ps[ii][ii]=1;
         }
 /************** Inverse of matrix **************/      }
 void ludcmp(double **a, int n, int *indx, double *d)      
 {  
   int i,imax,j,k;  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   double big,dum,sum,temp;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   double *vv;  /*         printf("ddd %lf ",ps[ii][jj]); */
    /*       } */
   vv=vector(1,n);  /*       printf("\n "); */
   *d=1.0;  /*        } */
   for (i=1;i<=n;i++) {  /*        printf("\n ");printf("%lf ",cov[2]); */
     big=0.0;         /*
     for (j=1;j<=n;j++)        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       if ((temp=fabs(a[i][j])) > big) big=temp;        goto end;*/
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      return ps;
     vv[i]=1.0/big;  }
   }  
   for (j=1;j<=n;j++) {  /**************** Product of 2 matrices ******************/
     for (i=1;i<j;i++) {  
       sum=a[i][j];  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  {
       a[i][j]=sum;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     }       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     big=0.0;    /* in, b, out are matrice of pointers which should have been initialized 
     for (i=j;i<=n;i++) {       before: only the contents of out is modified. The function returns
       sum=a[i][j];       a pointer to pointers identical to out */
       for (k=1;k<j;k++)    long i, j, k;
         sum -= a[i][k]*a[k][j];    for(i=nrl; i<= nrh; i++)
       a[i][j]=sum;      for(k=ncolol; k<=ncoloh; k++)
       if ( (dum=vv[i]*fabs(sum)) >= big) {        for(j=ncl,out[i][k]=0.; j<=nch; j++)
         big=dum;          out[i][k] +=in[i][j]*b[j][k];
         imax=i;  
       }    return out;
     }  }
     if (j != imax) {  
       for (k=1;k<=n;k++) {  
         dum=a[imax][k];  /************* Higher Matrix Product ***************/
         a[imax][k]=a[j][k];  
         a[j][k]=dum;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       }  {
       *d = -(*d);    /* Computes the transition matrix starting at age 'age' over 
       vv[imax]=vv[j];       'nhstepm*hstepm*stepm' months (i.e. until
     }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     indx[j]=imax;       nhstepm*hstepm matrices. 
     if (a[j][j] == 0.0) a[j][j]=TINY;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     if (j != n) {       (typically every 2 years instead of every month which is too big 
       dum=1.0/(a[j][j]);       for the memory).
       for (i=j+1;i<=n;i++) a[i][j] *= dum;       Model is determined by parameters x and covariates have to be 
     }       included manually here. 
   }  
   free_vector(vv,1,n);  /* Doesn't work */       */
 ;  
 }    int i, j, d, h, k;
     double **out, cov[NCOVMAX];
 void lubksb(double **a, int n, int *indx, double b[])    double **newm;
 {  
   int i,ii=0,ip,j;    /* Hstepm could be zero and should return the unit matrix */
   double sum;    for (i=1;i<=nlstate+ndeath;i++)
        for (j=1;j<=nlstate+ndeath;j++){
   for (i=1;i<=n;i++) {        oldm[i][j]=(i==j ? 1.0 : 0.0);
     ip=indx[i];        po[i][j][0]=(i==j ? 1.0 : 0.0);
     sum=b[ip];      }
     b[ip]=b[i];    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     if (ii)    for(h=1; h <=nhstepm; h++){
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      for(d=1; d <=hstepm; d++){
     else if (sum) ii=i;        newm=savm;
     b[i]=sum;        /* Covariates have to be included here again */
   }        cov[1]=1.;
   for (i=n;i>=1;i--) {        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     sum=b[i];        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        for (k=1; k<=cptcovage;k++)
     b[i]=sum/a[i][i];          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   }        for (k=1; k<=cptcovprod;k++)
 }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
 /************ Frequencies ********************/  
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
 {  /* Some frequencies */        /*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, 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   double ***freq; /* Frequencies */        savm=oldm;
   double *pp;        oldm=newm;
   double pos, k2, dateintsum=0,k2cpt=0;      }
   FILE *ficresp;      for(i=1; i<=nlstate+ndeath; i++)
   char fileresp[FILENAMELENGTH];        for(j=1;j<=nlstate+ndeath;j++) {
            po[i][j][h]=newm[i][j];
   pp=vector(1,nlstate);          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);           */
   strcpy(fileresp,"p");        }
   strcat(fileresp,fileres);    } /* end h */
   if((ficresp=fopen(fileresp,"w"))==NULL) {    return po;
     printf("Problem with prevalence resultfile: %s\n", fileresp);  }
     exit(0);  
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  /*************** log-likelihood *************/
   j1=0;  double func( double *x)
    {
   j=cptcoveff;    int i, ii, j, k, mi, d, kk;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    double l, ll[NLSTATEMAX], cov[NCOVMAX];
      double **out;
   for(k1=1; k1<=j;k1++){    double sw; /* Sum of weights */
     for(i1=1; i1<=ncodemax[k1];i1++){    double lli; /* Individual log likelihood */
       j1++;    int s1, s2;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    double bbh, survp;
         scanf("%d", i);*/    long ipmx;
       for (i=-1; i<=nlstate+ndeath; i++)      /*extern weight */
         for (jk=-1; jk<=nlstate+ndeath; jk++)      /* We are differentiating ll according to initial status */
           for(m=agemin; m <= agemax+3; m++)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
             freq[i][jk][m]=0;    /*for(i=1;i<imx;i++) 
            printf(" %d\n",s[4][i]);
       dateintsum=0;    */
       k2cpt=0;    cov[1]=1.;
       for (i=1; i<=imx; i++) {  
         bool=1;    for(k=1; k<=nlstate; k++) ll[k]=0.;
         if  (cptcovn>0) {  
           for (z1=1; z1<=cptcoveff; z1++)    if(mle==1){
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
               bool=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
         if (bool==1) {          for (ii=1;ii<=nlstate+ndeath;ii++)
           for(m=firstpass; m<=lastpass; m++){            for (j=1;j<=nlstate+ndeath;j++){
             k2=anint[m][i]+(mint[m][i]/12.);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             if ((k2>=dateprev1) && (k2<=dateprev2)) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
               if(agev[m][i]==0) agev[m][i]=agemax+1;            }
               if(agev[m][i]==1) agev[m][i]=agemax+2;          for(d=0; d<dh[mi][i]; d++){
               if (m<lastpass) {            newm=savm;
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];            for (kk=1; kk<=cptcovage;kk++) {
               }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                          }
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                 dateintsum=dateintsum+k2;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                 k2cpt++;            savm=oldm;
               }            oldm=newm;
             }          } /* end mult */
           }        
         }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       }          /* But now since version 0.9 we anticipate for bias at large stepm.
                   * If stepm is larger than one month (smallest stepm) and if the exact delay 
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);           * (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
       if  (cptcovn>0) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         fprintf(ficresp, "\n#********** Variable ");           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);           * probability in order to take into account the bias as a fraction of the way
         fprintf(ficresp, "**********\n#");           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
       }           * -stepm/2 to stepm/2 .
       for(i=1; i<=nlstate;i++)           * For stepm=1 the results are the same as for previous versions of Imach.
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);           * For stepm > 1 the results are less biased than in previous versions. 
       fprintf(ficresp, "\n");           */
                s1=s[mw[mi][i]][i];
       for(i=(int)agemin; i <= (int)agemax+3; i++){          s2=s[mw[mi+1][i]][i];
         if(i==(int)agemax+3)          bbh=(double)bh[mi][i]/(double)stepm; 
           printf("Total");          /* bias bh is positive if real duration
         else           * is higher than the multiple of stepm and negative otherwise.
           printf("Age %d", i);           */
         for(jk=1; jk <=nlstate ; 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=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          if( s2 > nlstate){ 
             pp[jk] += freq[jk][m][i];            /* 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 
         for(jk=1; jk <=nlstate ; jk++){               die between last step unit time and current  step unit time, 
           for(m=-1, pos=0; m <=0 ; m++)               which is also equal to probability to die before dh 
             pos += freq[jk][m][i];               minus probability to die before dh-stepm . 
           if(pp[jk]>=1.e-10)               In version up to 0.92 likelihood was computed
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          as if date of death was unknown. Death was treated as any other
           else          health state: the date of the interview describes the actual state
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          and not the date of a change in health state. The former idea was
         }          to consider that at each interview the state was recorded
           (healthy, disable or death) and IMaCh was corrected; but when we
         for(jk=1; jk <=nlstate ; jk++){          introduced the exact date of death then we should have modified
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          the contribution of an exact death to the likelihood. This new
             pp[jk] += freq[jk][m][i];          contribution is smaller and very dependent of the step unit
         }          stepm. It is no more the probability to die between last interview
           and month of death but the probability to survive from last
         for(jk=1,pos=0; jk <=nlstate ; jk++)          interview up to one month before death multiplied by the
           pos += pp[jk];          probability to die within a month. Thanks to Chris
         for(jk=1; jk <=nlstate ; jk++){          Jackson for correcting this bug.  Former versions increased
           if(pos>=1.e-5)          mortality artificially. The bad side is that we add another loop
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          which slows down the processing. The difference can be up to 10%
           else          lower mortality.
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            */
           if( i <= (int) agemax){            lli=log(out[s1][s2] - savm[s1][s2]);
             if(pos>=1.e-5){  
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  
               probs[i][jk][j1]= pp[jk]/pos;          } else if  (s2==-2) {
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/            for (j=1,survp=0. ; j<=nlstate; j++) 
             }              survp += out[s1][j];
             else            lli= survp;
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          }
           }  
         }  
                  else{
         for(jk=-1; jk <=nlstate+ndeath; jk++)            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           for(m=-1; m <=nlstate+ndeath; m++)            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          } 
         if(i <= (int) agemax)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           fprintf(ficresp,"\n");          /*if(lli ==000.0)*/
         printf("\n");          /*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); */
       }          ipmx +=1;
     }          sw += weight[i];
   }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   dateintmean=dateintsum/k2cpt;        } /* end of wave */
        } /* end of individual */
   fclose(ficresp);    }  else if(mle==2){
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   free_vector(pp,1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
   /* End of Freq */          for (ii=1;ii<=nlstate+ndeath;ii++)
 }            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 /************ Prevalence ********************/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)            }
 {  /* Some frequencies */          for(d=0; d<=dh[mi][i]; d++){
              newm=savm;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double ***freq; /* Frequencies */            for (kk=1; kk<=cptcovage;kk++) {
   double *pp;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double pos, k2;            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   pp=vector(1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            savm=oldm;
              oldm=newm;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          } /* end mult */
   j1=0;        
            s1=s[mw[mi][i]][i];
   j=cptcoveff;          s2=s[mw[mi+1][i]][i];
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          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 */
   for(k1=1; k1<=j;k1++){          ipmx +=1;
     for(i1=1; i1<=ncodemax[k1];i1++){          sw += weight[i];
       j1++;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
              } /* end of wave */
       for (i=-1; i<=nlstate+ndeath; i++)        } /* end of individual */
         for (jk=-1; jk<=nlstate+ndeath; jk++)      }  else if(mle==3){  /* exponential inter-extrapolation */
           for(m=agemin; m <= agemax+3; m++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             freq[i][jk][m]=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
              for(mi=1; mi<= wav[i]-1; mi++){
       for (i=1; i<=imx; i++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
         bool=1;            for (j=1;j<=nlstate+ndeath;j++){
         if  (cptcovn>0) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for (z1=1; z1<=cptcoveff; z1++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            }
               bool=0;          for(d=0; d<dh[mi][i]; d++){
         }            newm=savm;
         if (bool==1) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for(m=firstpass; m<=lastpass; m++){            for (kk=1; kk<=cptcovage;kk++) {
             k2=anint[m][i]+(mint[m][i]/12.);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            }
               if(agev[m][i]==0) agev[m][i]=agemax+1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
               if(agev[m][i]==1) agev[m][i]=agemax+2;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
               if (m<lastpass) {            savm=oldm;
                 if (calagedate>0)            oldm=newm;
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          } /* end mult */
                 else        
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          s1=s[mw[mi][i]][i];
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];          s2=s[mw[mi+1][i]][i];
               }          bbh=(double)bh[mi][i]/(double)stepm; 
             }          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
           }          ipmx +=1;
         }          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(i=(int)agemin; i <= (int)agemax+3; i++){        } /* end of wave */
         for(jk=1; jk <=nlstate ; jk++){      } /* end of individual */
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    }else if (mle==4){  /* ml=4 no inter-extrapolation */
             pp[jk] += freq[jk][m][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(jk=1; jk <=nlstate ; jk++){        for(mi=1; mi<= wav[i]-1; mi++){
           for(m=-1, pos=0; m <=0 ; m++)          for (ii=1;ii<=nlstate+ndeath;ii++)
             pos += freq[jk][m][i];            for (j=1;j<=nlstate+ndeath;j++){
         }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                      savm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(jk=1; jk <=nlstate ; jk++){            }
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          for(d=0; d<dh[mi][i]; d++){
             pp[jk] += freq[jk][m][i];            newm=savm;
         }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                    for (kk=1; kk<=cptcovage;kk++) {
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                    }
         for(jk=1; jk <=nlstate ; jk++){              
           if( i <= (int) agemax){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             if(pos>=1.e-5){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
               probs[i][jk][j1]= pp[jk]/pos;            savm=oldm;
             }            oldm=newm;
           }          } /* end mult */
         }        
                  s1=s[mw[mi][i]][i];
       }          s2=s[mw[mi+1][i]][i];
     }          if( s2 > nlstate){ 
   }            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
              lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          }
   free_vector(pp,1,nlstate);          ipmx +=1;
            sw += weight[i];
 }  /* End of Freq */          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]); */
 /************* Waves Concatenation ***************/        } /* end of wave */
       } /* end of individual */
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
 {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      Death is a valid wave (if date is known).        for(mi=1; mi<= wav[i]-1; mi++){
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          for (ii=1;ii<=nlstate+ndeath;ii++)
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            for (j=1;j<=nlstate+ndeath;j++){
      and mw[mi+1][i]. dh depends on stepm.              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   int i, mi, m;          for(d=0; d<dh[mi][i]; d++){
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;            newm=savm;
      double sum=0., jmean=0.;*/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   int j, k=0,jk, ju, jl;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double sum=0.;            }
   jmin=1e+5;          
   jmax=-1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   jmean=0.;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for(i=1; i<=imx; i++){            savm=oldm;
     mi=0;            oldm=newm;
     m=firstpass;          } /* end mult */
     while(s[m][i] <= nlstate){        
       if(s[m][i]>=1)          s1=s[mw[mi][i]][i];
         mw[++mi][i]=m;          s2=s[mw[mi+1][i]][i];
       if(m >=lastpass)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         break;          ipmx +=1;
       else          sw += weight[i];
         m++;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }/* end while */          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
     if (s[m][i] > nlstate){        } /* end of wave */
       mi++;     /* Death is another wave */      } /* end of individual */
       /* if(mi==0)  never been interviewed correctly before death */    } /* End of if */
          /* Only death is a correct wave */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       mw[mi][i]=m;    /* 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 */
     return -l;
     wav[i]=mi;  }
     if(mi==0)  
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  /*************** log-likelihood *************/
   }  double funcone( double *x)
   {
   for(i=1; i<=imx; i++){    /* Same as likeli but slower because of a lot of printf and if */
     for(mi=1; mi<wav[i];mi++){    int i, ii, j, k, mi, d, kk;
       if (stepm <=0)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         dh[mi][i]=1;    double **out;
       else{    double lli; /* Individual log likelihood */
         if (s[mw[mi+1][i]][i] > nlstate) {    double llt;
           if (agedc[i] < 2*AGESUP) {    int s1, s2;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    double bbh, survp;
           if(j==0) j=1;  /* Survives at least one month after exam */    /*extern weight */
           k=k+1;    /* We are differentiating ll according to initial status */
           if (j >= jmax) jmax=j;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           if (j <= jmin) jmin=j;    /*for(i=1;i<imx;i++) 
           sum=sum+j;      printf(" %d\n",s[4][i]);
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    */
           }    cov[1]=1.;
         }  
         else{    for(k=1; k<=nlstate; k++) ll[k]=0.;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  
           k=k+1;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           if (j >= jmax) jmax=j;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           else if (j <= jmin)jmin=j;      for(mi=1; mi<= wav[i]-1; mi++){
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        for (ii=1;ii<=nlstate+ndeath;ii++)
           sum=sum+j;          for (j=1;j<=nlstate+ndeath;j++){
         }            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         jk= j/stepm;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
         jl= j -jk*stepm;          }
         ju= j -(jk+1)*stepm;        for(d=0; d<dh[mi][i]; d++){
         if(jl <= -ju)          newm=savm;
           dh[mi][i]=jk;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         else          for (kk=1; kk<=cptcovage;kk++) {
           dh[mi][i]=jk+1;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         if(dh[mi][i]==0)          }
           dh[mi][i]=1; /* At least one step */          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }          savm=oldm;
   }          oldm=newm;
   jmean=sum/k;        } /* end mult */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        
  }        s1=s[mw[mi][i]][i];
 /*********** Tricode ****************************/        s2=s[mw[mi+1][i]][i];
 void tricode(int *Tvar, int **nbcode, int imx)        bbh=(double)bh[mi][i]/(double)stepm; 
 {        /* bias is positive if real duration
   int Ndum[20],ij=1, k, j, i;         * is higher than the multiple of stepm and negative otherwise.
   int cptcode=0;         */
   cptcoveff=0;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
            lli=log(out[s1][s2] - savm[s1][s2]);
   for (k=0; k<19; k++) Ndum[k]=0;        } else if (mle==1){
   for (k=1; k<=7; k++) ncodemax[k]=0;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     for (i=1; i<=imx; i++) {        } else if(mle==3){  /* exponential inter-extrapolation */
       ij=(int)(covar[Tvar[j]][i]);          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 */
       Ndum[ij]++;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          lli=log(out[s1][s2]); /* Original formula */
       if (ij > cptcode) cptcode=ij;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
     }          lli=log(out[s1][s2]); /* Original formula */
         } /* End of if */
     for (i=0; i<=cptcode; i++) {        ipmx +=1;
       if(Ndum[i]!=0) ncodemax[j]++;        sw += weight[i];
     }        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     ij=1;  /*       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(globpr){
           fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
     for (i=1; i<=ncodemax[j]; i++) {   %10.6f %10.6f %10.6f ", \
       for (k=0; k<=19; k++) {                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
         if (Ndum[k] != 0) {                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           nbcode[Tvar[j]][ij]=k;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
                      llt +=ll[k]*gipmx/gsw;
           ij++;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
         }          }
         if (ij > ncodemax[j]) break;          fprintf(ficresilk," %10.6f\n", -llt);
       }          }
     }      } /* end of wave */
   }      } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
  for (k=0; k<19; k++) Ndum[k]=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 */
  for (i=1; i<=ncovmodel-2; i++) {    if(globpr==0){ /* First time we count the contributions and weights */
       ij=Tvar[i];      gipmx=ipmx;
       Ndum[ij]++;      gsw=sw;
     }    }
     return -l;
  ij=1;  }
  for (i=1; i<=10; i++) {  
    if((Ndum[i]!=0) && (i<=ncovcol)){  
      Tvaraff[ij]=i;  /*************** function likelione ***********/
      ij++;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
    }  {
  }    /* This routine should help understanding what is done with 
         the selection of individuals/waves and
     cptcoveff=ij-1;       to check the exact contribution to the likelihood.
 }       Plotting could be done.
      */
 /*********** Health Expectancies ****************/    int k;
   
 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 )    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
 {      strcat(fileresilk,fileres);
   /* Health expectancies */      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;        printf("Problem with resultfile: %s\n", fileresilk);
   double age, agelim, hf;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   double ***p3mat,***varhe;      }
   double **dnewm,**doldm;      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");
   double *xp;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   double **gp, **gm;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   double ***gradg, ***trgradg;      for(k=1; k<=nlstate; k++) 
   int theta;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    }
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate*2,1,npar);    *fretone=(*funcone)(p);
   doldm=matrix(1,nlstate*2,1,nlstate*2);    if(*globpri !=0){
        fclose(ficresilk);
   fprintf(ficreseij,"# Health expectancies\n");      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   fprintf(ficreseij,"# Age");      fflush(fichtm); 
   for(i=1; i<=nlstate;i++)    } 
     for(j=1; j<=nlstate;j++)    return;
       fprintf(ficreseij," %1d-%1d (SE)",i,j);  }
   fprintf(ficreseij,"\n");  
   
   if(estepm < stepm){  /*********** Maximum Likelihood Estimation ***************/
     printf ("Problem %d lower than %d\n",estepm, stepm);  
   }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   else  hstepm=estepm;    {
   /* We compute the life expectancy from trapezoids spaced every estepm months    int i,j, iter;
    * This is mainly to measure the difference between two models: for example    double **xi;
    * if stepm=24 months pijx are given only every 2 years and by summing them    double fret;
    * we are calculating an estimate of the Life Expectancy assuming a linear    double fretone; /* Only one call to likelihood */
    * progression inbetween and thus overestimating or underestimating according    /*  char filerespow[FILENAMELENGTH];*/
    * to the curvature of the survival function. If, for the same date, we    xi=matrix(1,npar,1,npar);
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    for (i=1;i<=npar;i++)
    * to compare the new estimate of Life expectancy with the same linear      for (j=1;j<=npar;j++)
    * hypothesis. A more precise result, taking into account a more precise        xi[i][j]=(i==j ? 1.0 : 0.0);
    * curvature will be obtained if estepm is as small as stepm. */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
   /* For example we decided to compute the life expectancy with the smallest unit */    strcat(filerespow,fileres);
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    if((ficrespow=fopen(filerespow,"w"))==NULL) {
      nhstepm is the number of hstepm from age to agelim      printf("Problem with resultfile: %s\n", filerespow);
      nstepm is the number of stepm from age to agelin.      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
      Look at hpijx to understand the reason of that which relies in memory size    }
      and note for a fixed period like estepm months */    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    for (i=1;i<=nlstate;i++)
      survival function given by stepm (the optimization length). Unfortunately it      for(j=1;j<=nlstate+ndeath;j++)
      means that if the survival funtion is printed only each two years of age and if        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    fprintf(ficrespow,"\n");
      results. So we changed our mind and took the option of the best precision.  
   */    powell(p,xi,npar,ftol,&iter,&fret,func);
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  
     fclose(ficrespow);
   agelim=AGESUP;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     /* nhstepm age range expressed in number of stepm */    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     nstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */  }
     /* if (stepm >= YEARM) hstepm=1;*/  
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  /**** Computes Hessian and covariance matrix ***/
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);  {
     gp=matrix(0,nhstepm,1,nlstate*2);    double  **a,**y,*x,pd;
     gm=matrix(0,nhstepm,1,nlstate*2);    double **hess;
     int i, j,jk;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    int *indx;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
      double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     void lubksb(double **a, int npar, int *indx, double b[]) ;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    void ludcmp(double **a, int npar, int *indx, double *d) ;
     double gompertz(double p[]);
     /* Computing Variances of health expectancies */    hess=matrix(1,npar,1,npar);
   
      for(theta=1; theta <=npar; theta++){    printf("\nCalculation of the hessian matrix. Wait...\n");
       for(i=1; i<=npar; i++){    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    for (i=1;i<=npar;i++){
       }      printf("%d",i);fflush(stdout);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        fprintf(ficlog,"%d",i);fflush(ficlog);
       
       cptj=0;       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       for(j=1; j<= nlstate; j++){      
         for(i=1; i<=nlstate; i++){      /*  printf(" %f ",p[i]);
           cptj=cptj+1;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    }
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    
           }    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);
       for(i=1; i<=npar; i++)          hess[i][j]=hessij(p,delti,i,j,func,npar);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            hess[j][i]=hess[i][j];    
                /*printf(" %lf ",hess[i][j]);*/
       cptj=0;        }
       for(j=1; j<= nlstate; j++){      }
         for(i=1;i<=nlstate;i++){    }
           cptj=cptj+1;    printf("\n");
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    fprintf(ficlog,"\n");
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
         }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       }    
       for(j=1; j<= nlstate*2; j++)    a=matrix(1,npar,1,npar);
         for(h=0; h<=nhstepm-1; h++){    y=matrix(1,npar,1,npar);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    x=vector(1,npar);
         }    indx=ivector(1,npar);
      }    for (i=1;i<=npar;i++)
          for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
 /* End theta */    ludcmp(a,npar,indx,&pd);
   
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
      for(h=0; h<=nhstepm-1; h++)      x[j]=1;
       for(j=1; j<=nlstate*2;j++)      lubksb(a,npar,indx,x);
         for(theta=1; theta <=npar; theta++)      for (i=1;i<=npar;i++){ 
           trgradg[h][j][theta]=gradg[h][theta][j];        matcov[i][j]=x[i];
            }
     }
      for(i=1;i<=nlstate*2;i++)  
       for(j=1;j<=nlstate*2;j++)    printf("\n#Hessian matrix#\n");
         varhe[i][j][(int)age] =0.;    fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
      printf("%d|",(int)age);fflush(stdout);      for (j=1;j<=npar;j++) { 
      for(h=0;h<=nhstepm-1;h++){        printf("%.3e ",hess[i][j]);
       for(k=0;k<=nhstepm-1;k++){        fprintf(ficlog,"%.3e ",hess[i][j]);
         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]);      printf("\n");
         for(i=1;i<=nlstate*2;i++)      fprintf(ficlog,"\n");
           for(j=1;j<=nlstate*2;j++)    }
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;  
       }    /* Recompute Inverse */
     }    for (i=1;i<=npar;i++)
     /* Computing expectancies */      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     for(i=1; i<=nlstate;i++)    ludcmp(a,npar,indx,&pd);
       for(j=1; j<=nlstate;j++)  
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    /*  printf("\n#Hessian matrix recomputed#\n");
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;  
              for (j=1;j<=npar;j++) {
 /* 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]);*/      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
         }      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
     fprintf(ficreseij,"%3.0f",age );        y[i][j]=x[i];
     cptj=0;        printf("%.3e ",y[i][j]);
     for(i=1; i<=nlstate;i++)        fprintf(ficlog,"%.3e ",y[i][j]);
       for(j=1; j<=nlstate;j++){      }
         cptj++;      printf("\n");
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      fprintf(ficlog,"\n");
       }    }
     fprintf(ficreseij,"\n");    */
      
     free_matrix(gm,0,nhstepm,1,nlstate*2);    free_matrix(a,1,npar,1,npar);
     free_matrix(gp,0,nhstepm,1,nlstate*2);    free_matrix(y,1,npar,1,npar);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    free_vector(x,1,npar);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);    free_ivector(indx,1,npar);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_matrix(hess,1,npar,1,npar);
   }  
   printf("\n");  
   }
   free_vector(xp,1,npar);  
   free_matrix(dnewm,1,nlstate*2,1,npar);  /*************** hessian matrix ****************/
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);  {
 }    int i;
     int l=1, lmax=20;
 /************ Variance ******************/    double k1,k2;
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)    double p2[NPARMAX+1];
 {    double res;
   /* Variance of health expectancies */    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    double fx;
   double **newm;    int k=0,kmax=10;
   double **dnewm,**doldm;    double l1;
   int i, j, nhstepm, hstepm, h, nstepm ;  
   int k, cptcode;    fx=func(x);
   double *xp;    for (i=1;i<=npar;i++) p2[i]=x[i];
   double **gp, **gm;    for(l=0 ; l <=lmax; l++){
   double ***gradg, ***trgradg;      l1=pow(10,l);
   double ***p3mat;      delts=delt;
   double age,agelim, hf;      for(k=1 ; k <kmax; k=k+1){
   int theta;        delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
   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");        k1=func(p2)-fx;
   fprintf(ficresvij,"# Age");        p2[theta]=x[theta]-delt;
   for(i=1; i<=nlstate;i++)        k2=func(p2)-fx;
     for(j=1; j<=nlstate;j++)        /*res= (k1-2.0*fx+k2)/delt/delt; */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   fprintf(ficresvij,"\n");        
   #ifdef DEBUG
   xp=vector(1,npar);        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);
   dnewm=matrix(1,nlstate,1,npar);        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);
   doldm=matrix(1,nlstate,1,nlstate);  #endif
          /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   if(estepm < stepm){        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     printf ("Problem %d lower than %d\n",estepm, stepm);          k=kmax;
   }        }
   else  hstepm=estepm;          else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   /* For example we decided to compute the life expectancy with the smallest unit */          k=kmax; l=lmax*10.;
   /* 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        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
      nstepm is the number of stepm from age to agelin.          delts=delt;
      Look at hpijx to understand the reason of that which relies in memory size        }
      and note for a fixed period like k years */      }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    }
      survival function given by stepm (the optimization length). Unfortunately it    delti[theta]=delts;
      means that if the survival funtion is printed only each two years of age and if    return res; 
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    
      results. So we changed our mind and took the option of the best precision.  }
   */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   agelim = AGESUP;  {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    int i;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    int l=1, l1, lmax=20;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    double k1,k2,k3,k4,res,fx;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double p2[NPARMAX+1];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    int k;
     gp=matrix(0,nhstepm,1,nlstate);  
     gm=matrix(0,nhstepm,1,nlstate);    fx=func(x);
     for (k=1; k<=2; k++) {
     for(theta=1; theta <=npar; theta++){      for (i=1;i<=npar;i++) p2[i]=x[i];
       for(i=1; i<=npar; i++){ /* Computes gradient */      p2[thetai]=x[thetai]+delti[thetai]/k;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       }      k1=func(p2)-fx;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       if (popbased==1) {      k2=func(p2)-fx;
         for(i=1; i<=nlstate;i++)    
           prlim[i][i]=probs[(int)age][i][ij];      p2[thetai]=x[thetai]-delti[thetai]/k;
       }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
        k3=func(p2)-fx;
       for(j=1; j<= nlstate; j++){    
         for(h=0; h<=nhstepm; h++){      p2[thetai]=x[thetai]-delti[thetai]/k;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      k4=func(p2)-fx;
         }      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       }  #ifdef DEBUG
          printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       for(i=1; i<=npar; i++) /* Computes gradient */      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);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  #endif
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    return res;
    }
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)  /************** Inverse of matrix **************/
           prlim[i][i]=probs[(int)age][i][ij];  void ludcmp(double **a, int n, int *indx, double *d) 
       }  { 
     int i,imax,j,k; 
       for(j=1; j<= nlstate; j++){    double big,dum,sum,temp; 
         for(h=0; h<=nhstepm; h++){    double *vv; 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)   
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    vv=vector(1,n); 
         }    *d=1.0; 
       }    for (i=1;i<=n;i++) { 
       big=0.0; 
       for(j=1; j<= nlstate; j++)      for (j=1;j<=n;j++) 
         for(h=0; h<=nhstepm; h++){        if ((temp=fabs(a[i][j])) > big) big=temp; 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         }      vv[i]=1.0/big; 
     } /* End theta */    } 
     for (j=1;j<=n;j++) { 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      for (i=1;i<j;i++) { 
         sum=a[i][j]; 
     for(h=0; h<=nhstepm; h++)        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       for(j=1; j<=nlstate;j++)        a[i][j]=sum; 
         for(theta=1; theta <=npar; theta++)      } 
           trgradg[h][j][theta]=gradg[h][theta][j];      big=0.0; 
       for (i=j;i<=n;i++) { 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        sum=a[i][j]; 
     for(i=1;i<=nlstate;i++)        for (k=1;k<j;k++) 
       for(j=1;j<=nlstate;j++)          sum -= a[i][k]*a[k][j]; 
         vareij[i][j][(int)age] =0.;        a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
     for(h=0;h<=nhstepm;h++){          big=dum; 
       for(k=0;k<=nhstepm;k++){          imax=i; 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        } 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      } 
         for(i=1;i<=nlstate;i++)      if (j != imax) { 
           for(j=1;j<=nlstate;j++)        for (k=1;k<=n;k++) { 
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          dum=a[imax][k]; 
       }          a[imax][k]=a[j][k]; 
     }          a[j][k]=dum; 
         } 
     fprintf(ficresvij,"%.0f ",age );        *d = -(*d); 
     for(i=1; i<=nlstate;i++)        vv[imax]=vv[j]; 
       for(j=1; j<=nlstate;j++){      } 
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);      indx[j]=imax; 
       }      if (a[j][j] == 0.0) a[j][j]=TINY; 
     fprintf(ficresvij,"\n");      if (j != n) { 
     free_matrix(gp,0,nhstepm,1,nlstate);        dum=1.0/(a[j][j]); 
     free_matrix(gm,0,nhstepm,1,nlstate);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      } 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    } 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_vector(vv,1,n);  /* Doesn't work */
   } /* End age */  ;
    } 
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);  void lubksb(double **a, int n, int *indx, double b[]) 
   free_matrix(dnewm,1,nlstate,1,nlstate);  { 
     int i,ii=0,ip,j; 
 }    double sum; 
    
 /************ Variance of prevlim ******************/    for (i=1;i<=n;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)      ip=indx[i]; 
 {      sum=b[ip]; 
   /* Variance of prevalence limit */      b[ip]=b[i]; 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      if (ii) 
   double **newm;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   double **dnewm,**doldm;      else if (sum) ii=i; 
   int i, j, nhstepm, hstepm;      b[i]=sum; 
   int k, cptcode;    } 
   double *xp;    for (i=n;i>=1;i--) { 
   double *gp, *gm;      sum=b[i]; 
   double **gradg, **trgradg;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   double age,agelim;      b[i]=sum/a[i][i]; 
   int theta;    } 
      } 
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");  
   fprintf(ficresvpl,"# Age");  /************ Frequencies ********************/
   for(i=1; i<=nlstate;i++)  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(ficresvpl," %1d-%1d",i,i);  {  /* Some frequencies */
   fprintf(ficresvpl,"\n");    
     int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   xp=vector(1,npar);    int first;
   dnewm=matrix(1,nlstate,1,npar);    double ***freq; /* Frequencies */
   doldm=matrix(1,nlstate,1,nlstate);    double *pp, **prop;
      double pos,posprop, k2, dateintsum=0,k2cpt=0;
   hstepm=1*YEARM; /* Every year of age */    FILE *ficresp;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    char fileresp[FILENAMELENGTH];
   agelim = AGESUP;    
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    pp=vector(1,nlstate);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    prop=matrix(1,nlstate,iagemin,iagemax+3);
     if (stepm >= YEARM) hstepm=1;    strcpy(fileresp,"p");
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    strcat(fileresp,fileres);
     gradg=matrix(1,npar,1,nlstate);    if((ficresp=fopen(fileresp,"w"))==NULL) {
     gp=vector(1,nlstate);      printf("Problem with prevalence resultfile: %s\n", fileresp);
     gm=vector(1,nlstate);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       exit(0);
     for(theta=1; theta <=npar; theta++){    }
       for(i=1; i<=npar; i++){ /* Computes gradient */    freq= ma3x(-2,nlstate+ndeath,-2,nlstate+ndeath,iagemin,iagemax+3);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    j1=0;
       }    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    j=cptcoveff;
       for(i=1;i<=nlstate;i++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         gp[i] = prlim[i][i];  
        first=1;
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    for(k1=1; k1<=j;k1++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      for(i1=1; i1<=ncodemax[k1];i1++){
       for(i=1;i<=nlstate;i++)        j1++;
         gm[i] = prlim[i][i];        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           scanf("%d", i);*/
       for(i=1;i<=nlstate;i++)        for (i=-2; i<=nlstate+ndeath; i++)  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          for (jk=-2; jk<=nlstate+ndeath; jk++)  
     } /* End theta */            for(m=iagemin; m <= iagemax+3; m++)
               freq[i][jk][m]=0;
     trgradg =matrix(1,nlstate,1,npar);  
       for (i=1; i<=nlstate; i++)  
     for(j=1; j<=nlstate;j++)        for(m=iagemin; m <= iagemax+3; m++)
       for(theta=1; theta <=npar; theta++)          prop[i][m]=0;
         trgradg[j][theta]=gradg[theta][j];        
         dateintsum=0;
     for(i=1;i<=nlstate;i++)        k2cpt=0;
       varpl[i][(int)age] =0.;        for (i=1; i<=imx; i++) {
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          bool=1;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          if  (cptcovn>0) {
     for(i=1;i<=nlstate;i++)            for (z1=1; z1<=cptcoveff; z1++) 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
     fprintf(ficresvpl,"%.0f ",age );          }
     for(i=1; i<=nlstate;i++)          if (bool==1){
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            for(m=firstpass; m<=lastpass; m++){
     fprintf(ficresvpl,"\n");              k2=anint[m][i]+(mint[m][i]/12.);
     free_vector(gp,1,nlstate);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     free_vector(gm,1,nlstate);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     free_matrix(gradg,1,npar,1,nlstate);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     free_matrix(trgradg,1,nlstate,1,npar);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   } /* End age */                if (m<lastpass) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   free_vector(xp,1,npar);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   free_matrix(doldm,1,nlstate,1,npar);                }
   free_matrix(dnewm,1,nlstate,1,nlstate);                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
 }                  dateintsum=dateintsum+k2;
                   k2cpt++;
 /************ 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)                /*}*/
 {            }
   int i, j,  i1, k1, l1;          }
   int k2, l2, j1,  z1;        }
   int k=0,l, cptcode;         
   int first=1;        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;  
   double **dnewm,**doldm;        if  (cptcovn>0) {
   double *xp;          fprintf(ficresp, "\n#********** Variable "); 
   double *gp, *gm;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   double **gradg, **trgradg;          fprintf(ficresp, "**********\n#");
   double **mu;        }
   double age,agelim, cov[NCOVMAX];        for(i=1; i<=nlstate;i++) 
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   int theta;        fprintf(ficresp, "\n");
   char fileresprob[FILENAMELENGTH];        
   char fileresprobcov[FILENAMELENGTH];        for(i=iagemin; i <= iagemax+3; i++){
   char fileresprobcor[FILENAMELENGTH];          if(i==iagemax+3){
             fprintf(ficlog,"Total");
   double ***varpij;          }else{
             if(first==1){
   strcpy(fileresprob,"prob");              first=0;
   strcat(fileresprob,fileres);              printf("See log file for details...\n");
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {            }
     printf("Problem with resultfile: %s\n", fileresprob);            fprintf(ficlog,"Age %d", i);
   }          }
   strcpy(fileresprobcov,"probcov");          for(jk=1; jk <=nlstate ; jk++){
   strcat(fileresprobcov,fileres);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {              pp[jk] += freq[jk][m][i]; 
     printf("Problem with resultfile: %s\n", fileresprobcov);          }
   }          for(jk=1; jk <=nlstate ; jk++){
   strcpy(fileresprobcor,"probcor");            for(m=-1, pos=0; m <=0 ; m++)
   strcat(fileresprobcor,fileres);              pos += freq[jk][m][i];
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {            if(pp[jk]>=1.e-10){
     printf("Problem with resultfile: %s\n", fileresprobcor);              if(first==1){
   }              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   printf("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," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);            }else{
                if(first==1)
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   fprintf(ficresprob,"# Age");              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");            }
   fprintf(ficresprobcov,"# Age");          }
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");  
   fprintf(ficresprobcov,"# Age");          for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
   for(i=1; i<=nlstate;i++)          }       
     for(j=1; j<=(nlstate+ndeath);j++){          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);            pos += pp[jk];
       fprintf(ficresprobcov," p%1d-%1d ",i,j);            posprop += prop[jk][i];
       fprintf(ficresprobcor," p%1d-%1d ",i,j);          }
     }            for(jk=1; jk <=nlstate ; jk++){
   fprintf(ficresprob,"\n");            if(pos>=1.e-5){
   fprintf(ficresprobcov,"\n");              if(first==1)
   fprintf(ficresprobcor,"\n");                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   xp=vector(1,npar);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);            }else{
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));              if(first==1)
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   first=1;            }
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {            if( i <= iagemax){
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);              if(pos>=1.e-5){
     exit(0);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   }                /*probs[i][jk][j1]= pp[jk]/pos;*/
   else{                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     fprintf(ficgp,"\n# Routine varprob");              }
   }              else
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     printf("Problem with html file: %s\n", optionfilehtm);            }
     exit(0);          }
   }          
   else{          for(jk=-1; jk <=nlstate+ndeath; jk++)
     fprintf(fichtm,"\n<H2> Computing matrix of variance-covariance of step probabilities</h2>\n");            for(m=-1; m <=nlstate+ndeath; m++)
     fprintf(fichtm,"\n<br> We 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");              if(freq[jk][m][i] !=0 ) {
     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");              if(first==1)
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   cov[1]=1;              }
   j=cptcoveff;          if(i <= iagemax)
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            fprintf(ficresp,"\n");
   j1=0;          if(first==1)
   for(k1=1; k1<=1;k1++){            printf("Others in log...\n");
     for(i1=1; i1<=ncodemax[k1];i1++){          fprintf(ficlog,"\n");
     j1++;        }
       }
     if  (cptcovn>0) {    }
       fprintf(ficresprob, "\n#********** Variable ");    dateintmean=dateintsum/k2cpt; 
       fprintf(ficresprobcov, "\n#********** Variable ");   
       fprintf(ficgp, "\n#********** Variable ");    fclose(ficresp);
       fprintf(fichtm, "\n<h4>********** Variable</h4>\n ");    free_ma3x(freq,-2,nlstate+ndeath,-2,nlstate+ndeath, iagemin, iagemax+3);
       fprintf(ficresprobcor, "\n#********** Variable ");    free_vector(pp,1,nlstate);
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       fprintf(ficresprob, "**********\n#");    /* End of Freq */
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  }
       fprintf(ficresprobcov, "**********\n#");  
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  /************ Prevalence ********************/
       fprintf(ficgp, "**********\n#");  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  {  
       fprintf(ficgp, "**********\n#");    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);       in each health status at the date of interview (if between dateprev1 and dateprev2).
       fprintf(fichtm, "**********\n#");       We still use firstpass and lastpass as another selection.
     }    */
       
       for (age=bage; age<=fage; age ++){    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
         cov[2]=age;    double ***freq; /* Frequencies */
         for (k=1; k<=cptcovn;k++) {    double *pp, **prop;
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    double pos,posprop; 
         }    double  y2; /* in fractional years */
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    int iagemin, iagemax;
         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]]];    iagemin= (int) agemin;
            iagemax= (int) agemax;
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));    /*pp=vector(1,nlstate);*/
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
         gp=vector(1,(nlstate)*(nlstate+ndeath));    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
         gm=vector(1,(nlstate)*(nlstate+ndeath));    j1=0;
        
         for(theta=1; theta <=npar; theta++){    j=cptcoveff;
           for(i=1; i<=npar; i++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    
              for(k1=1; k1<=j;k1++){
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      for(i1=1; i1<=ncodemax[k1];i1++){
                  j1++;
           k=0;        
           for(i=1; i<= (nlstate); i++){        for (i=1; i<=nlstate; i++)  
             for(j=1; j<=(nlstate+ndeath);j++){          for(m=iagemin; m <= iagemax+3; m++)
               k=k+1;            prop[i][m]=0.0;
               gp[k]=pmmij[i][j];       
             }        for (i=1; i<=imx; i++) { /* Each individual */
           }          bool=1;
                    if  (cptcovn>0) {
           for(i=1; i<=npar; i++)            for (z1=1; z1<=cptcoveff; z1++) 
             xp[i] = x[i] - (i==theta ?delti[theta]:0);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                    bool=0;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          } 
           k=0;          if (bool==1) { 
           for(i=1; i<=(nlstate); i++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
             for(j=1; j<=(nlstate+ndeath);j++){              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
               k=k+1;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
               gm[k]=pmmij[i][j];                if(agev[m][i]==0) agev[m][i]=iagemax+1;
             }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                      if (s[m][i]>0 && s[m][i]<=nlstate) { 
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)                  /*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]]);*/
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                    prop[s[m][i]][(int)agev[m][i]] += weight[i];
         }                  prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)              }
           for(theta=1; theta <=npar; theta++)            } /* end selection of waves */
             trgradg[j][theta]=gradg[theta][j];          }
                }
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);        for(i=iagemin; i <= iagemax+3; i++){  
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);          
                  for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         pmij(pmmij,cov,ncovmodel,x,nlstate);            posprop += prop[jk][i]; 
                  } 
         k=0;  
         for(i=1; i<=(nlstate); i++){          for(jk=1; jk <=nlstate ; jk++){     
           for(j=1; j<=(nlstate+ndeath);j++){            if( i <=  iagemax){ 
             k=k+1;              if(posprop>=1.e-5){ 
             mu[k][(int) age]=pmmij[i][j];                probs[i][jk][j1]= prop[jk][i]/posprop;
           }              } 
         }            } 
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)          }/* end jk */ 
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)        }/* end i */ 
             varpij[i][j][(int)age] = doldm[i][j];      } /* end i1 */
     } /* end k1 */
         /*printf("\n%d ",(int)age);    
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    /*free_vector(pp,1,nlstate);*/
      }*/    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
         fprintf(ficresprob,"\n%d ",(int)age);  
         fprintf(ficresprobcov,"\n%d ",(int)age);  /************* Waves Concatenation ***************/
         fprintf(ficresprobcor,"\n%d ",(int)age);  
   void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)  {
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){       Death is a valid wave (if date is known).
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         }       and mw[mi+1][i]. dh depends on stepm.
         i=0;       */
         for (k=1; k<=(nlstate);k++){  
           for (l=1; l<=(nlstate+ndeath);l++){    int i, mi, m;
             i=i++;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);       double sum=0., jmean=0.;*/
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);    int first;
             for (j=1; j<=i;j++){    int j, k=0,jk, ju, jl;
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);    double sum=0.;
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));    first=0;
             }    jmin=1e+5;
           }    jmax=-1;
         }/* end of loop for state */    jmean=0.;
       } /* end of loop for age */    for(i=1; i<=imx; i++){
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/      mi=0;
       for (k1=1; k1<=(nlstate);k1++){      m=firstpass;
         for (l1=1; l1<=(nlstate+ndeath);l1++){      while(s[m][i] <= nlstate){
           if(l1==k1) continue;        if(s[m][i]>=1 || s[m][i]==-2)
           i=(k1-1)*(nlstate+ndeath)+l1;          mw[++mi][i]=m;
           for (k2=1; k2<=(nlstate);k2++){        if(m >=lastpass)
             for (l2=1; l2<=(nlstate+ndeath);l2++){          break;
               if(l2==k2) continue;        else
               j=(k2-1)*(nlstate+ndeath)+l2;          m++;
               if(j<=i) continue;      }/* end while */
               for (age=bage; age<=fage; age ++){      if (s[m][i] > nlstate){
                 if ((int)age %5==0){        mi++;     /* Death is another wave */
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;        /* if(mi==0)  never been interviewed correctly before death */
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;           /* Only death is a correct wave */
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;        mw[mi][i]=m;
                   mu1=mu[i][(int) age]/stepm*YEARM ;      }
                   mu2=mu[j][(int) age]/stepm*YEARM;  
                   /* Computing eigen value of matrix of covariance */      wav[i]=mi;
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));      if(mi==0){
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));        nbwarn++;
                   printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);        if(first==0){
                   /* Eigen vectors */          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));          first=1;
                   v21=sqrt(1.-v11*v11);        }
                   v12=-v21;        if(first==1){
                   v22=v11;          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
                   /*printf(fignu*/        }
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */      } /* end mi==0 */
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */    } /* End individuals */
                   if(first==1){  
                     first=0;    for(i=1; i<=imx; i++){
                     fprintf(ficgp,"\nset parametric;set nolabel");      for(mi=1; mi<wav[i];mi++){
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);        if (stepm <=0)
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");          dh[mi][i]=1;
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%1d%1d-%1d%1d.png\">varpijgr%s%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1);        else{
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%1d%1d-%1d%1d.png\">, ",optionfilefiname,k2,l2,k1,l1);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                     fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\"",optionfilefiname,k2,l2,k1,l1);            if (agedc[i] < 2*AGESUP) {
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);              if(j==0) j=1;  /* Survives at least one month after exam */
                     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)) t \"%d\"",\              else if(j<0){
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \                nberr++;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);                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]);
                   }else{                j=1; /* Temporary Dangerous patch */
                     first=0;                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(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);                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(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);                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);
                     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)) t \"%d\"",\              }
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \              k=k+1;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);              if (j >= jmax) jmax=j;
                   }/* if first */              if (j <= jmin) jmin=j;
                 } /* age mod 5 */              sum=sum+j;
               } /* end loop age */              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\";replot;",optionfilefiname,k2,l2,k1,l1);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
               first=1;            }
             } /*l12 */          }
           } /* k12 */          else{
         } /*l1 */            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       }/* k1 */  /*        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]); */
     } /* loop covariates */  
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);            k=k+1;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));            if (j >= jmax) jmax=j;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));            else if (j <= jmin)jmin=j;
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            /*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]);*/
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            if(j<0){
   }              nberr++;
   free_vector(xp,1,npar);              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]);
   fclose(ficresprob);              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]);
   fclose(ficresprobcov);            }
   fclose(ficresprobcor);            sum=sum+j;
   fclose(ficgp);          }
   fclose(fichtm);          jk= j/stepm;
 }          jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
 /******************* Printing html file ***********/            if(jl==0){
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \              dh[mi][i]=jk;
                   int lastpass, int stepm, int weightopt, char model[],\              bh[mi][i]=0;
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\            }else{ /* We want a negative bias in order to only have interpolation ie
                   int popforecast, int estepm ,\                    * at the price of an extra matrix product in likelihood */
                   double jprev1, double mprev1,double anprev1, \              dh[mi][i]=jk+1;
                   double jprev2, double mprev2,double anprev2){              bh[mi][i]=ju;
   int jj1, k1, i1, cpt;            }
   /*char optionfilehtm[FILENAMELENGTH];*/          }else{
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {            if(jl <= -ju){
     printf("Problem with %s \n",optionfilehtm), exit(0);              dh[mi][i]=jk;
   }              bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\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            else{
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n              dh[mi][i]=jk+1;
  - Life expectancies by age and initial health status (estepm=%2d months):              bh[mi][i]=ju;
    <a href=\"e%s\">e%s</a> <br>\n</li>", \            }
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);            if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n              bh[mi][i]=ju; /* At least one step */
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\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);*/
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n            }
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n          } /* end if mle */
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n        }
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n      } /* end wave */
  - 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);    jmean=sum/k;
     printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
  if(popforecast==1) fprintf(fichtm,"\n    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n   }
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n  
         <br>",fileres,fileres,fileres,fileres);  /*********** Tricode ****************************/
  else  void tricode(int *Tvar, int **nbcode, int imx)
    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(fichtm," <li>Graphs</li><p>");    
     int Ndum[20],ij=1, k, j, i, maxncov=19;
  m=cptcoveff;    int cptcode=0;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    cptcoveff=0; 
    
  jj1=0;    for (k=0; k<maxncov; k++) Ndum[k]=0;
  for(k1=1; k1<=m;k1++){    for (k=1; k<=7; k++) ncodemax[k]=0;
    for(i1=1; i1<=ncodemax[k1];i1++){  
      jj1++;    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
      if (cptcovn > 0) {      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");                                 modality*/ 
        for (cpt=1; cpt<=cptcoveff;cpt++)        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);        Ndum[ij]++; /*store the modality */
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        /*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 
      /* Pij */                                         Tvar[j]. If V=sex and male is 0 and 
      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>                                         female is 1, then  cptcode=1.*/
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          }
      /* Quasi-incidences */  
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>      for (i=0; i<=cptcode; i++) {
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        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 */
        /* Stable prevalence in each health state */      }
        for(cpt=1; cpt<nlstate;cpt++){  
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>      ij=1; 
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      for (i=1; i<=ncodemax[j]; i++) {
        }        for (k=0; k<= maxncov; k++) {
     for(cpt=1; cpt<=nlstate;cpt++) {          if (Ndum[k] != 0) {
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident            nbcode[Tvar[j]][ij]=k; 
 interval) in state (%d): v%s%d%d.png <br>            /* 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; */
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              
      }            ij++;
      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 (ij > ncodemax[j]) break; 
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        }  
      }      } 
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    }  
 health expectancies in states (1) and (2): e%s%d.png<br>  
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);   for (k=0; k< maxncov; k++) Ndum[k]=0;
    }  
  }   for (i=1; i<=ncovmodel-2; i++) { 
 fclose(fichtm);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
 }     ij=Tvar[i];
      Ndum[ij]++;
 /******************* Gnuplot file **************/   }
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  
    ij=1;
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;   for (i=1; i<= maxncov; i++) {
   int ng;     if((Ndum[i]!=0) && (i<=ncovcol)){
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {       Tvaraff[ij]=i; /*For printing */
     printf("Problem with file %s",optionfilegnuplot);       ij++;
   }     }
    }
 #ifdef windows   
     fprintf(ficgp,"cd \"%s\" \n",pathc);   cptcoveff=ij-1; /*Number of simple covariates*/
 #endif  }
 m=pow(2,cptcoveff);  
    /*********** Health Expectancies ****************/
  /* 1eme*/  
   for (cpt=1; cpt<= nlstate ; cpt ++) {  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 (k1=1; k1<= m ; k1 ++) {  
   {
 #ifdef windows    /* Health expectancies */
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
      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);    double age, agelim, hf;
 #endif    double ***p3mat,***varhe;
 #ifdef unix    double **dnewm,**doldm;
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    double *xp;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    double **gp, **gm;
 #endif    double ***gradg, ***trgradg;
     int theta;
 for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    xp=vector(1,npar);
 }    dnewm=matrix(1,nlstate*nlstate,1,npar);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     for (i=1; i<= nlstate ; i ++) {    
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficreseij,"# Health expectancies\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficreseij,"# Age");
 }    for(i=1; i<=nlstate;i++)
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      for(j=1; j<=nlstate;j++)
      for (i=1; i<= nlstate ; i ++) {        fprintf(ficreseij," %1d-%1d (SE)",i,j);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficreseij,"\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      if(estepm < stepm){
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      printf ("Problem %d lower than %d\n",estepm, stepm);
 #ifdef unix    }
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");    else  hstepm=estepm;   
 #endif    /* We compute the life expectancy from trapezoids spaced every estepm months
    }     * This is mainly to measure the difference between two models: for example
   }     * if stepm=24 months pijx are given only every 2 years and by summing them
   /*2 eme*/     * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
   for (k1=1; k1<= m ; k1 ++) {     * to the curvature of the survival function. If, for the same date, we 
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);     * to compare the new estimate of Life expectancy with the same linear 
         * hypothesis. A more precise result, taking into account a more precise
     for (i=1; i<= nlstate+1 ; i ++) {     * curvature will be obtained if estepm is as small as stepm. */
       k=2*i;  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    /* For example we decided to compute the life expectancy with the smallest unit */
       for (j=1; j<= nlstate+1 ; j ++) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");       nhstepm is the number of hstepm from age to agelim 
   else fprintf(ficgp," \%%*lf (\%%*lf)");       nstepm is the number of stepm from age to agelin. 
 }         Look at hpijx to understand the reason of that which relies in memory size
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");       and note for a fixed period like estepm months */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);       survival function given by stepm (the optimization length). Unfortunately it
       for (j=1; j<= nlstate+1 ; j ++) {       means that if the survival funtion is printed only each two years of age and if
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         else fprintf(ficgp," \%%*lf (\%%*lf)");       results. So we changed our mind and took the option of the best precision.
 }      */
       fprintf(ficgp,"\" t\"\" w l 0,");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {    agelim=AGESUP;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      /* nhstepm age range expressed in number of stepm */
 }        nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       else fprintf(ficgp,"\" t\"\" w l 0,");      /* if (stepm >= YEARM) hstepm=1;*/
     }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   /*3eme*/      gp=matrix(0,nhstepm,1,nlstate*nlstate);
       gm=matrix(0,nhstepm,1,nlstate*nlstate);
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<= nlstate ; cpt ++) {      /* Computed by stepm unit matrices, product of hstepm matrices, stored
       k=2+nlstate*(2*cpt-2);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);   
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);      /* Computing  Variances of health expectancies */
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");  
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
 */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       for (i=1; i< nlstate ; i ++) {        }
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);        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++){
              cptj=cptj+1;
   /* CV preval stat */            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
     for (k1=1; k1<= m ; k1 ++) {              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     for (cpt=1; cpt<nlstate ; cpt ++) {            }
       k=3;          }
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        }
       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 (i=1; i< nlstate ; i ++)        for(i=1; i<=npar; i++) 
         fprintf(ficgp,"+$%d",k+i+1);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
              
       l=3+(nlstate+ndeath)*cpt;        cptj=0;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        for(j=1; j<= nlstate; j++){
       for (i=1; i< nlstate ; i ++) {          for(i=1;i<=nlstate;i++){
         l=3+(nlstate+ndeath)*cpt;            cptj=cptj+1;
         fprintf(ficgp,"+$%d",l+i+1);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     }            }
   }            }
          }
   /* proba elementaires */        for(j=1; j<= nlstate*nlstate; j++)
    for(i=1,jk=1; i <=nlstate; i++){          for(h=0; h<=nhstepm-1; h++){
     for(k=1; k <=(nlstate+ndeath); k++){            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       if (k != i) {          }
         for(j=1; j <=ncovmodel; j++){       } 
             
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  /* End theta */
           jk++;  
           fprintf(ficgp,"\n");       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
         }  
       }       for(h=0; h<=nhstepm-1; h++)
     }        for(j=1; j<=nlstate*nlstate;j++)
    }          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/       
      for(jk=1; jk <=m; jk++) {  
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);       for(i=1;i<=nlstate*nlstate;i++)
        if (ng==2)        for(j=1;j<=nlstate*nlstate;j++)
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");          varhe[i][j][(int)age] =0.;
        else  
          fprintf(ficgp,"\nset title \"Probability\"\n");       printf("%d|",(int)age);fflush(stdout);
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        i=1;       for(h=0;h<=nhstepm-1;h++){
        for(k2=1; k2<=nlstate; k2++) {        for(k=0;k<=nhstepm-1;k++){
          k3=i;          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
          for(k=1; k<=(nlstate+ndeath); k++) {          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
            if (k != k2){          for(i=1;i<=nlstate*nlstate;i++)
              if(ng==2)            for(j=1;j<=nlstate*nlstate;j++)
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
              else        }
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      }
              ij=1;      /* Computing expectancies */
              for(j=3; j <=ncovmodel; j++) {      for(i=1; i<=nlstate;i++)
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        for(j=1; j<=nlstate;j++)
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                  ij++;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
                }            
                else  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
              }          }
              fprintf(ficgp,")/(1");  
                    fprintf(ficreseij,"%3.0f",age );
              for(k1=1; k1 <=nlstate; k1++){        cptj=0;
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      for(i=1; i<=nlstate;i++)
                ij=1;        for(j=1; j<=nlstate;j++){
                for(j=3; j <=ncovmodel; j++){          cptj++;
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        }
                    ij++;      fprintf(ficreseij,"\n");
                  }     
                  else      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
                }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
                fprintf(ficgp,")");      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
              }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);    }
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    printf("\n");
              i=i+ncovmodel;    fprintf(ficlog,"\n");
            }  
          }    free_vector(xp,1,npar);
        }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
      }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
    }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
    fclose(ficgp);  }
 }  /* end gnuplot */  
   /************ Variance ******************/
   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)
 /*************** Moving average **************/  {
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   int i, cpt, cptcod;    /* double **newm;*/
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    double **dnewm,**doldm;
       for (i=1; i<=nlstate;i++)    double **dnewmp,**doldmp;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    int i, j, nhstepm, hstepm, h, nstepm ;
           mobaverage[(int)agedeb][i][cptcod]=0.;    int k, cptcode;
        double *xp;
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    double **gp, **gm;  /* for var eij */
       for (i=1; i<=nlstate;i++){    double ***gradg, ***trgradg; /*for var eij */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    double **gradgp, **trgradgp; /* for var p point j */
           for (cpt=0;cpt<=4;cpt++){    double *gpp, *gmp; /* for var p point j */
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
           }    double ***p3mat;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    double age,agelim, hf;
         }    double ***mobaverage;
       }    int theta;
     }    char digit[4];
        char digitp[25];
 }  
     char fileresprobmorprev[FILENAMELENGTH];
   
 /************** Forecasting ******************/    if(popbased==1){
 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){      if(mobilav!=0)
          strcpy(digitp,"-populbased-mobilav-");
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      else strcpy(digitp,"-populbased-nomobil-");
   int *popage;    }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    else 
   double *popeffectif,*popcount;      strcpy(digitp,"-stablbased-");
   double ***p3mat;  
   char fileresf[FILENAMELENGTH];    if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  agelim=AGESUP;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      }
      }
    
   strcpy(fileresf,"f");    strcpy(fileresprobmorprev,"prmorprev"); 
   strcat(fileresf,fileres);    sprintf(digit,"%-d",ij);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     printf("Problem with forecast resultfile: %s\n", fileresf);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   printf("Computing forecasting: result on file '%s' \n", fileresf);    strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   if (mobilav==1) {    }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     movingaverage(agedeb, fage, ageminpar, mobaverage);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   }    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   if (stepm<=12) stepsize=1;      fprintf(ficresprobmorprev," p.%-d SE",j);
        for(i=1; i<=nlstate;i++)
   agelim=AGESUP;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
      }  
   hstepm=1;    fprintf(ficresprobmorprev,"\n");
   hstepm=hstepm/stepm;    fprintf(ficgp,"\n# Routine varevsij");
   yp1=modf(dateintmean,&yp);    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");
   anprojmean=yp;    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   yp2=modf((yp1*12),&yp);  /*   } */
   mprojmean=yp;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;    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(jprojmean==0) jprojmean=1;    fprintf(ficresvij,"# Age");
   if(mprojmean==0) jprojmean=1;    for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
      fprintf(ficresvij,"\n");
   for(cptcov=1;cptcov<=i2;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    xp=vector(1,npar);
       k=k+1;    dnewm=matrix(1,nlstate,1,npar);
       fprintf(ficresf,"\n#******");    doldm=matrix(1,nlstate,1,nlstate);
       for(j=1;j<=cptcoveff;j++) {    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       }  
       fprintf(ficresf,"******\n");    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       fprintf(ficresf,"# StartingAge FinalAge");    gpp=vector(nlstate+1,nlstate+ndeath);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    gmp=vector(nlstate+1,nlstate+ndeath);
          trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
          
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    if(estepm < stepm){
         fprintf(ficresf,"\n");      printf ("Problem %d lower than %d\n",estepm, stepm);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      }
     else  hstepm=estepm;   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    /* For example we decided to compute the life expectancy with the smallest unit */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           nhstepm = nhstepm/hstepm;       nhstepm is the number of hstepm from age to agelim 
                 nstepm is the number of stepm from age to agelin. 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       Look at hpijx to understand the reason of that which relies in memory size
           oldm=oldms;savm=savms;       and note for a fixed period like k years */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      /* We decided (b) to get a life expectancy respecting the most precise curvature of the
               survival function given by stepm (the optimization length). Unfortunately it
           for (h=0; h<=nhstepm; h++){       means that if the survival funtion is printed every two years of age and if
             if (h==(int) (calagedate+YEARM*cpt)) {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);       results. So we changed our mind and took the option of the best precision.
             }    */
             for(j=1; j<=nlstate+ndeath;j++) {    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
               kk1=0.;kk2=0;    agelim = AGESUP;
               for(i=1; i<=nlstate;i++) {                  for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                 if (mobilav==1)      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                 else {      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
                 }      gp=matrix(0,nhstepm,1,nlstate);
                      gm=matrix(0,nhstepm,1,nlstate);
               }  
               if (h==(int)(calagedate+12*cpt)){  
                 fprintf(ficresf," %.3f", kk1);      for(theta=1; theta <=npar; theta++){
                                for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
               }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             }        }
           }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         }  
       }        if (popbased==1) {
     }          if(mobilav ==0){
   }            for(i=1; i<=nlstate;i++)
                      prlim[i][i]=probs[(int)age][i][ij];
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
   fclose(ficresf);              prlim[i][i]=mobaverage[(int)age][i][ij];
 }          }
 /************** 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){    
          for(j=1; j<= nlstate; j++){
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          for(h=0; h<=nhstepm; h++){
   int *popage;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   double *popeffectif,*popcount;          }
   double ***p3mat,***tabpop,***tabpopprev;        }
   char filerespop[FILENAMELENGTH];        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);           as a weighted average of prlim.
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        */
   agelim=AGESUP;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          for(i=1,gpp[j]=0.; i<= nlstate; i++)
              gpp[j] += prlim[i][i]*p3mat[i][j][1];
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        }    
          /* end probability of death */
    
   strcpy(filerespop,"pop");        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   strcat(filerespop,fileres);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     printf("Problem with forecast resultfile: %s\n", filerespop);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   }   
   printf("Computing forecasting: result on file '%s' \n", filerespop);        if (popbased==1) {
           if(mobilav ==0){
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
   if (mobilav==1) {          }else{ /* mobilav */ 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(i=1; i<=nlstate;i++)
     movingaverage(agedeb, fage, ageminpar, mobaverage);              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
         }
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   if (stepm<=12) stepsize=1;        for(j=1; j<= nlstate; j++){
            for(h=0; h<=nhstepm; h++){
   agelim=AGESUP;            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   hstepm=1;          }
   hstepm=hstepm/stepm;        }
          /* This for computing probability of death (h=1 means
   if (popforecast==1) {           computed over hstepm matrices product = hstepm*stepm months) 
     if((ficpop=fopen(popfile,"r"))==NULL) {           as a weighted average of prlim.
       printf("Problem with population file : %s\n",popfile);exit(0);        */
     }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     popage=ivector(0,AGESUP);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     popeffectif=vector(0,AGESUP);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     popcount=vector(0,AGESUP);        }    
            /* end probability of death */
     i=1;    
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        for(j=1; j<= nlstate; j++) /* vareij */
              for(h=0; h<=nhstepm; h++){
     imx=i;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          }
   }  
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   for(cptcov=1;cptcov<=i2;cptcov++){          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        }
       k=k+1;  
       fprintf(ficrespop,"\n#******");      } /* End theta */
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       }  
       fprintf(ficrespop,"******\n");      for(h=0; h<=nhstepm; h++) /* veij */
       fprintf(ficrespop,"# Age");        for(j=1; j<=nlstate;j++)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);          for(theta=1; theta <=npar; theta++)
       if (popforecast==1)  fprintf(ficrespop," [Population]");            trgradg[h][j][theta]=gradg[h][theta][j];
        
       for (cpt=0; cpt<=0;cpt++) {      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          for(theta=1; theta <=npar; theta++)
                  trgradgp[j][theta]=gradgp[theta][j];
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                for(i=1;i<=nlstate;i++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(j=1;j<=nlstate;j++)
           oldm=oldms;savm=savms;          vareij[i][j][(int)age] =0.;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
              for(h=0;h<=nhstepm;h++){
           for (h=0; h<=nhstepm; h++){        for(k=0;k<=nhstepm;k++){
             if (h==(int) (calagedate+YEARM*cpt)) {          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
             }          for(i=1;i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++) {            for(j=1;j<=nlstate;j++)
               kk1=0.;kk2=0;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
               for(i=1; i<=nlstate;i++) {                      }
                 if (mobilav==1)      }
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    
                 else {      /* pptj */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      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++)
               if (h==(int)(calagedate+12*cpt)){        for(i=nlstate+1;i<=nlstate+ndeath;i++)
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          varppt[j][i]=doldmp[j][i];
                   /*fprintf(ficrespop," %.3f", kk1);      /* end ppptj */
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      /*  x centered again */
               }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
             }      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
             for(i=1; i<=nlstate;i++){   
               kk1=0.;      if (popbased==1) {
                 for(j=1; j<=nlstate;j++){        if(mobilav ==0){
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          for(i=1; i<=nlstate;i++)
                 }            prlim[i][i]=probs[(int)age][i][ij];
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];        }else{ /* mobilav */ 
             }          for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        }
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      }
           }               
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* This for computing probability of death (h=1 means
         }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       }         as a weighted average of prlim.
        */
   /******/      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
         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--){      /* end probability of death */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
                for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
           oldm=oldms;savm=savms;        for(i=1; i<=nlstate;i++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
           for (h=0; h<=nhstepm; h++){        }
             if (h==(int) (calagedate+YEARM*cpt)) {      } 
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      fprintf(ficresprobmorprev,"\n");
             }  
             for(j=1; j<=nlstate+ndeath;j++) {      fprintf(ficresvij,"%.0f ",age );
               kk1=0.;kk2=0;      for(i=1; i<=nlstate;i++)
               for(i=1; i<=nlstate;i++) {                      for(j=1; j<=nlstate;j++){
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
               }        }
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);      fprintf(ficresvij,"\n");
             }      free_matrix(gp,0,nhstepm,1,nlstate);
           }      free_matrix(gm,0,nhstepm,1,nlstate);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
         }      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    }    } /* End age */
   }    free_vector(gpp,nlstate+1,nlstate+ndeath);
      free_vector(gmp,nlstate+1,nlstate+ndeath);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   if (popforecast==1) {    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     free_ivector(popage,0,AGESUP);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     free_vector(popeffectif,0,AGESUP);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     free_vector(popcount,0,AGESUP);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
   fclose(ficrespop);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
 }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
 /***********************************************/    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
 /**************** Main Program *****************/    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
 /***********************************************/  */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
 int main(int argc, char *argv[])    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
 {  
     free_vector(xp,1,npar);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    free_matrix(doldm,1,nlstate,1,nlstate);
   double agedeb, agefin,hf;    free_matrix(dnewm,1,nlstate,1,npar);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   double fret;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   double **xi,tmp,delta;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
   double dum; /* Dummy variable */    fflush(ficgp);
   double ***p3mat;    fflush(fichtm); 
   int *indx;  }  /* end varevsij */
   char line[MAXLINE], linepar[MAXLINE];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  /************ Variance of prevlim ******************/
   int firstobs=1, lastobs=10;  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 sdeb, sfin; /* Status at beginning and end */  {
   int c,  h , cpt,l;    /* Variance of prevalence limit */
   int ju,jl, mi;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    double **newm;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    double **dnewm,**doldm;
   int mobilav=0,popforecast=0;    int i, j, nhstepm, hstepm;
   int hstepm, nhstepm;    int k, cptcode;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    double *xp;
     double *gp, *gm;
   double bage, fage, age, agelim, agebase;    double **gradg, **trgradg;
   double ftolpl=FTOL;    double age,agelim;
   double **prlim;    int theta;
   double *severity;     
   double ***param; /* Matrix of parameters */    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   double  *p;    fprintf(ficresvpl,"# Age");
   double **matcov; /* Matrix of covariance */    for(i=1; i<=nlstate;i++)
   double ***delti3; /* Scale */        fprintf(ficresvpl," %1d-%1d",i,i);
   double *delti; /* Scale */    fprintf(ficresvpl,"\n");
   double ***eij, ***vareij;  
   double **varpl; /* Variances of prevalence limits by age */    xp=vector(1,npar);
   double *epj, vepp;    dnewm=matrix(1,nlstate,1,npar);
   double kk1, kk2;    doldm=matrix(1,nlstate,1,nlstate);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    
      hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   char *alph[]={"a","a","b","c","d","e"}, str[4];    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   char z[1]="c", occ;      if (stepm >= YEARM) hstepm=1;
 #include <sys/time.h>      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
 #include <time.h>      gradg=matrix(1,npar,1,nlstate);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      gp=vector(1,nlstate);
        gm=vector(1,nlstate);
   /* long total_usecs;  
   struct timeval start_time, end_time;      for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ /* Computes gradient */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   getcwd(pathcd, size);        }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   printf("\n%s",version);        for(i=1;i<=nlstate;i++)
   if(argc <=1){          gp[i] = prlim[i][i];
     printf("\nEnter the parameter file name: ");      
     scanf("%s",pathtot);        for(i=1; i<=npar; i++) /* Computes gradient */
   }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   else{        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     strcpy(pathtot,argv[1]);        for(i=1;i<=nlstate;i++)
   }          gm[i] = prlim[i][i];
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/  
   /*cygwin_split_path(pathtot,path,optionfile);        for(i=1;i<=nlstate;i++)
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   /* cutv(path,optionfile,pathtot,'\\');*/      } /* End theta */
   
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);      trgradg =matrix(1,nlstate,1,npar);
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  
   chdir(path);      for(j=1; j<=nlstate;j++)
   replace(pathc,path);        for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
 /*-------- arguments in the command line --------*/  
       for(i=1;i<=nlstate;i++)
   strcpy(fileres,"r");        varpl[i][(int)age] =0.;
   strcat(fileres, optionfilefiname);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   strcat(fileres,".txt");    /* Other files have txt extension */      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
   /*---------arguments file --------*/        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      fprintf(ficresvpl,"%.0f ",age );
     printf("Problem with optionfile %s\n",optionfile);      for(i=1; i<=nlstate;i++)
     goto end;        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   }      fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
   strcpy(filereso,"o");      free_vector(gm,1,nlstate);
   strcat(filereso,fileres);      free_matrix(gradg,1,npar,1,nlstate);
   if((ficparo=fopen(filereso,"w"))==NULL) {      free_matrix(trgradg,1,nlstate,1,npar);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    } /* End age */
   }  
     free_vector(xp,1,npar);
   /* Reads comments: lines beginning with '#' */    free_matrix(doldm,1,nlstate,1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){    free_matrix(dnewm,1,nlstate,1,nlstate);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  }
     puts(line);  
     fputs(line,ficparo);  /************ 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)
   ungetc(c,ficpar);  {
     int i, j=0,  i1, k1, l1, t, tj;
   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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    int k2, l2, j1,  z1;
   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);    int k=0,l, cptcode;
   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);    int first=1, first1;
 while((c=getc(ficpar))=='#' && c!= EOF){    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     ungetc(c,ficpar);    double **dnewm,**doldm;
     fgets(line, MAXLINE, ficpar);    double *xp;
     puts(line);    double *gp, *gm;
     fputs(line,ficparo);    double **gradg, **trgradg;
   }    double **mu;
   ungetc(c,ficpar);    double age,agelim, cov[NCOVMAX];
      double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
        int theta;
   covar=matrix(0,NCOVMAX,1,n);    char fileresprob[FILENAMELENGTH];
   cptcovn=0;    char fileresprobcov[FILENAMELENGTH];
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    char fileresprobcor[FILENAMELENGTH];
   
   ncovmodel=2+cptcovn;    double ***varpij;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
      strcpy(fileresprob,"prob"); 
   /* Read guess parameters */    strcat(fileresprob,fileres);
   /* Reads comments: lines beginning with '#' */    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   while((c=getc(ficpar))=='#' && c!= EOF){      printf("Problem with resultfile: %s\n", fileresprob);
     ungetc(c,ficpar);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    strcpy(fileresprobcov,"probcov"); 
     fputs(line,ficparo);    strcat(fileresprobcov,fileres);
   }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   ungetc(c,ficpar);      printf("Problem with resultfile: %s\n", fileresprobcov);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    }
     for(i=1; i <=nlstate; i++)    strcpy(fileresprobcor,"probcor"); 
     for(j=1; j <=nlstate+ndeath-1; j++){    strcat(fileresprobcor,fileres);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       fprintf(ficparo,"%1d%1d",i1,j1);      printf("Problem with resultfile: %s\n", fileresprobcor);
       printf("%1d%1d",i,j);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
       for(k=1; k<=ncovmodel;k++){    }
         fscanf(ficpar," %lf",&param[i][j][k]);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
         printf(" %lf",param[i][j][k]);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
         fprintf(ficparo," %lf",param[i][j][k]);    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);
       fscanf(ficpar,"\n");    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       printf("\n");    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       fprintf(ficparo,"\n");    
     }    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
      fprintf(ficresprob,"# Age");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
   p=param[1][1];    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
      fprintf(ficresprobcov,"# Age");
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);      for(j=1; j<=(nlstate+ndeath);j++){
     puts(line);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
     fputs(line,ficparo);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   ungetc(c,ficpar);      }  
    /* fprintf(ficresprob,"\n");
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    fprintf(ficresprobcov,"\n");
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    fprintf(ficresprobcor,"\n");
   for(i=1; i <=nlstate; i++){   */
     for(j=1; j <=nlstate+ndeath-1; j++){   xp=vector(1,npar);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       printf("%1d%1d",i,j);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
       fprintf(ficparo,"%1d%1d",i1,j1);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
       for(k=1; k<=ncovmodel;k++){    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
         fscanf(ficpar,"%le",&delti3[i][j][k]);    first=1;
         printf(" %le",delti3[i][j][k]);    fprintf(ficgp,"\n# Routine varprob");
         fprintf(ficparo," %le",delti3[i][j][k]);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       }    fprintf(fichtm,"\n");
       fscanf(ficpar,"\n");  
       printf("\n");    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
       fprintf(ficparo,"\n");    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     }    file %s<br>\n",optionfilehtmcov);
   }    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   delti=delti3[1][1];  and drawn. It helps understanding how is the covariance between two incidences.\
     They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   /* Reads comments: lines beginning with '#' */    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. \
   while((c=getc(ficpar))=='#' && c!= EOF){  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
     ungetc(c,ficpar);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
     fgets(line, MAXLINE, ficpar);  standard deviations wide on each axis. <br>\
     puts(line);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
     fputs(line,ficparo);   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   }  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   ungetc(c,ficpar);  
      cov[1]=1;
   matcov=matrix(1,npar,1,npar);    tj=cptcoveff;
   for(i=1; i <=npar; i++){    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     fscanf(ficpar,"%s",&str);    j1=0;
     printf("%s",str);    for(t=1; t<=tj;t++){
     fprintf(ficparo,"%s",str);      for(i1=1; i1<=ncodemax[t];i1++){ 
     for(j=1; j <=i; j++){        j1++;
       fscanf(ficpar," %le",&matcov[i][j]);        if  (cptcovn>0) {
       printf(" %.5le",matcov[i][j]);          fprintf(ficresprob, "\n#********** Variable "); 
       fprintf(ficparo," %.5le",matcov[i][j]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     }          fprintf(ficresprob, "**********\n#\n");
     fscanf(ficpar,"\n");          fprintf(ficresprobcov, "\n#********** Variable "); 
     printf("\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fprintf(ficparo,"\n");          fprintf(ficresprobcov, "**********\n#\n");
   }          
   for(i=1; i <=npar; i++)          fprintf(ficgp, "\n#********** Variable "); 
     for(j=i+1;j<=npar;j++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       matcov[i][j]=matcov[j][i];          fprintf(ficgp, "**********\n#\n");
              
   printf("\n");          
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     /*-------- Rewriting paramater file ----------*/          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
      strcpy(rfileres,"r");    /* "Rparameterfile */          
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/          fprintf(ficresprobcor, "\n#********** Variable ");    
      strcat(rfileres,".");    /* */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */          fprintf(ficresprobcor, "**********\n#");    
     if((ficres =fopen(rfileres,"w"))==NULL) {        }
       printf("Problem writing new parameter file: %s\n", fileres);goto end;        
     }        for (age=bage; age<=fage; age ++){ 
     fprintf(ficres,"#%s\n",version);          cov[2]=age;
              for (k=1; k<=cptcovn;k++) {
     /*-------- data file ----------*/            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     if((fic=fopen(datafile,"r"))==NULL)    {          }
       printf("Problem with datafile: %s\n", datafile);goto end;          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     }          for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     n= lastobs;          
     severity = vector(1,maxwav);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     outcome=imatrix(1,maxwav+1,1,n);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     num=ivector(1,n);          gp=vector(1,(nlstate)*(nlstate+ndeath));
     moisnais=vector(1,n);          gm=vector(1,(nlstate)*(nlstate+ndeath));
     annais=vector(1,n);      
     moisdc=vector(1,n);          for(theta=1; theta <=npar; theta++){
     andc=vector(1,n);            for(i=1; i<=npar; i++)
     agedc=vector(1,n);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
     cod=ivector(1,n);            
     weight=vector(1,n);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */            
     mint=matrix(1,maxwav,1,n);            k=0;
     anint=matrix(1,maxwav,1,n);            for(i=1; i<= (nlstate); i++){
     s=imatrix(1,maxwav+1,1,n);              for(j=1; j<=(nlstate+ndeath);j++){
     adl=imatrix(1,maxwav+1,1,n);                    k=k+1;
     tab=ivector(1,NCOVMAX);                gp[k]=pmmij[i][j];
     ncodemax=ivector(1,8);              }
             }
     i=1;            
     while (fgets(line, MAXLINE, fic) != NULL)    {            for(i=1; i<=npar; i++)
       if ((i >= firstobs) && (i <=lastobs)) {              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
              
         for (j=maxwav;j>=1;j--){            pmij(pmmij,cov,ncovmodel,xp,nlstate);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);            k=0;
           strcpy(line,stra);            for(i=1; i<=(nlstate); i++){
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              for(j=1; j<=(nlstate+ndeath);j++){
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                k=k+1;
         }                gm[k]=pmmij[i][j];
                      }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);            }
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);       
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
         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=1; j<=(nlstate)*(nlstate+ndeath);j++)
         for (j=ncovcol;j>=1;j--){            for(theta=1; theta <=npar; theta++)
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);              trgradg[j][theta]=gradg[theta][j];
         }          
         num[i]=atol(stra);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
                  matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           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;}*/          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         i=i+1;          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       }  
     }          pmij(pmmij,cov,ncovmodel,x,nlstate);
     /* printf("ii=%d", ij);          
        scanf("%d",i);*/          k=0;
   imx=i-1; /* Number of individuals */          for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
   /* for (i=1; i<=imx; i++){              k=k+1;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;              mu[k][(int) age]=pmmij[i][j];
     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<=(nlstate)*(nlstate+ndeath);i++)
    /*  for (i=1; i<=imx; i++){            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
      if (s[4][i]==9)  s[4][i]=-1;              varpij[i][j][(int)age] = doldm[i][j];
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/  
            /*printf("\n%d ",(int)age);
              for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   /* Calculation of the number of parameter from char model*/            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   Tvar=ivector(1,15);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   Tprod=ivector(1,15);            }*/
   Tvaraff=ivector(1,15);  
   Tvard=imatrix(1,15,1,2);          fprintf(ficresprob,"\n%d ",(int)age);
   Tage=ivector(1,15);                fprintf(ficresprobcov,"\n%d ",(int)age);
              fprintf(ficresprobcor,"\n%d ",(int)age);
   if (strlen(model) >1){  
     j=0, j1=0, k1=1, k2=1;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     j=nbocc(model,'+');            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     j1=nbocc(model,'*');          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     cptcovn=j+1;            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     cptcovprod=j1;            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
              }
     strcpy(modelsav,model);          i=0;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          for (k=1; k<=(nlstate);k++){
       printf("Error. Non available option model=%s ",model);            for (l=1; l<=(nlstate+ndeath);l++){ 
       goto end;              i=i++;
     }              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
                  fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     for(i=(j+1); i>=1;i--){              for (j=1; j<=i;j++){
       cutv(stra,strb,modelsav,'+');                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/              }
       /*scanf("%d",i);*/            }
       if (strchr(strb,'*')) {          }/* end of loop for state */
         cutv(strd,strc,strb,'*');        } /* end of loop for age */
         if (strcmp(strc,"age")==0) {  
           cptcovprod--;        /* Confidence intervalle of pij  */
           cutv(strb,stre,strd,'V');        /*
           Tvar[i]=atoi(stre);          fprintf(ficgp,"\nset noparametric;unset label");
           cptcovage++;          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
             Tage[cptcovage]=i;          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
             /*printf("stre=%s ", stre);*/          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);
         else if (strcmp(strd,"age")==0) {          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           cptcovprod--;          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
           cutv(strb,stre,strc,'V');        */
           Tvar[i]=atoi(stre);  
           cptcovage++;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
           Tage[cptcovage]=i;        first1=1;
         }        for (k2=1; k2<=(nlstate);k2++){
         else {          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
           cutv(strb,stre,strc,'V');            if(l2==k2) continue;
           Tvar[i]=ncovcol+k1;            j=(k2-1)*(nlstate+ndeath)+l2;
           cutv(strb,strc,strd,'V');            for (k1=1; k1<=(nlstate);k1++){
           Tprod[k1]=i;              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
           Tvard[k1][1]=atoi(strc);                if(l1==k1) continue;
           Tvard[k1][2]=atoi(stre);                i=(k1-1)*(nlstate+ndeath)+l1;
           Tvar[cptcovn+k2]=Tvard[k1][1];                if(i<=j) continue;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                for (age=bage; age<=fage; age ++){ 
           for (k=1; k<=lastobs;k++)                  if ((int)age %5==0){
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
           k1++;                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
           k2=k2+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;
       else {                    c12=cv12/sqrt(v1*v2);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/                    /* Computing eigen value of matrix of covariance */
        /*  scanf("%d",i);*/                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       cutv(strd,strc,strb,'V');                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       Tvar[i]=atoi(strc);                    /* Eigen vectors */
       }                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
       strcpy(modelsav,stra);                      /*v21=sqrt(1.-v11*v11); *//* error */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                    v21=(lc1-v1)/cv12*v11;
         scanf("%d",i);*/                    v12=-v21;
     }                    v22=v11;
 }                    tnalp=v21/v11;
                      if(first1==1){
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);                      first1=0;
   printf("cptcovprod=%d ", cptcovprod);                      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);
   scanf("%d ",i);*/                    }
     fclose(fic);                    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*/
     /*  if(mle==1){*/                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     if (weightopt != 1) { /* Maximisation without weights*/                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
       for(i=1;i<=n;i++) weight[i]=1.0;                    if(first==1){
     }                      first=0;
     /*-calculation of age at interview from date of interview and age at death -*/                      fprintf(ficgp,"\nset parametric;unset label");
     agev=matrix(1,maxwav,1,imx);                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     for (i=1; i<=imx; i++) {                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
       for(m=2; (m<= maxwav); m++) {   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
          anint[m][i]=9999;                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
          s[m][i]=-1;                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
        }                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
       }                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     for (i=1; i<=imx; i++)  {                      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",\
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       for(m=1; (m<= maxwav); m++){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
         if(s[m][i] >0){                    }else{
           if (s[m][i] >= nlstate+1) {                      first=0;
             if(agedc[i]>0)                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
               if(moisdc[i]!=99 && andc[i]!=9999)                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                 agev[m][i]=agedc[i];                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/                      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",\
            else {                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
               if (andc[i]!=9999){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                    }/* if first */
               agev[m][i]=-1;                  } /* age mod 5 */
               }                } /* end loop age */
             }                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           }                first=1;
           else if(s[m][i] !=9){ /* Should no more exist */              } /*l12 */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);            } /* k12 */
             if(mint[m][i]==99 || anint[m][i]==9999)          } /*l1 */
               agev[m][i]=1;        }/* k1 */
             else if(agev[m][i] <agemin){      } /* loop covariates */
               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);*/    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
             }    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
             else if(agev[m][i] >agemax){    free_vector(xp,1,npar);
               agemax=agev[m][i];    fclose(ficresprob);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    fclose(ficresprobcov);
             }    fclose(ficresprobcor);
             /*agev[m][i]=anint[m][i]-annais[i];*/    fflush(ficgp);
             /*   agev[m][i] = age[i]+2*m;*/    fflush(fichtmcov);
           }  }
           else { /* =9 */  
             agev[m][i]=1;  
             s[m][i]=-1;  /******************* Printing html file ***********/
           }  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
         }                    int lastpass, int stepm, int weightopt, char model[],\
         else /*= 0 Unknown */                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
           agev[m][i]=1;                    int popforecast, int estepm ,\
       }                    double jprev1, double mprev1,double anprev1, \
                        double jprev2, double mprev2,double anprev2){
     }    int jj1, k1, i1, cpt;
     for (i=1; i<=imx; i++)  {  
       for(m=1; (m<= maxwav); m++){     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
         if (s[m][i] > (nlstate+ndeath)) {   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
           printf("Error: Wrong value in nlstate or ndeath\n");               jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
           goto end;     fprintf(fichtm,"\
         }   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
       }             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
     }     fprintf(fichtm,"\
    - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
     free_vector(severity,1,maxwav);   - Life expectancies by age and initial health status (estepm=%2d months): \
     free_imatrix(outcome,1,maxwav+1,1,n);     <a href=\"%s\">%s</a> <br>\n</li>",
     free_vector(moisnais,1,n);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
     free_vector(annais,1,n);  
     /* free_matrix(mint,1,maxwav,1,n);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
        free_matrix(anint,1,maxwav,1,n);*/  
     free_vector(moisdc,1,n);   m=cptcoveff;
     free_vector(andc,1,n);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
       jj1=0;
     wav=ivector(1,imx);   for(k1=1; k1<=m;k1++){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);     for(i1=1; i1<=ncodemax[k1];i1++){
     mw=imatrix(1,lastpass-firstpass+1,1,imx);       jj1++;
           if (cptcovn > 0) {
     /* Concatenates waves */         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);         for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       Tcode=ivector(1,100);       }
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);       /* Pij */
       ncodemax[1]=1;       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> \
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
             /* Quasi-incidences */
    codtab=imatrix(1,100,1,10);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    h=0;   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
    m=pow(2,cptcoveff);  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
           /* Stable prevalence in each health state */
    for(k=1;k<=cptcoveff; k++){         for(cpt=1; cpt<nlstate;cpt++){
      for(i=1; i <=(m/pow(2,k));i++){           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
        for(j=1; j <= ncodemax[k]; j++){  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){         }
            h++;       for(cpt=1; cpt<=nlstate;cpt++) {
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
          }       }
        }     } /* end i1 */
      }   }/* End k1 */
    }   fprintf(fichtm,"</ul>");
    /* 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++){   fprintf(fichtm,"\
       for(k=1; k <=cptcovn; k++){  \n<br><li><h4> Result files (second order: variances)</h4>\n\
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
       }  
       printf("\n");   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
       }           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
       scanf("%d",i);*/   fprintf(fichtm,"\
       - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
    /* Calculates basic frequencies. Computes observed prevalence at single age           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
        and prints on file fileres'p'. */  
    fprintf(fichtm,"\
       - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
               subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   fprintf(fichtm,"\
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   fprintf(fichtm,"\
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
                 subdirf2(fileres,"t"),subdirf2(fileres,"t"));
     /* For Powell, parameters are in a vector p[] starting at p[1]   fprintf(fichtm,"\
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
     if(mle==1){  /*  if(popforecast==1) fprintf(fichtm,"\n */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
     }  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
      /*      <br>",fileres,fileres,fileres,fileres); */
     /*--------- results files --------------*/  /*  else  */
     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(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
     fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
    jk=1;  
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");   m=cptcoveff;
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    for(i=1,jk=1; i <=nlstate; i++){  
      for(k=1; k <=(nlstate+ndeath); k++){   jj1=0;
        if (k != i)   for(k1=1; k1<=m;k1++){
          {     for(i1=1; i1<=ncodemax[k1];i1++){
            printf("%d%d ",i,k);       jj1++;
            fprintf(ficres,"%1d%1d ",i,k);       if (cptcovn > 0) {
            for(j=1; j <=ncovmodel; j++){         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
              printf("%f ",p[jk]);         for (cpt=1; cpt<=cptcoveff;cpt++) 
              fprintf(ficres,"%f ",p[jk]);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
              jk++;         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
            }       }
            printf("\n");       for(cpt=1; cpt<=nlstate;cpt++) {
            fprintf(ficres,"\n");         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
          }  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
      }  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
    }       }
  if(mle==1){       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
     /* Computing hessian and covariance matrix */  health expectancies in states (1) and (2): %s%d.png<br>\
     ftolhess=ftol; /* Usually correct */  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
     hesscov(matcov, p, npar, delti, ftolhess, func);     } /* end i1 */
  }   }/* End k1 */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");   fprintf(fichtm,"</ul>");
     printf("# Scales (for hessian or gradient estimation)\n");   fflush(fichtm);
      for(i=1,jk=1; i <=nlstate; i++){  }
       for(j=1; j <=nlstate+ndeath; j++){  
         if (j!=i) {  /******************* Gnuplot file **************/
           fprintf(ficres,"%1d%1d",i,j);  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
           printf("%1d%1d",i,j);  
           for(k=1; k<=ncovmodel;k++){    char dirfileres[132],optfileres[132];
             printf(" %.5e",delti[jk]);    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
             fprintf(ficres," %.5e",delti[jk]);    int ng;
             jk++;  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
           }  /*     printf("Problem with file %s",optionfilegnuplot); */
           printf("\n");  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
           fprintf(ficres,"\n");  /*   } */
         }  
       }    /*#ifdef windows */
      }    fprintf(ficgp,"cd \"%s\" \n",pathc);
          /*#endif */
     k=1;    m=pow(2,cptcoveff);
     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");  
     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");    strcpy(dirfileres,optionfilefiname);
     for(i=1;i<=npar;i++){    strcpy(optfileres,"vpl");
       /*  if (k>nlstate) k=1;   /* 1eme*/
       i1=(i-1)/(ncovmodel*nlstate)+1;    for (cpt=1; cpt<= nlstate ; cpt ++) {
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);     for (k1=1; k1<= m ; k1 ++) {
       printf("%s%d%d",alph[k],i1,tab[i]);*/       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
       fprintf(ficres,"%3d",i);       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
       printf("%3d",i);       fprintf(ficgp,"set xlabel \"Age\" \n\
       for(j=1; j<=i;j++){  set ylabel \"Probability\" \n\
         fprintf(ficres," %.5e",matcov[i][j]);  set ter png small\n\
         printf(" %.5e",matcov[i][j]);  set size 0.65,0.65\n\
       }  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
       fprintf(ficres,"\n");  
       printf("\n");       for (i=1; i<= nlstate ; i ++) {
       k++;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     }         else fprintf(ficgp," \%%*lf (\%%*lf)");
           }
     while((c=getc(ficpar))=='#' && c!= EOF){       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);
       ungetc(c,ficpar);       for (i=1; i<= nlstate ; i ++) {
       fgets(line, MAXLINE, ficpar);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       puts(line);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       fputs(line,ficparo);       } 
     }       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
     ungetc(c,ficpar);       for (i=1; i<= nlstate ; i ++) {
     estepm=0;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     if (estepm==0 || estepm < stepm) estepm=stepm;       }  
     if (fage <= 2) {       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
       bage = ageminpar;     }
       fage = agemaxpar;    }
     }    /*2 eme*/
        
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    for (k1=1; k1<= m ; k1 ++) { 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
        
     while((c=getc(ficpar))=='#' && c!= EOF){      for (i=1; i<= nlstate+1 ; i ++) {
     ungetc(c,ficpar);        k=2*i;
     fgets(line, MAXLINE, ficpar);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     puts(line);        for (j=1; j<= nlstate+1 ; j ++) {
     fputs(line,ficparo);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   }          else fprintf(ficgp," \%%*lf (\%%*lf)");
   ungetc(c,ficpar);        }   
          if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        for (j=1; j<= nlstate+1 ; j ++) {
                if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   while((c=getc(ficpar))=='#' && c!= EOF){          else fprintf(ficgp," \%%*lf (\%%*lf)");
     ungetc(c,ficpar);        }   
     fgets(line, MAXLINE, ficpar);        fprintf(ficgp,"\" t\"\" w l 0,");
     puts(line);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     fputs(line,ficparo);        for (j=1; j<= nlstate+1 ; j ++) {
   }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   ungetc(c,ficpar);          else fprintf(ficgp," \%%*lf (\%%*lf)");
          }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        else fprintf(ficgp,"\" t\"\" w l 0,");
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      }
     }
   fscanf(ficpar,"pop_based=%d\n",&popbased);    
   fprintf(ficparo,"pop_based=%d\n",popbased);      /*3eme*/
   fprintf(ficres,"pop_based=%d\n",popbased);      
      for (k1=1; k1<= m ; k1 ++) { 
   while((c=getc(ficpar))=='#' && c!= EOF){      for (cpt=1; cpt<= nlstate ; cpt ++) {
     ungetc(c,ficpar);        k=2+nlstate*(2*cpt-2);
     fgets(line, MAXLINE, ficpar);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
     puts(line);        fprintf(ficgp,"set ter png small\n\
     fputs(line,ficparo);  set size 0.65,0.65\n\
   }  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
   ungetc(c,ficpar);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
 while((c=getc(ficpar))=='#' && c!= EOF){        */
     ungetc(c,ficpar);        for (i=1; i< nlstate ; i ++) {
     fgets(line, MAXLINE, ficpar);          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);
     puts(line);          
     fputs(line,ficparo);        } 
   }      }
   ungetc(c,ficpar);    }
     
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    /* CV preval stable (period) */
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    for (k1=1; k1<= m ; k1 ++) { 
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
 /*------------ gnuplot -------------*/  set ter png small\nset size 0.65,0.65\n\
   strcpy(optionfilegnuplot,optionfilefiname);  unset log y\n\
   strcat(optionfilegnuplot,".gp");  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        
     printf("Problem with file %s",optionfilegnuplot);        for (i=1; i< nlstate ; i ++)
   }          fprintf(ficgp,"+$%d",k+i+1);
   fclose(ficgp);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);        
 /*--------- index.htm --------*/        l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
   strcpy(optionfilehtm,optionfile);        for (i=1; i< nlstate ; i ++) {
   strcat(optionfilehtm,".htm");          l=3+(nlstate+ndeath)*cpt;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          fprintf(ficgp,"+$%d",l+i+1);
     printf("Problem with %s \n",optionfilehtm), exit(0);        }
   }        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+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    /* proba elementaires */
 Total number of observations=%d <br>\n    for(i=1,jk=1; i <=nlstate; i++){
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      for(k=1; k <=(nlstate+ndeath); k++){
 <hr  size=\"2\" color=\"#EC5E5E\">        if (k != i) {
  <ul><li>Parameter files<br>\n          for(j=1; j <=ncovmodel; j++){
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);            jk++; 
   fclose(fichtm);            fprintf(ficgp,"\n");
           }
  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);  
       for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
  free_ivector(wav,1,imx);       for(jk=1; jk <=m; jk++) {
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);           if (ng==2)
  free_ivector(num,1,n);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
  free_vector(agedc,1,n);         else
  /*free_matrix(covar,1,NCOVMAX,1,n);*/           fprintf(ficgp,"\nset title \"Probability\"\n");
  fclose(ficparo);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
  fclose(ficres);         i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
   /*--------------- Prevalence limit --------------*/           for(k=1; k<=(nlstate+ndeath); k++) {
               if (k != k2){
   strcpy(filerespl,"pl");               if(ng==2)
   strcat(filerespl,fileres);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {               else
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
   }               ij=1;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);               for(j=3; j <=ncovmodel; j++) {
   fprintf(ficrespl,"#Prevalence limit\n");                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   fprintf(ficrespl,"#Age ");                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);                   ij++;
   fprintf(ficrespl,"\n");                 }
                   else
   prlim=matrix(1,nlstate,1,nlstate);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */               }
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */               fprintf(ficgp,")/(1");
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */               
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */               for(k1=1; k1 <=nlstate; k1++){   
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
   k=0;                 ij=1;
   agebase=ageminpar;                 for(j=3; j <=ncovmodel; j++){
   agelim=agemaxpar;                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   ftolpl=1.e-10;                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   i1=cptcoveff;                     ij++;
   if (cptcovn < 1){i1=1;}                   }
                    else
   for(cptcov=1;cptcov<=i1;cptcov++){                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                 }
         k=k+1;                 fprintf(ficgp,")");
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/               }
         fprintf(ficrespl,"\n#******");               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
         for(j=1;j<=cptcoveff;j++)               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);               i=i+ncovmodel;
         fprintf(ficrespl,"******\n");             }
                   } /* end k */
         for (age=agebase; age<=agelim; age++){         } /* end k2 */
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);       } /* end jk */
           fprintf(ficrespl,"%.0f",age );     } /* end ng */
           for(i=1; i<=nlstate;i++)     fflush(ficgp); 
           fprintf(ficrespl," %.5f", prlim[i][i]);  }  /* end gnuplot */
           fprintf(ficrespl,"\n");  
         }  
       }  /*************** Moving average **************/
     }  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   fclose(ficrespl);  
     int i, cpt, cptcod;
   /*------------- h Pij x at various ages ------------*/    int modcovmax =1;
      int mobilavrange, mob;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    double age;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
   }                             a covariate has 2 modalities */
   printf("Computing pij: result on file '%s' \n", filerespij);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
    
   stepsize=(int) (stepm+YEARM-1)/YEARM;    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
   /*if (stepm<=24) stepsize=2;*/      if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
   agelim=AGESUP;      for (age=bage; age<=fage; age++)
   hstepm=stepsize*YEARM; /* Every year of age */        for (i=1; i<=nlstate;i++)
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          for (cptcod=1;cptcod<=modcovmax;cptcod++)
              mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   k=0;      /* We keep the original values on the extreme ages bage, fage and for 
   for(cptcov=1;cptcov<=i1;cptcov++){         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         we use a 5 terms etc. until the borders are no more concerned. 
       k=k+1;      */ 
         fprintf(ficrespij,"\n#****** ");      for (mob=3;mob <=mobilavrange;mob=mob+2){
         for(j=1;j<=cptcoveff;j++)        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for (i=1; i<=nlstate;i++){
         fprintf(ficrespij,"******\n");            for (cptcod=1;cptcod<=modcovmax;cptcod++){
                      mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                for (cpt=1;cpt<=(mob-1)/2;cpt++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                }
           oldm=oldms;savm=savms;              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              }
           fprintf(ficrespij,"# Age");          }
           for(i=1; i<=nlstate;i++)        }/* end age */
             for(j=1; j<=nlstate+ndeath;j++)      }/* end mob */
               fprintf(ficrespij," %1d-%1d",i,j);    }else return -1;
           fprintf(ficrespij,"\n");    return 0;
            for (h=0; h<=nhstepm; h++){  }/* End movingaverage */
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)  
               for(j=1; j<=nlstate+ndeath;j++)  /************** Forecasting ******************/
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  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){
             fprintf(ficrespij,"\n");    /* proj1, year, month, day of starting projection 
              }       agemin, agemax range of age
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       dateprev1 dateprev2 range of dates during which prevalence is computed
           fprintf(ficrespij,"\n");       anproj2 year of en of projection (same day and month as proj1).
         }    */
     }    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
   }    int *popage;
     double agec; /* generic age */
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
   fclose(ficrespij);    double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   /*---------- Forecasting ------------------*/  
   if((stepm == 1) && (strcmp(model,".")==0)){    agelim=AGESUP;
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);   
   }    strcpy(fileresf,"f"); 
   else{    strcat(fileresf,fileres);
     erreur=108;    if((ficresf=fopen(fileresf,"w"))==NULL) {
     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);      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);
   /*---------- Health expectancies and variances ------------*/    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
   strcpy(filerest,"t");    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   strcat(filerest,fileres);  
   if((ficrest=fopen(filerest,"w"))==NULL) {    if (mobilav!=0) {
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   }      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   printf("Computing Total LEs with variances: file '%s' \n", filerest);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
   strcpy(filerese,"e");    }
   strcat(filerese,fileres);  
   if((ficreseij=fopen(filerese,"w"))==NULL) {    stepsize=(int) (stepm+YEARM-1)/YEARM;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    if (stepm<=12) stepsize=1;
   }    if(estepm < stepm){
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
  strcpy(fileresv,"v");    else  hstepm=estepm;   
   strcat(fileresv,fileres);  
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    hstepm=hstepm/stepm; 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
   }                                 fractional in yp1 */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    anprojmean=yp;
   calagedate=-1;    yp2=modf((yp1*12),&yp);
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
   k=0;    jprojmean=yp;
   for(cptcov=1;cptcov<=i1;cptcov++){    if(jprojmean==0) jprojmean=1;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    if(mprojmean==0) jprojmean=1;
       k=k+1;  
       fprintf(ficrest,"\n#****** ");    i1=cptcoveff;
       for(j=1;j<=cptcoveff;j++)    if (cptcovn < 1){i1=1;}
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
       fprintf(ficrest,"******\n");    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
       fprintf(ficreseij,"\n#****** ");    fprintf(ficresf,"#****** Routine prevforecast **\n");
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*            if (h==(int)(YEARM*yearp)){ */
       fprintf(ficreseij,"******\n");    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       fprintf(ficresvij,"\n#****** ");        k=k+1;
       for(j=1;j<=cptcoveff;j++)        fprintf(ficresf,"\n#******");
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(j=1;j<=cptcoveff;j++) {
       fprintf(ficresvij,"******\n");          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]]);
         }
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        fprintf(ficresf,"******\n");
       oldm=oldms;savm=savms;        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);          for(j=1; j<=nlstate+ndeath;j++){ 
            for(i=1; i<=nlstate;i++)              
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            fprintf(ficresf," p%d%d",i,j);
       oldm=oldms;savm=savms;          fprintf(ficresf," p.%d",j);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);        }
            for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
            fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          for (agec=fage; agec>=(ageminpar-1); agec--){ 
       fprintf(ficrest,"\n");            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
       epj=vector(1,nlstate+1);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(age=bage; age <=fage ;age++){            oldm=oldms;savm=savms;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
         if (popbased==1) {          
           for(i=1; i<=nlstate;i++)            for (h=0; h<=nhstepm; h++){
             prlim[i][i]=probs[(int)age][i][k];              if (h*hstepm/YEARM*stepm ==yearp) {
         }                fprintf(ficresf,"\n");
                        for(j=1;j<=cptcoveff;j++) 
         fprintf(ficrest," %4.0f",age);                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {              } 
             epj[j] += prlim[i][i]*eij[i][j][(int)age];              for(j=1; j<=nlstate+ndeath;j++) {
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/                ppij=0.;
           }                for(i=1; i<=nlstate;i++) {
           epj[nlstate+1] +=epj[j];                  if (mobilav==1) 
         }                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
         for(i=1, vepp=0.;i <=nlstate;i++)                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
           for(j=1;j <=nlstate;j++)                  }
             vepp += vareij[i][j][(int)age];                  if (h*hstepm/YEARM*stepm== yearp) {
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
         for(j=1;j <=nlstate;j++){                  }
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));                } /* end i */
         }                if (h*hstepm/YEARM*stepm==yearp) {
         fprintf(ficrest,"\n");                  fprintf(ficresf," %.3f", ppij);
       }                }
     }              }/* end j */
   }            } /* end h */
 free_matrix(mint,1,maxwav,1,n);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);          } /* end agec */
     free_vector(weight,1,n);        } /* end yearp */
   fclose(ficreseij);      } /* end cptcod */
   fclose(ficresvij);    } /* end  cptcov */
   fclose(ficrest);         
   fclose(ficpar);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_vector(epj,1,nlstate+1);  
      fclose(ficresf);
   /*------- Variance limit prevalence------*/    }
   
   strcpy(fileresvpl,"vpl");  /************** Forecasting *****not tested NB*************/
   strcat(fileresvpl,fileres);  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){
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     exit(0);    int *popage;
   }    double calagedatem, agelim, kk1, kk2;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
   k=0;    double ***mobaverage;
   for(cptcov=1;cptcov<=i1;cptcov++){    char filerespop[FILENAMELENGTH];
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fprintf(ficresvpl,"\n#****** ");    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(j=1;j<=cptcoveff;j++)    agelim=AGESUP;
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
       fprintf(ficresvpl,"******\n");    
          prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       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);    strcpy(filerespop,"pop"); 
     }    strcat(filerespop,fileres);
  }    if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
   fclose(ficresvpl);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
   /*---------- End : free ----------------*/    printf("Computing forecasting: result on file '%s' \n", filerespop);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
      if (mobilav!=0) {
        mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      }
      }
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);    stepsize=(int) (stepm+YEARM-1)/YEARM;
   free_matrix(agev,1,maxwav,1,imx);    if (stepm<=12) stepsize=1;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    
     agelim=AGESUP;
   fprintf(fichtm,"\n</body>");    
   fclose(fichtm);    hstepm=1;
   fclose(ficgp);    hstepm=hstepm/stepm; 
      
     if (popforecast==1) {
   if(erreur >0)      if((ficpop=fopen(popfile,"r"))==NULL) {
     printf("End of Imach with error or warning %d\n",erreur);        printf("Problem with population file : %s\n",popfile);exit(0);
   else   printf("End of Imach\n");        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      } 
        popage=ivector(0,AGESUP);
   /* 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);*/      popeffectif=vector(0,AGESUP);
   /*printf("Total time was %d uSec.\n", total_usecs);*/      popcount=vector(0,AGESUP);
   /*------ End -----------*/      
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
  end:     
 #ifdef windows      imx=i;
   /* chdir(pathcd);*/      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
 #endif    }
  /*system("wgnuplot graph.plt");*/  
  /*system("../gp37mgw/wgnuplot graph.plt");*/    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
  /*system("cd ../gp37mgw");*/     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        k=k+1;
  strcpy(plotcmd,GNUPLOTPROGRAM);        fprintf(ficrespop,"\n#******");
  strcat(plotcmd," ");        for(j=1;j<=cptcoveff;j++) {
  strcat(plotcmd,optionfilegnuplot);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
  system(plotcmd);        }
         fprintf(ficrespop,"******\n");
 #ifdef windows        fprintf(ficrespop,"# Age");
   while (z[0] != 'q') {        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
     /* chdir(path); */        if (popforecast==1)  fprintf(ficrespop," [Population]");
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");        
     scanf("%s",z);        for (cpt=0; cpt<=0;cpt++) { 
     if (z[0] == 'c') system("./imach");          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
     else if (z[0] == 'e') system(optionfilehtm);          
     else if (z[0] == 'g') system(plotcmd);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
     else if (z[0] == 'q') exit(0);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   }            nhstepm = nhstepm/hstepm; 
 #endif            
 }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i]==1 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i]==0 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         if (wav[i]>1 & agecens[i]>15) {
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov){
     int i;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
         for(j=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.1.47  
changed lines
  Added in v.1.104


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