Diff for /imach/src/imach.c between versions 1.31 and 1.102

version 1.31, 2002/03/10 13:43:02 version 1.102, 2004/09/15 17:31:30
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.102  2004/09/15 17:31:30  brouard
      Add the possibility to read data file including tab characters.
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.101  2004/09/15 10:38:38  brouard
   first survey ("cross") where individuals from different ages are    Fix on curr_time
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.100  2004/07/12 18:29:06  brouard
   second wave of interviews ("longitudinal") which measure each change    Add version for Mac OS X. Just define UNIX in Makefile
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.99  2004/06/05 08:57:40  brouard
   model. More health states you consider, more time is necessary to reach the    *** empty log message ***
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.98  2004/05/16 15:05:56  brouard
   probabibility to be observed in state j at the second wave    New version 0.97 . First attempt to estimate force of mortality
   conditional to be observed in state i at the first wave. Therefore    directly from the data i.e. without the need of knowing the health
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    state at each age, but using a Gompertz model: log u =a + b*age .
   'age' is age and 'sex' is a covariate. If you want to have a more    This is the basic analysis of mortality and should be done before any
   complex model than "constant and age", you should modify the program    other analysis, in order to test if the mortality estimated from the
   where the markup *Covariates have to be included here again* invites    cross-longitudinal survey is different from the mortality estimated
   you to do it.  More covariates you add, slower the    from other sources like vital statistic data.
   convergence.  
     The same imach parameter file can be used but the option for mle should be -3.
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Agnès, who wrote this part of the code, tried to keep most of the
   identical for each individual. Also, if a individual missed an    former routines in order to include the new code within the former code.
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      The output is very simple: only an estimate of the intercept and of
     the slope with 95% confident intervals.
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    Current limitations:
   split into an exact number (nh*stepm) of unobserved intermediate    A) Even if you enter covariates, i.e. with the
   states. This elementary transition (by month or quarter trimester,    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   semester or year) is model as a multinomial logistic.  The hPx    B) There is no computation of Life Expectancy nor Life Table.
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.97  2004/02/20 13:25:42  lievre
   hPijx.    Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.96  2003/07/15 15:38:55  brouard
      * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    rewritten within the same printf. Workaround: many printfs.
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.95  2003/07/08 07:54:34  brouard
   from the European Union.    * imach.c (Repository):
   It is copyrighted identically to a GNU software product, ie programme and    (Repository): Using imachwizard code to output a more meaningful covariance
   software can be distributed freely for non commercial use. Latest version    matrix (cov(a12,c31) instead of numbers.
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.94  2003/06/27 13:00:02  brouard
      Just cleaning
 #include <math.h>  
 #include <stdio.h>    Revision 1.93  2003/06/25 16:33:55  brouard
 #include <stdlib.h>    (Module): On windows (cygwin) function asctime_r doesn't
 #include <unistd.h>    exist so I changed back to asctime which exists.
     (Module): Version 0.96b
 #define MAXLINE 256  
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    Revision 1.92  2003/06/25 16:30:45  brouard
 #define FILENAMELENGTH 80    (Module): On windows (cygwin) function asctime_r doesn't
 /*#define DEBUG*/    exist so I changed back to asctime which exists.
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.91  2003/06/25 15:30:29  brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    helps to forecast when convergence will be reached. Elapsed time
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    is stamped in powell.  We created a new html file for the graphs
     concerning matrix of covariance. It has extension -cov.htm.
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.90  2003/06/24 12:34:15  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    (Module): Some bugs corrected for windows. Also, when
 #define NCOVMAX 8 /* Maximum number of covariates */    mle=-1 a template is output in file "or"mypar.txt with the design
 #define MAXN 20000    of the covariance matrix to be input.
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.89  2003/06/24 12:30:52  brouard
 #define AGEBASE 40    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
 int erreur; /* Error number */  
 int nvar;    Revision 1.88  2003/06/23 17:54:56  brouard
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    * 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 npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Revision 1.87  2003/06/18 12:26:01  brouard
 int ndeath=1; /* Number of dead states */    Version 0.96
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
 int *wav; /* Number of waves for this individuual 0 is possible */    routine fileappend.
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.85  2003/06/17 13:12:43  brouard
 int mle, weightopt;    * imach.c (Repository): Check when date of death was earlier that
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    current date of interview. It may happen when the death was just
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    prior to the death. In this case, dh was negative and likelihood
 double jmean; /* Mean space between 2 waves */    was wrong (infinity). We still send an "Error" but patch by
 double **oldm, **newm, **savm; /* Working pointers to matrices */    assuming that the date of death was just one stepm after the
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    interview.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    (Repository): Because some people have very long ID (first column)
 FILE *ficgp,*ficresprob,*ficpop;    we changed int to long in num[] and we added a new lvector for
 FILE *ficreseij;    memory allocation. But we also truncated to 8 characters (left
   char filerese[FILENAMELENGTH];    truncation)
  FILE  *ficresvij;    (Repository): No more line truncation errors.
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.84  2003/06/13 21:44:43  brouard
   char fileresvpl[FILENAMELENGTH];    * imach.c (Repository): Replace "freqsummary" at a correct
     place. It differs from routine "prevalence" which may be called
 #define NR_END 1    many times. Probs is memory consuming and must be used with
 #define FREE_ARG char*    parcimony.
 #define FTOL 1.0e-10    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 #define NRANSI    Revision 1.83  2003/06/10 13:39:11  lievre
 #define ITMAX 200    *** empty log message ***
   
 #define TOL 2.0e-4    Revision 1.82  2003/06/05 15:57:20  brouard
     Add log in  imach.c and  fullversion number is now printed.
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10  */
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  /*
      Interpolated Markov Chain
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Short summary of the programme:
 #define TINY 1.0e-20    
     This program computes Healthy Life Expectancies from
 static double maxarg1,maxarg2;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    first survey ("cross") where individuals from different ages are
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    interviewed on their health status or degree of disability (in the
      case of a health survey which is our main interest) -2- at least a
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    second wave of interviews ("longitudinal") which measure each change
 #define rint(a) floor(a+0.5)    (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
 static double sqrarg;    model. More health states you consider, more time is necessary to reach the
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Maximum Likelihood of the parameters involved in the model.  The
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
 int imx;    conditional to be observed in state i at the first wave. Therefore
 int stepm;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 /* Stepm, step in month: minimum step interpolation*/    'age' is age and 'sex' is a covariate. If you want to have a more
     complex model than "constant and age", you should modify the program
 int m,nb;    where the markup *Covariates have to be included here again* invites
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    you to do it.  More covariates you add, slower the
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    convergence.
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;    The advantage of this computer programme, compared to a simple
     multinomial logistic model, is clear when the delay between waves is not
 double *weight;    identical for each individual. Also, if a individual missed an
 int **s; /* Status */    intermediate interview, the information is lost, but taken into
 double *agedc, **covar, idx;    account using an interpolation or extrapolation.  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     hPijx is the probability to be observed in state i at age x+h
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    conditional to the observed state i at age x. The delay 'h' can be
 double ftolhess; /* Tolerance for computing hessian */    split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
 /**************** split *************************/    semester or year) is modelled as a multinomial logistic.  The hPx
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    matrix is simply the matrix product of nh*stepm elementary matrices
 {    and the contribution of each individual to the likelihood is simply
    char *s;                             /* pointer */    hPijx.
    int  l1, l2;                         /* length counters */  
     Also this programme outputs the covariance matrix of the parameters but also
    l1 = strlen( path );                 /* length of path */    of the life expectancies. It also computes the stable prevalence. 
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    
 #ifdef windows    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
    s = strrchr( path, '\\' );           /* find last / */             Institut national d'études démographiques, Paris.
 #else    This software have been partly granted by Euro-REVES, a concerted action
    s = strrchr( path, '/' );            /* find last / */    from the European Union.
 #endif    It is copyrighted identically to a GNU software product, ie programme and
    if ( s == NULL ) {                   /* no directory, so use current */    software can be distributed freely for non commercial use. Latest version
 #if     defined(__bsd__)                /* get current working directory */    can be accessed at http://euroreves.ined.fr/imach .
       extern char       *getwd( );  
     Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
       if ( getwd( dirc ) == NULL ) {    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #else    
       extern char       *getcwd( );    **********************************************************************/
   /*
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    main
 #endif    read parameterfile
          return( GLOCK_ERROR_GETCWD );    read datafile
       }    concatwav
       strcpy( name, path );             /* we've got it */    freqsummary
    } else {                             /* strip direcotry from path */    if (mle >= 1)
       s++;                              /* after this, the filename */      mlikeli
       l2 = strlen( s );                 /* length of filename */    print results files
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    if mle==1 
       strcpy( name, s );                /* save file name */       computes hessian
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    read end of parameter file: agemin, agemax, bage, fage, estepm
       dirc[l1-l2] = 0;                  /* add zero */        begin-prev-date,...
    }    open gnuplot file
    l1 = strlen( dirc );                 /* length of directory */    open html file
 #ifdef windows    stable prevalence
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }     for age prevalim()
 #else    h Pij x
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    variance of p varprob
 #endif    forecasting if prevfcast==1 prevforecast call prevalence()
    s = strrchr( name, '.' );            /* find last / */    health expectancies
    s++;    Variance-covariance of DFLE
    strcpy(ext,s);                       /* save extension */    prevalence()
    l1= strlen( name);     movingaverage()
    l2= strlen( s)+1;    varevsij() 
    strncpy( finame, name, l1-l2);    if popbased==1 varevsij(,popbased)
    finame[l1-l2]= 0;    total life expectancies
    return( 0 );                         /* we're done */    Variance of stable prevalence
 }   end
   */
   
 /******************************************/  
   
 void replace(char *s, char*t)   
 {  #include <math.h>
   int i;  #include <stdio.h>
   int lg=20;  #include <stdlib.h>
   i=0;  #include <unistd.h>
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {  /* #include <sys/time.h> */
     (s[i] = t[i]);  #include <time.h>
     if (t[i]== '\\') s[i]='/';  #include "timeval.h"
   }  
 }  /* #include <libintl.h> */
   /* #define _(String) gettext (String) */
 int nbocc(char *s, char occ)  
 {  #define MAXLINE 256
   int i,j=0;  #define GNUPLOTPROGRAM "gnuplot"
   int lg=20;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   i=0;  #define FILENAMELENGTH 132
   lg=strlen(s);  /*#define DEBUG*/
   for(i=0; i<= lg; i++) {  /*#define windows*/
   if  (s[i] == occ ) j++;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   }  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   return j;  
 }  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 void cutv(char *u,char *v, char*t, char occ)  
 {  #define NINTERVMAX 8
   int i,lg,j,p=0;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   i=0;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   for(j=0; j<=strlen(t)-1; j++) {  #define NCOVMAX 8 /* Maximum number of covariates */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  #define MAXN 20000
   }  #define YEARM 12. /* Number of months per year */
   #define AGESUP 130
   lg=strlen(t);  #define AGEBASE 40
   for(j=0; j<p; j++) {  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
     (u[j] = t[j]);  #ifdef UNIX
   }  #define DIRSEPARATOR '/'
      u[p]='\0';  #define ODIRSEPARATOR '\\'
   #else
    for(j=0; j<= lg; j++) {  #define DIRSEPARATOR '\\'
     if (j>=(p+1))(v[j-p-1] = t[j]);  #define ODIRSEPARATOR '/'
   }  #endif
 }  
   /* $Id$ */
 /********************** nrerror ********************/  /* $State$ */
   
 void nrerror(char error_text[])  char version[]="Imach version 0.97c, September 2004, INED-EUROREVES ";
 {  char fullversion[]="$Revision$ $Date$"; 
   fprintf(stderr,"ERREUR ...\n");  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   fprintf(stderr,"%s\n",error_text);  int nvar;
   exit(1);  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 }  int npar=NPARMAX;
 /*********************** vector *******************/  int nlstate=2; /* Number of live states */
 double *vector(int nl, int nh)  int ndeath=1; /* Number of dead states */
 {  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   double *v;  int popbased=0;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  int *wav; /* Number of waves for this individuual 0 is possible */
   return v-nl+NR_END;  int maxwav; /* Maxim number of waves */
 }  int jmin, jmax; /* min, max spacing between 2 waves */
   int gipmx, gsw; /* Global variables on the number of contributions 
 /************************ free vector ******************/                     to the likelihood and the sum of weights (done by funcone)*/
 void free_vector(double*v, int nl, int nh)  int mle, weightopt;
 {  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   free((FREE_ARG)(v+nl-NR_END));  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
              * wave mi and wave mi+1 is not an exact multiple of stepm. */
 /************************ivector *******************************/  double jmean; /* Mean space between 2 waves */
 int *ivector(long nl,long nh)  double **oldm, **newm, **savm; /* Working pointers to matrices */
 {  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   int *v;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  FILE *ficlog, *ficrespow;
   if (!v) nrerror("allocation failure in ivector");  int globpr; /* Global variable for printing or not */
   return v-nl+NR_END;  double fretone; /* Only one call to likelihood */
 }  long ipmx; /* Number of contributions */
   double sw; /* Sum of weights */
 /******************free ivector **************************/  char filerespow[FILENAMELENGTH];
 void free_ivector(int *v, long nl, long nh)  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 {  FILE *ficresilk;
   free((FREE_ARG)(v+nl-NR_END));  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 }  FILE *ficresprobmorprev;
   FILE *fichtm, *fichtmcov; /* Html File */
 /******************* imatrix *******************************/  FILE *ficreseij;
 int **imatrix(long nrl, long nrh, long ncl, long nch)  char filerese[FILENAMELENGTH];
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  FILE  *ficresvij;
 {  char fileresv[FILENAMELENGTH];
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  FILE  *ficresvpl;
   int **m;  char fileresvpl[FILENAMELENGTH];
    char title[MAXLINE];
   /* allocate pointers to rows */  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   if (!m) nrerror("allocation failure 1 in matrix()");  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   m += NR_END;  char command[FILENAMELENGTH];
   m -= nrl;  int  outcmd=0;
    
    char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  char filelog[FILENAMELENGTH]; /* Log file */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  char filerest[FILENAMELENGTH];
   m[nrl] += NR_END;  char fileregp[FILENAMELENGTH];
   m[nrl] -= ncl;  char popfile[FILENAMELENGTH];
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
    
   /* return pointer to array of pointers to rows */  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   return m;  struct timezone tzp;
 }  extern int gettimeofday();
   struct tm tmg, tm, tmf, *gmtime(), *localtime();
 /****************** free_imatrix *************************/  long time_value;
 void free_imatrix(m,nrl,nrh,ncl,nch)  extern long time();
       int **m;  char strcurr[80], strfor[80];
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */  #define NR_END 1
 {  #define FREE_ARG char*
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #define FTOL 1.0e-10
   free((FREE_ARG) (m+nrl-NR_END));  
 }  #define NRANSI 
   #define ITMAX 200 
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  #define TOL 2.0e-4 
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  #define CGOLD 0.3819660 
   double **m;  #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  #define GOLD 1.618034 
   m += NR_END;  #define GLIMIT 100.0 
   m -= nrl;  #define TINY 1.0e-20 
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  static double maxarg1,maxarg2;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   m[nrl] += NR_END;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   m[nrl] -= ncl;    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define rint(a) floor(a+0.5)
   return m;  
 }  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 /*************************free matrix ************************/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  int agegomp= AGEGOMP;
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int imx; 
   free((FREE_ARG)(m+nrl-NR_END));  int stepm=1;
 }  /* Stepm, step in month: minimum step interpolation*/
   
 /******************* ma3x *******************************/  int estepm;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  int m,nb;
   double ***m;  long *num;
   int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   if (!m) nrerror("allocation failure 1 in matrix()");  double **pmmij, ***probs;
   m += NR_END;  double *ageexmed,*agecens;
   m -= nrl;  double dateintmean=0;
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  double *weight;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int **s; /* Status */
   m[nrl] += NR_END;  double *agedc, **covar, idx;
   m[nrl] -= ncl;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   double ftolhess; /* Tolerance for computing hessian */
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  /**************** split *************************/
   m[nrl][ncl] += NR_END;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   m[nrl][ncl] -= nll;  {
   for (j=ncl+1; j<=nch; j++)    /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
     m[nrl][j]=m[nrl][j-1]+nlay;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
      */ 
   for (i=nrl+1; i<=nrh; i++) {    char  *ss;                            /* pointer */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    int   l1, l2;                         /* length counters */
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;    l1 = strlen(path );                   /* length of path */
   }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   return m;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 }    if ( ss == NULL ) {                   /* no directory, so use current */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 /*************************free ma3x ************************/        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)      /* get current working directory */
 {      /*    extern  char* getcwd ( char *buf , int len);*/
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   free((FREE_ARG)(m[nrl]+ncl-NR_END));        return( GLOCK_ERROR_GETCWD );
   free((FREE_ARG)(m+nrl-NR_END));      }
 }      strcpy( name, path );               /* we've got it */
     } else {                              /* strip direcotry from path */
 /***************** f1dim *************************/      ss++;                               /* after this, the filename */
 extern int ncom;      l2 = strlen( ss );                  /* length of filename */
 extern double *pcom,*xicom;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 extern double (*nrfunc)(double []);      strcpy( name, ss );         /* save file name */
        strncpy( dirc, path, l1 - l2 );     /* now the directory */
 double f1dim(double x)      dirc[l1-l2] = 0;                    /* add zero */
 {    }
   int j;    l1 = strlen( dirc );                  /* length of directory */
   double f;    /*#ifdef windows
   double *xt;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
    #else
   xt=vector(1,ncom);    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #endif
   f=(*nrfunc)(xt);    */
   free_vector(xt,1,ncom);    ss = strrchr( name, '.' );            /* find last / */
   return f;    if (ss >0){
 }      ss++;
       strcpy(ext,ss);                     /* save extension */
 /*****************brent *************************/      l1= strlen( name);
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)      l2= strlen(ss)+1;
 {      strncpy( finame, name, l1-l2);
   int iter;      finame[l1-l2]= 0;
   double a,b,d,etemp;    }
   double fu,fv,fw,fx;    return( 0 );                          /* we're done */
   double ftemp;  }
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  
    /******************************************/
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);  void replace_back_to_slash(char *s, char*t)
   x=w=v=bx;  {
   fw=fv=fx=(*f)(x);    int i;
   for (iter=1;iter<=ITMAX;iter++) {    int lg=0;
     xm=0.5*(a+b);    i=0;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    lg=strlen(t);
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    for(i=0; i<= lg; i++) {
     printf(".");fflush(stdout);      (s[i] = t[i]);
 #ifdef DEBUG      if (t[i]== '\\') s[i]='/';
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    }
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  }
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  int nbocc(char *s, char occ)
       *xmin=x;  {
       return fx;    int i,j=0;
     }    int lg=20;
     ftemp=fu;    i=0;
     if (fabs(e) > tol1) {    lg=strlen(s);
       r=(x-w)*(fx-fv);    for(i=0; i<= lg; i++) {
       q=(x-v)*(fx-fw);    if  (s[i] == occ ) j++;
       p=(x-v)*q-(x-w)*r;    }
       q=2.0*(q-r);    return j;
       if (q > 0.0) p = -p;  }
       q=fabs(q);  
       etemp=e;  void cutv(char *u,char *v, char*t, char occ)
       e=d;  {
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       else {       gives u="abcedf" and v="ghi2j" */
         d=p/q;    int i,lg,j,p=0;
         u=x+d;    i=0;
         if (u-a < tol2 || b-u < tol2)    for(j=0; j<=strlen(t)-1; j++) {
           d=SIGN(tol1,xm-x);      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
       }    }
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    lg=strlen(t);
     }    for(j=0; j<p; j++) {
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));      (u[j] = t[j]);
     fu=(*f)(u);    }
     if (fu <= fx) {       u[p]='\0';
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)     for(j=0; j<= lg; j++) {
         SHFT(fv,fw,fx,fu)      if (j>=(p+1))(v[j-p-1] = t[j]);
         } else {    }
           if (u < x) a=u; else b=u;  }
           if (fu <= fw || w == x) {  
             v=w;  /********************** nrerror ********************/
             w=u;  
             fv=fw;  void nrerror(char error_text[])
             fw=fu;  {
           } else if (fu <= fv || v == x || v == w) {    fprintf(stderr,"ERREUR ...\n");
             v=u;    fprintf(stderr,"%s\n",error_text);
             fv=fu;    exit(EXIT_FAILURE);
           }  }
         }  /*********************** vector *******************/
   }  double *vector(int nl, int nh)
   nrerror("Too many iterations in brent");  {
   *xmin=x;    double *v;
   return fx;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 }    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
 /****************** mnbrak ***********************/  }
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  /************************ free vector ******************/
             double (*func)(double))  void free_vector(double*v, int nl, int nh)
 {  {
   double ulim,u,r,q, dum;    free((FREE_ARG)(v+nl-NR_END));
   double fu;  }
    
   *fa=(*func)(*ax);  /************************ivector *******************************/
   *fb=(*func)(*bx);  int *ivector(long nl,long nh)
   if (*fb > *fa) {  {
     SHFT(dum,*ax,*bx,dum)    int *v;
       SHFT(dum,*fb,*fa,dum)    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       }    if (!v) nrerror("allocation failure in ivector");
   *cx=(*bx)+GOLD*(*bx-*ax);    return v-nl+NR_END;
   *fc=(*func)(*cx);  }
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  /******************free ivector **************************/
     q=(*bx-*cx)*(*fb-*fa);  void free_ivector(int *v, long nl, long nh)
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  {
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    free((FREE_ARG)(v+nl-NR_END));
     ulim=(*bx)+GLIMIT*(*cx-*bx);  }
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);  /************************lvector *******************************/
     } else if ((*cx-u)*(u-ulim) > 0.0) {  long *lvector(long nl,long nh)
       fu=(*func)(u);  {
       if (fu < *fc) {    long *v;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
           SHFT(*fb,*fc,fu,(*func)(u))    if (!v) nrerror("allocation failure in ivector");
           }    return v-nl+NR_END;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  }
       u=ulim;  
       fu=(*func)(u);  /******************free lvector **************************/
     } else {  void free_lvector(long *v, long nl, long nh)
       u=(*cx)+GOLD*(*cx-*bx);  {
       fu=(*func)(u);    free((FREE_ARG)(v+nl-NR_END));
     }  }
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)  /******************* imatrix *******************************/
       }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
 }       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   { 
 /*************** linmin ************************/    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     int **m; 
 int ncom;    
 double *pcom,*xicom;    /* allocate pointers to rows */ 
 double (*nrfunc)(double []);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
      if (!m) nrerror("allocation failure 1 in matrix()"); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    m += NR_END; 
 {    m -= nrl; 
   double brent(double ax, double bx, double cx,    
                double (*f)(double), double tol, double *xmin);    
   double f1dim(double x);    /* allocate rows and set pointers to them */ 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
               double *fc, double (*func)(double));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   int j;    m[nrl] += NR_END; 
   double xx,xmin,bx,ax;    m[nrl] -= ncl; 
   double fx,fb,fa;    
      for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   ncom=n;    
   pcom=vector(1,n);    /* return pointer to array of pointers to rows */ 
   xicom=vector(1,n);    return m; 
   nrfunc=func;  } 
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];  /****************** free_imatrix *************************/
     xicom[j]=xi[j];  void free_imatrix(m,nrl,nrh,ncl,nch)
   }        int **m;
   ax=0.0;        long nch,ncl,nrh,nrl; 
   xx=1.0;       /* free an int matrix allocated by imatrix() */ 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  { 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 #ifdef DEBUG    free((FREE_ARG) (m+nrl-NR_END)); 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  } 
 #endif  
   for (j=1;j<=n;j++) {  /******************* matrix *******************************/
     xi[j] *= xmin;  double **matrix(long nrl, long nrh, long ncl, long nch)
     p[j] += xi[j];  {
   }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   free_vector(xicom,1,n);    double **m;
   free_vector(pcom,1,n);  
 }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 /*************** powell ************************/    m += NR_END;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    m -= nrl;
             double (*func)(double []))  
 {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   void linmin(double p[], double xi[], int n, double *fret,    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
               double (*func)(double []));    m[nrl] += NR_END;
   int i,ibig,j;    m[nrl] -= ncl;
   double del,t,*pt,*ptt,*xit;  
   double fp,fptt;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double *xits;    return m;
   pt=vector(1,n);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   ptt=vector(1,n);     */
   xit=vector(1,n);  }
   xits=vector(1,n);  
   *fret=(*func)(p);  /*************************free matrix ************************/
   for (j=1;j<=n;j++) pt[j]=p[j];  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   for (*iter=1;;++(*iter)) {  {
     fp=(*fret);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     ibig=0;    free((FREE_ARG)(m+nrl-NR_END));
     del=0.0;  }
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     for (i=1;i<=n;i++)  /******************* ma3x *******************************/
       printf(" %d %.12f",i, p[i]);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     printf("\n");  {
     for (i=1;i<=n;i++) {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    double ***m;
       fptt=(*fret);  
 #ifdef DEBUG    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       printf("fret=%lf \n",*fret);    if (!m) nrerror("allocation failure 1 in matrix()");
 #endif    m += NR_END;
       printf("%d",i);fflush(stdout);    m -= nrl;
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         del=fabs(fptt-(*fret));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         ibig=i;    m[nrl] += NR_END;
       }    m[nrl] -= ncl;
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       for (j=1;j<=n;j++) {  
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         printf(" x(%d)=%.12e",j,xit[j]);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       }    m[nrl][ncl] += NR_END;
       for(j=1;j<=n;j++)    m[nrl][ncl] -= nll;
         printf(" p=%.12e",p[j]);    for (j=ncl+1; j<=nch; j++) 
       printf("\n");      m[nrl][j]=m[nrl][j-1]+nlay;
 #endif    
     }    for (i=nrl+1; i<=nrh; i++) {
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 #ifdef DEBUG      for (j=ncl+1; j<=nch; j++) 
       int k[2],l;        m[i][j]=m[i][j-1]+nlay;
       k[0]=1;    }
       k[1]=-1;    return m; 
       printf("Max: %.12e",(*func)(p));    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       for (j=1;j<=n;j++)             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
         printf(" %.12e",p[j]);    */
       printf("\n");  }
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {  /*************************free ma3x ************************/
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  {
         }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       }    free((FREE_ARG)(m+nrl-NR_END));
 #endif  }
   
   /*************** function subdirf ***********/
       free_vector(xit,1,n);  char *subdirf(char fileres[])
       free_vector(xits,1,n);  {
       free_vector(ptt,1,n);    /* Caution optionfilefiname is hidden */
       free_vector(pt,1,n);    strcpy(tmpout,optionfilefiname);
       return;    strcat(tmpout,"/"); /* Add to the right */
     }    strcat(tmpout,fileres);
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    return tmpout;
     for (j=1;j<=n;j++) {  }
       ptt[j]=2.0*p[j]-pt[j];  
       xit[j]=p[j]-pt[j];  /*************** function subdirf2 ***********/
       pt[j]=p[j];  char *subdirf2(char fileres[], char *preop)
     }  {
     fptt=(*func)(ptt);    
     if (fptt < fp) {    /* Caution optionfilefiname is hidden */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    strcpy(tmpout,optionfilefiname);
       if (t < 0.0) {    strcat(tmpout,"/");
         linmin(p,xit,n,fret,func);    strcat(tmpout,preop);
         for (j=1;j<=n;j++) {    strcat(tmpout,fileres);
           xi[j][ibig]=xi[j][n];    return tmpout;
           xi[j][n]=xit[j];  }
         }  
 #ifdef DEBUG  /*************** function subdirf3 ***********/
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  char *subdirf3(char fileres[], char *preop, char *preop2)
         for(j=1;j<=n;j++)  {
           printf(" %.12e",xit[j]);    
         printf("\n");    /* Caution optionfilefiname is hidden */
 #endif    strcpy(tmpout,optionfilefiname);
       }    strcat(tmpout,"/");
     }    strcat(tmpout,preop);
   }    strcat(tmpout,preop2);
 }    strcat(tmpout,fileres);
     return tmpout;
 /**** Prevalence limit ****************/  }
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  /***************** f1dim *************************/
 {  extern int ncom; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  extern double *pcom,*xicom;
      matrix by transitions matrix until convergence is reached */  extern double (*nrfunc)(double []); 
    
   int i, ii,j,k;  double f1dim(double x) 
   double min, max, maxmin, maxmax,sumnew=0.;  { 
   double **matprod2();    int j; 
   double **out, cov[NCOVMAX], **pmij();    double f;
   double **newm;    double *xt; 
   double agefin, delaymax=50 ; /* Max number of years to converge */   
     xt=vector(1,ncom); 
   for (ii=1;ii<=nlstate+ndeath;ii++)    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     for (j=1;j<=nlstate+ndeath;j++){    f=(*nrfunc)(xt); 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    free_vector(xt,1,ncom); 
     }    return f; 
   } 
    cov[1]=1.;  
    /*****************brent *************************/
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  { 
     newm=savm;    int iter; 
     /* Covariates have to be included here again */    double a,b,d,etemp;
      cov[2]=agefin;    double fu,fv,fw,fx;
      double ftemp;
       for (k=1; k<=cptcovn;k++) {    double p,q,r,tol1,tol2,u,v,w,x,xm; 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    double e=0.0; 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/   
       }    a=(ax < cx ? ax : cx); 
       for (k=1; k<=cptcovage;k++)    b=(ax > cx ? ax : cx); 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    x=w=v=bx; 
       for (k=1; k<=cptcovprod;k++)    fw=fv=fx=(*f)(x); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    for (iter=1;iter<=ITMAX;iter++) { 
       xm=0.5*(a+b); 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       printf(".");fflush(stdout);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      fprintf(ficlog,".");fflush(ficlog);
   #ifdef DEBUG
     savm=oldm;      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);
     oldm=newm;      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);
     maxmax=0.;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     for(j=1;j<=nlstate;j++){  #endif
       min=1.;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       max=0.;        *xmin=x; 
       for(i=1; i<=nlstate; i++) {        return fx; 
         sumnew=0;      } 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      ftemp=fu;
         prlim[i][j]= newm[i][j]/(1-sumnew);      if (fabs(e) > tol1) { 
         max=FMAX(max,prlim[i][j]);        r=(x-w)*(fx-fv); 
         min=FMIN(min,prlim[i][j]);        q=(x-v)*(fx-fw); 
       }        p=(x-v)*q-(x-w)*r; 
       maxmin=max-min;        q=2.0*(q-r); 
       maxmax=FMAX(maxmax,maxmin);        if (q > 0.0) p = -p; 
     }        q=fabs(q); 
     if(maxmax < ftolpl){        etemp=e; 
       return prlim;        e=d; 
     }        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)); 
 }        else { 
           d=p/q; 
 /*************** transition probabilities ***************/          u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )            d=SIGN(tol1,xm-x); 
 {        } 
   double s1, s2;      } else { 
   /*double t34;*/        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   int i,j,j1, nc, ii, jj;      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     for(i=1; i<= nlstate; i++){      fu=(*f)(u); 
     for(j=1; j<i;j++){      if (fu <= fx) { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        if (u >= x) a=x; else b=x; 
         /*s2 += param[i][j][nc]*cov[nc];*/        SHFT(v,w,x,u) 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          SHFT(fv,fw,fx,fu) 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/          } else { 
       }            if (u < x) a=u; else b=u; 
       ps[i][j]=s2;            if (fu <= fw || w == x) { 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/              v=w; 
     }              w=u; 
     for(j=i+1; j<=nlstate+ndeath;j++){              fv=fw; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){              fw=fu; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];            } else if (fu <= fv || v == x || v == w) { 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/              v=u; 
       }              fv=fu; 
       ps[i][j]=s2;            } 
     }          } 
   }    } 
     /*ps[3][2]=1;*/    nrerror("Too many iterations in brent"); 
     *xmin=x; 
   for(i=1; i<= nlstate; i++){    return fx; 
      s1=0;  } 
     for(j=1; j<i; j++)  
       s1+=exp(ps[i][j]);  /****************** mnbrak ***********************/
     for(j=i+1; j<=nlstate+ndeath; j++)  
       s1+=exp(ps[i][j]);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     ps[i][i]=1./(s1+1.);              double (*func)(double)) 
     for(j=1; j<i; j++)  { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    double ulim,u,r,q, dum;
     for(j=i+1; j<=nlstate+ndeath; j++)    double fu; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];   
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    *fa=(*func)(*ax); 
   } /* end i */    *fb=(*func)(*bx); 
     if (*fb > *fa) { 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      SHFT(dum,*ax,*bx,dum) 
     for(jj=1; jj<= nlstate+ndeath; jj++){        SHFT(dum,*fb,*fa,dum) 
       ps[ii][jj]=0;        } 
       ps[ii][ii]=1;    *cx=(*bx)+GOLD*(*bx-*ax); 
     }    *fc=(*func)(*cx); 
   }    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     for(jj=1; jj<= nlstate+ndeath; jj++){        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
      printf("%lf ",ps[ii][jj]);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
    }      if ((*bx-u)*(u-*cx) > 0.0) { 
     printf("\n ");        fu=(*func)(u); 
     }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     printf("\n ");printf("%lf ",cov[2]);*/        fu=(*func)(u); 
 /*        if (fu < *fc) { 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   goto end;*/            SHFT(*fb,*fc,fu,(*func)(u)) 
     return ps;            } 
 }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         u=ulim; 
 /**************** Product of 2 matrices ******************/        fu=(*func)(u); 
       } else { 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        u=(*cx)+GOLD*(*cx-*bx); 
 {        fu=(*func)(u); 
   /* 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(...) */      SHFT(*ax,*bx,*cx,u) 
   /* in, b, out are matrice of pointers which should have been initialized        SHFT(*fa,*fb,*fc,fu) 
      before: only the contents of out is modified. The function returns        } 
      a pointer to pointers identical to out */  } 
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)  /*************** linmin ************************/
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  int ncom; 
         out[i][k] +=in[i][j]*b[j][k];  double *pcom,*xicom;
   double (*nrfunc)(double []); 
   return out;   
 }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   { 
     double brent(double ax, double bx, double cx, 
 /************* Higher Matrix Product ***************/                 double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 {                double *fc, double (*func)(double)); 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    int j; 
      duration (i.e. until    double xx,xmin,bx,ax; 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    double fx,fb,fa;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step   
      (typically every 2 years instead of every month which is too big).    ncom=n; 
      Model is determined by parameters x and covariates have to be    pcom=vector(1,n); 
      included manually here.    xicom=vector(1,n); 
     nrfunc=func; 
      */    for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
   int i, j, d, h, k;      xicom[j]=xi[j]; 
   double **out, cov[NCOVMAX];    } 
   double **newm;    ax=0.0; 
     xx=1.0; 
   /* Hstepm could be zero and should return the unit matrix */    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   for (i=1;i<=nlstate+ndeath;i++)    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     for (j=1;j<=nlstate+ndeath;j++){  #ifdef DEBUG
       oldm[i][j]=(i==j ? 1.0 : 0.0);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       po[i][j][0]=(i==j ? 1.0 : 0.0);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     }  #endif
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    for (j=1;j<=n;j++) { 
   for(h=1; h <=nhstepm; h++){      xi[j] *= xmin; 
     for(d=1; d <=hstepm; d++){      p[j] += xi[j]; 
       newm=savm;    } 
       /* Covariates have to be included here again */    free_vector(xicom,1,n); 
       cov[1]=1.;    free_vector(pcom,1,n); 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  } 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
       for (k=1; k<=cptcovage;k++)  char *asc_diff_time(long time_sec, char ascdiff[])
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  {
       for (k=1; k<=cptcovprod;k++)    long sec_left, days, hours, minutes;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    sec_left = (sec_left) %(60*60);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    minutes = (sec_left) /60;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    sec_left = (sec_left) % (60);
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
       savm=oldm;    return ascdiff;
       oldm=newm;  }
     }  
     for(i=1; i<=nlstate+ndeath; i++)  /*************** powell ************************/
       for(j=1;j<=nlstate+ndeath;j++) {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         po[i][j][h]=newm[i][j];              double (*func)(double [])) 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  { 
          */    void linmin(double p[], double xi[], int n, double *fret, 
       }                double (*func)(double [])); 
   } /* end h */    int i,ibig,j; 
   return po;    double del,t,*pt,*ptt,*xit;
 }    double fp,fptt;
     double *xits;
     int niterf, itmp;
 /*************** log-likelihood *************/  
 double func( double *x)    pt=vector(1,n); 
 {    ptt=vector(1,n); 
   int i, ii, j, k, mi, d, kk;    xit=vector(1,n); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    xits=vector(1,n); 
   double **out;    *fret=(*func)(p); 
   double sw; /* Sum of weights */    for (j=1;j<=n;j++) pt[j]=p[j]; 
   double lli; /* Individual log likelihood */    for (*iter=1;;++(*iter)) { 
   long ipmx;      fp=(*fret); 
   /*extern weight */      ibig=0; 
   /* We are differentiating ll according to initial status */      del=0.0; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      last_time=curr_time;
   /*for(i=1;i<imx;i++)      (void) gettimeofday(&curr_time,&tzp);
     printf(" %d\n",s[4][i]);      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
   */      /*    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
   cov[1]=1.;      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       */
   for(k=1; k<=nlstate; k++) ll[k]=0.;     for (i=1;i<=n;i++) {
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        printf(" %d %.12f",i, p[i]);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        fprintf(ficlog," %d %.12lf",i, p[i]);
     for(mi=1; mi<= wav[i]-1; mi++){        fprintf(ficrespow," %.12lf", p[i]);
       for (ii=1;ii<=nlstate+ndeath;ii++)      }
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      printf("\n");
       for(d=0; d<dh[mi][i]; d++){      fprintf(ficlog,"\n");
         newm=savm;      fprintf(ficrespow,"\n");fflush(ficrespow);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      if(*iter <=3){
         for (kk=1; kk<=cptcovage;kk++) {        tm = *localtime(&curr_time.tv_sec);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        strcpy(strcurr,asctime(&tm));
         }  /*       asctime_r(&tm,strcurr); */
                forecast_time=curr_time; 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        itmp = strlen(strcurr);
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         savm=oldm;          strcurr[itmp-1]='\0';
         oldm=newm;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
                fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
                for(niterf=10;niterf<=30;niterf+=10){
       } /* end mult */          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
                tmf = *localtime(&forecast_time.tv_sec);
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  /*      asctime_r(&tmf,strfor); */
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/          strcpy(strfor,asctime(&tmf));
       ipmx +=1;          itmp = strlen(strfor);
       sw += weight[i];          if(strfor[itmp-1]=='\n')
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          strfor[itmp-1]='\0';
     } /* end of wave */          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);
   } /* end of individual */          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);
         }
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      }
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      for (i=1;i<=n;i++) { 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   return -l;        fptt=(*fret); 
 }  #ifdef DEBUG
         printf("fret=%lf \n",*fret);
         fprintf(ficlog,"fret=%lf \n",*fret);
 /*********** Maximum Likelihood Estimation ***************/  #endif
         printf("%d",i);fflush(stdout);
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        fprintf(ficlog,"%d",i);fflush(ficlog);
 {        linmin(p,xit,n,fret,func); 
   int i,j, iter;        if (fabs(fptt-(*fret)) > del) { 
   double **xi,*delti;          del=fabs(fptt-(*fret)); 
   double fret;          ibig=i; 
   xi=matrix(1,npar,1,npar);        } 
   for (i=1;i<=npar;i++)  #ifdef DEBUG
     for (j=1;j<=npar;j++)        printf("%d %.12e",i,(*fret));
       xi[i][j]=(i==j ? 1.0 : 0.0);        fprintf(ficlog,"%d %.12e",i,(*fret));
   printf("Powell\n");        for (j=1;j<=n;j++) {
   powell(p,xi,npar,ftol,&iter,&fret,func);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           printf(" x(%d)=%.12e",j,xit[j]);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        }
         for(j=1;j<=n;j++) {
 }          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
 /**** Computes Hessian and covariance matrix ***/        }
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        printf("\n");
 {        fprintf(ficlog,"\n");
   double  **a,**y,*x,pd;  #endif
   double **hess;      } 
   int i, j,jk;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   int *indx;  #ifdef DEBUG
         int k[2],l;
   double hessii(double p[], double delta, int theta, double delti[]);        k[0]=1;
   double hessij(double p[], double delti[], int i, int j);        k[1]=-1;
   void lubksb(double **a, int npar, int *indx, double b[]) ;        printf("Max: %.12e",(*func)(p));
   void ludcmp(double **a, int npar, int *indx, double *d) ;        fprintf(ficlog,"Max: %.12e",(*func)(p));
         for (j=1;j<=n;j++) {
   hess=matrix(1,npar,1,npar);          printf(" %.12e",p[j]);
           fprintf(ficlog," %.12e",p[j]);
   printf("\nCalculation of the hessian matrix. Wait...\n");        }
   for (i=1;i<=npar;i++){        printf("\n");
     printf("%d",i);fflush(stdout);        fprintf(ficlog,"\n");
     hess[i][i]=hessii(p,ftolhess,i,delti);        for(l=0;l<=1;l++) {
     /*printf(" %f ",p[i]);*/          for (j=1;j<=n;j++) {
     /*printf(" %lf ",hess[i][i]);*/            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   }            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
              fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   for (i=1;i<=npar;i++) {          }
     for (j=1;j<=npar;j++)  {          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       if (j>i) {          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         printf(".%d%d",i,j);fflush(stdout);        }
         hess[i][j]=hessij(p,delti,i,j);  #endif
         hess[j][i]=hess[i][j];      
         /*printf(" %lf ",hess[i][j]);*/  
       }        free_vector(xit,1,n); 
     }        free_vector(xits,1,n); 
   }        free_vector(ptt,1,n); 
   printf("\n");        free_vector(pt,1,n); 
         return; 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      } 
        if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   a=matrix(1,npar,1,npar);      for (j=1;j<=n;j++) { 
   y=matrix(1,npar,1,npar);        ptt[j]=2.0*p[j]-pt[j]; 
   x=vector(1,npar);        xit[j]=p[j]-pt[j]; 
   indx=ivector(1,npar);        pt[j]=p[j]; 
   for (i=1;i<=npar;i++)      } 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];      fptt=(*func)(ptt); 
   ludcmp(a,npar,indx,&pd);      if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   for (j=1;j<=npar;j++) {        if (t < 0.0) { 
     for (i=1;i<=npar;i++) x[i]=0;          linmin(p,xit,n,fret,func); 
     x[j]=1;          for (j=1;j<=n;j++) { 
     lubksb(a,npar,indx,x);            xi[j][ibig]=xi[j][n]; 
     for (i=1;i<=npar;i++){            xi[j][n]=xit[j]; 
       matcov[i][j]=x[i];          }
     }  #ifdef DEBUG
   }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   printf("\n#Hessian matrix#\n");          for(j=1;j<=n;j++){
   for (i=1;i<=npar;i++) {            printf(" %.12e",xit[j]);
     for (j=1;j<=npar;j++) {            fprintf(ficlog," %.12e",xit[j]);
       printf("%.3e ",hess[i][j]);          }
     }          printf("\n");
     printf("\n");          fprintf(ficlog,"\n");
   }  #endif
         }
   /* Recompute Inverse */      } 
   for (i=1;i<=npar;i++)    } 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  } 
   ludcmp(a,npar,indx,&pd);  
   /**** Prevalence limit (stable prevalence)  ****************/
   /*  printf("\n#Hessian matrix recomputed#\n");  
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   for (j=1;j<=npar;j++) {  {
     for (i=1;i<=npar;i++) x[i]=0;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     x[j]=1;       matrix by transitions matrix until convergence is reached */
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){    int i, ii,j,k;
       y[i][j]=x[i];    double min, max, maxmin, maxmax,sumnew=0.;
       printf("%.3e ",y[i][j]);    double **matprod2();
     }    double **out, cov[NCOVMAX], **pmij();
     printf("\n");    double **newm;
   }    double agefin, delaymax=50 ; /* Max number of years to converge */
   */  
     for (ii=1;ii<=nlstate+ndeath;ii++)
   free_matrix(a,1,npar,1,npar);      for (j=1;j<=nlstate+ndeath;j++){
   free_matrix(y,1,npar,1,npar);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(x,1,npar);      }
   free_ivector(indx,1,npar);  
   free_matrix(hess,1,npar,1,npar);     cov[1]=1.;
    
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 }    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       newm=savm;
 /*************** hessian matrix ****************/      /* Covariates have to be included here again */
 double hessii( double x[], double delta, int theta, double delti[])       cov[2]=agefin;
 {    
   int i;        for (k=1; k<=cptcovn;k++) {
   int l=1, lmax=20;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double k1,k2;          /*      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]]);*/
   double p2[NPARMAX+1];        }
   double res;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        for (k=1; k<=cptcovprod;k++)
   double fx;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   int k=0,kmax=10;  
   double l1;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   fx=func(x);        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   for (i=1;i<=npar;i++) p2[i]=x[i];      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   for(l=0 ; l <=lmax; l++){  
     l1=pow(10,l);      savm=oldm;
     delts=delt;      oldm=newm;
     for(k=1 ; k <kmax; k=k+1){      maxmax=0.;
       delt = delta*(l1*k);      for(j=1;j<=nlstate;j++){
       p2[theta]=x[theta] +delt;        min=1.;
       k1=func(p2)-fx;        max=0.;
       p2[theta]=x[theta]-delt;        for(i=1; i<=nlstate; i++) {
       k2=func(p2)-fx;          sumnew=0;
       /*res= (k1-2.0*fx+k2)/delt/delt; */          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          prlim[i][j]= newm[i][j]/(1-sumnew);
                max=FMAX(max,prlim[i][j]);
 #ifdef DEBUG          min=FMIN(min,prlim[i][j]);
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        }
 #endif        maxmin=max-min;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        maxmax=FMAX(maxmax,maxmin);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      }
         k=kmax;      if(maxmax < ftolpl){
       }        return prlim;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      }
         k=kmax; l=lmax*10.;    }
       }  }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  
         delts=delt;  /*************** transition probabilities ***************/ 
       }  
     }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   }  {
   delti[theta]=delts;    double s1, s2;
   return res;    /*double t34;*/
      int i,j,j1, nc, ii, jj;
 }  
       for(i=1; i<= nlstate; i++){
 double hessij( double x[], double delti[], int thetai,int thetaj)        for(j=1; j<i;j++){
 {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   int i;            /*s2 += param[i][j][nc]*cov[nc];*/
   int l=1, l1, lmax=20;            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   double k1,k2,k3,k4,res,fx;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
   double p2[NPARMAX+1];          }
   int k;          ps[i][j]=s2;
   /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
   fx=func(x);        }
   for (k=1; k<=2; k++) {        for(j=i+1; j<=nlstate+ndeath;j++){
     for (i=1;i<=npar;i++) p2[i]=x[i];          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     p2[thetai]=x[thetai]+delti[thetai]/k;            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     k1=func(p2)-fx;          }
            ps[i][j]=s2;
     p2[thetai]=x[thetai]+delti[thetai]/k;        }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      }
     k2=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;
     k3=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]);
     k4=func(p2)-fx;        ps[i][i]=1./(s1+1.);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        for(j=1; j<i; j++)
 #ifdef DEBUG          ps[i][j]= exp(ps[i][j])*ps[i][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);        for(j=i+1; j<=nlstate+ndeath; j++)
 #endif          ps[i][j]= exp(ps[i][j])*ps[i][i];
   }        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   return res;      } /* end i */
 }      
       for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
 /************** Inverse of matrix **************/        for(jj=1; jj<= nlstate+ndeath; jj++){
 void ludcmp(double **a, int n, int *indx, double *d)          ps[ii][jj]=0;
 {          ps[ii][ii]=1;
   int i,imax,j,k;        }
   double big,dum,sum,temp;      }
   double *vv;      
    
   vv=vector(1,n);  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   *d=1.0;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   for (i=1;i<=n;i++) {  /*         printf("ddd %lf ",ps[ii][jj]); */
     big=0.0;  /*       } */
     for (j=1;j<=n;j++)  /*       printf("\n "); */
       if ((temp=fabs(a[i][j])) > big) big=temp;  /*        } */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  /*        printf("\n ");printf("%lf ",cov[2]); */
     vv[i]=1.0/big;         /*
   }        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   for (j=1;j<=n;j++) {        goto end;*/
     for (i=1;i<j;i++) {      return ps;
       sum=a[i][j];  }
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;  /**************** Product of 2 matrices ******************/
     }  
     big=0.0;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     for (i=j;i<=n;i++) {  {
       sum=a[i][j];    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       for (k=1;k<j;k++)       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         sum -= a[i][k]*a[k][j];    /* in, b, out are matrice of pointers which should have been initialized 
       a[i][j]=sum;       before: only the contents of out is modified. The function returns
       if ( (dum=vv[i]*fabs(sum)) >= big) {       a pointer to pointers identical to out */
         big=dum;    long i, j, k;
         imax=i;    for(i=nrl; i<= nrh; i++)
       }      for(k=ncolol; k<=ncoloh; k++)
     }        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     if (j != imax) {          out[i][k] +=in[i][j]*b[j][k];
       for (k=1;k<=n;k++) {  
         dum=a[imax][k];    return out;
         a[imax][k]=a[j][k];  }
         a[j][k]=dum;  
       }  
       *d = -(*d);  /************* Higher Matrix Product ***************/
       vv[imax]=vv[j];  
     }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     indx[j]=imax;  {
     if (a[j][j] == 0.0) a[j][j]=TINY;    /* Computes the transition matrix starting at age 'age' over 
     if (j != n) {       'nhstepm*hstepm*stepm' months (i.e. until
       dum=1.0/(a[j][j]);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;       nhstepm*hstepm matrices. 
     }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   }       (typically every 2 years instead of every month which is too big 
   free_vector(vv,1,n);  /* Doesn't work */       for the memory).
 ;       Model is determined by parameters x and covariates have to be 
 }       included manually here. 
   
 void lubksb(double **a, int n, int *indx, double b[])       */
 {  
   int i,ii=0,ip,j;    int i, j, d, h, k;
   double sum;    double **out, cov[NCOVMAX];
      double **newm;
   for (i=1;i<=n;i++) {  
     ip=indx[i];    /* Hstepm could be zero and should return the unit matrix */
     sum=b[ip];    for (i=1;i<=nlstate+ndeath;i++)
     b[ip]=b[i];      for (j=1;j<=nlstate+ndeath;j++){
     if (ii)        oldm[i][j]=(i==j ? 1.0 : 0.0);
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        po[i][j][0]=(i==j ? 1.0 : 0.0);
     else if (sum) ii=i;      }
     b[i]=sum;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   }    for(h=1; h <=nhstepm; h++){
   for (i=n;i>=1;i--) {      for(d=1; d <=hstepm; d++){
     sum=b[i];        newm=savm;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        /* Covariates have to be included here again */
     b[i]=sum/a[i][i];        cov[1]=1.;
   }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
 }        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
 /************ Frequencies ********************/          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 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)        for (k=1; k<=cptcovprod;k++)
 {  /* Some frequencies */          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
    
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   double *pp;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   double pos, k2, dateintsum=0,k2cpt=0;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   FILE *ficresp;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   char fileresp[FILENAMELENGTH];        savm=oldm;
          oldm=newm;
   pp=vector(1,nlstate);      }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      for(i=1; i<=nlstate+ndeath; i++)
   strcpy(fileresp,"p");        for(j=1;j<=nlstate+ndeath;j++) {
   strcat(fileresp,fileres);          po[i][j][h]=newm[i][j];
   if((ficresp=fopen(fileresp,"w"))==NULL) {          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     printf("Problem with prevalence resultfile: %s\n", fileresp);           */
     exit(0);        }
   }    } /* end h */
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    return po;
   j1=0;  }
   
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  /*************** log-likelihood *************/
   double func( double *x)
   for(k1=1; k1<=j;k1++){  {
    for(i1=1; i1<=ncodemax[k1];i1++){    int i, ii, j, k, mi, d, kk;
        j1++;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    double **out;
          scanf("%d", i);*/    double sw; /* Sum of weights */
         for (i=-1; i<=nlstate+ndeath; i++)      double lli; /* Individual log likelihood */
          for (jk=-1; jk<=nlstate+ndeath; jk++)      int s1, s2;
            for(m=agemin; m <= agemax+3; m++)    double bbh, survp;
              freq[i][jk][m]=0;    long ipmx;
     /*extern weight */
         dateintsum=0;    /* We are differentiating ll according to initial status */
         k2cpt=0;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
        for (i=1; i<=imx; i++) {    /*for(i=1;i<imx;i++) 
          bool=1;      printf(" %d\n",s[4][i]);
          if  (cptcovn>0) {    */
            for (z1=1; z1<=cptcoveff; z1++)    cov[1]=1.;
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
                bool=0;    for(k=1; k<=nlstate; k++) ll[k]=0.;
          }  
          if (bool==1) {    if(mle==1){
            for(m=firstpass; m<=lastpass; m++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
              k2=anint[m][i]+(mint[m][i]/12.);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
              if ((k2>=dateprev1) && (k2<=dateprev2)) {        for(mi=1; mi<= wav[i]-1; mi++){
                if(agev[m][i]==0) agev[m][i]=agemax+1;          for (ii=1;ii<=nlstate+ndeath;ii++)
                if(agev[m][i]==1) agev[m][i]=agemax+2;            for (j=1;j<=nlstate+ndeath;j++){
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {            }
                  dateintsum=dateintsum+k2;          for(d=0; d<dh[mi][i]; d++){
                  k2cpt++;            newm=savm;
                }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
              }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
            }            }
          }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
        }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                    savm=oldm;
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            oldm=newm;
           } /* end mult */
         if  (cptcovn>0) {        
          fprintf(ficresp, "\n#********** Variable ");          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          /* But now since version 0.9 we anticipate for bias at large stepm.
        fprintf(ficresp, "**********\n#");           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         }           * (in months) between two waves is not a multiple of stepm, we rounded to 
        for(i=1; i<=nlstate;i++)           * the nearest (and in case of equal distance, to the lowest) interval but now
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
        fprintf(ficresp, "\n");           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
                   * probability in order to take into account the bias as a fraction of the way
   for(i=(int)agemin; i <= (int)agemax+3; i++){           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
     if(i==(int)agemax+3)           * -stepm/2 to stepm/2 .
       printf("Total");           * For stepm=1 the results are the same as for previous versions of Imach.
     else           * For stepm > 1 the results are less biased than in previous versions. 
       printf("Age %d", i);           */
     for(jk=1; jk <=nlstate ; jk++){          s1=s[mw[mi][i]][i];
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          s2=s[mw[mi+1][i]][i];
         pp[jk] += freq[jk][m][i];          bbh=(double)bh[mi][i]/(double)stepm; 
     }          /* bias bh is positive if real duration
     for(jk=1; jk <=nlstate ; jk++){           * is higher than the multiple of stepm and negative otherwise.
       for(m=-1, pos=0; m <=0 ; m++)           */
         pos += freq[jk][m][i];          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       if(pp[jk]>=1.e-10)          if( s2 > nlstate){ 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            /* i.e. if s2 is a death state and if the date of death is known then the contribution
       else               to the likelihood is the probability to die between last step unit time and current 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);               step unit time, which is also equal to probability to die before dh 
     }               minus probability to die before dh-stepm . 
                In version up to 0.92 likelihood was computed
      for(jk=1; jk <=nlstate ; jk++){          as if date of death was unknown. Death was treated as any other
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          health state: the date of the interview describes the actual state
         pp[jk] += freq[jk][m][i];          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,pos=0; jk <=nlstate ; jk++)          introduced the exact date of death then we should have modified
       pos += pp[jk];          the contribution of an exact death to the likelihood. This new
     for(jk=1; jk <=nlstate ; jk++){          contribution is smaller and very dependent of the step unit
       if(pos>=1.e-5)          stepm. It is no more the probability to die between last interview
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          and month of death but the probability to survive from last
       else          interview up to one month before death multiplied by the
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          probability to die within a month. Thanks to Chris
       if( i <= (int) agemax){          Jackson for correcting this bug.  Former versions increased
         if(pos>=1.e-5){          mortality artificially. The bad side is that we add another loop
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          which slows down the processing. The difference can be up to 10%
           probs[i][jk][j1]= pp[jk]/pos;          lower mortality.
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/            */
         }            lli=log(out[s1][s2] - savm[s1][s2]);
       else          }else{
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
     }          } 
     for(jk=-1; jk <=nlstate+ndeath; jk++)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       for(m=-1; m <=nlstate+ndeath; m++)          /*if(lli ==000.0)*/
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     if(i <= (int) agemax)          ipmx +=1;
       fprintf(ficresp,"\n");          sw += weight[i];
     printf("\n");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
     }      } /* end of individual */
  }    }  else if(mle==2){
   dateintmean=dateintsum/k2cpt;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   fclose(ficresp);        for(mi=1; mi<= wav[i]-1; mi++){
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          for (ii=1;ii<=nlstate+ndeath;ii++)
   free_vector(pp,1,nlstate);            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* End of Freq */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 }            }
           for(d=0; d<=dh[mi][i]; d++){
 /************ Prevalence ********************/            newm=savm;
 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)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 {  /* Some frequencies */            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;            }
   double ***freq; /* Frequencies */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double *pp;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double pos, k2;            savm=oldm;
             oldm=newm;
   pp=vector(1,nlstate);          } /* end mult */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        
            s1=s[mw[mi][i]][i];
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          s2=s[mw[mi+1][i]][i];
   j1=0;          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 */
   j=cptcoveff;          ipmx +=1;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
  for(k1=1; k1<=j;k1++){        } /* end of wave */
     for(i1=1; i1<=ncodemax[k1];i1++){      } /* end of individual */
       j1++;    }  else if(mle==3){  /* exponential inter-extrapolation */
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (i=-1; i<=nlstate+ndeath; i++)          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for (jk=-1; jk<=nlstate+ndeath; jk++)          for(mi=1; mi<= wav[i]-1; mi++){
           for(m=agemin; m <= agemax+3; m++)          for (ii=1;ii<=nlstate+ndeath;ii++)
             freq[i][jk][m]=0;            for (j=1;j<=nlstate+ndeath;j++){
                    oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (i=1; i<=imx; i++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         bool=1;            }
         if  (cptcovn>0) {          for(d=0; d<dh[mi][i]; d++){
           for (z1=1; z1<=cptcoveff; z1++)            newm=savm;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
               bool=0;            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         if (bool==1) {            }
           for(m=firstpass; m<=lastpass; m++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             k2=anint[m][i]+(mint[m][i]/12.);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            savm=oldm;
               if(agev[m][i]==0) agev[m][i]=agemax+1;            oldm=newm;
               if(agev[m][i]==1) agev[m][i]=agemax+2;          } /* end mult */
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */          s1=s[mw[mi][i]][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;
         for(i=(int)agemin; i <= (int)agemax+3; i++){          sw += weight[i];
           for(jk=1; jk <=nlstate ; jk++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        } /* end of wave */
               pp[jk] += freq[jk][m][i];      } /* end of individual */
           }    }else if (mle==4){  /* ml=4 no inter-extrapolation */
           for(jk=1; jk <=nlstate ; jk++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             for(m=-1, pos=0; m <=0 ; m++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             pos += freq[jk][m][i];        for(mi=1; mi<= wav[i]-1; mi++){
         }          for (ii=1;ii<=nlstate+ndeath;ii++)
                    for (j=1;j<=nlstate+ndeath;j++){
          for(jk=1; jk <=nlstate ; jk++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              pp[jk] += freq[jk][m][i];            }
          }          for(d=0; d<dh[mi][i]; d++){
                      newm=savm;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
          for(jk=1; jk <=nlstate ; jk++){                        cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
            if( i <= (int) agemax){            }
              if(pos>=1.e-5){          
                probs[i][jk][j1]= pp[jk]/pos;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
              }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
            }            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]);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          }else{
   free_vector(pp,1,nlstate);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
            }
 }  /* End of Freq */          ipmx +=1;
           sw += weight[i];
 /************* Waves Concatenation ***************/          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]); */
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        } /* end of wave */
 {      } /* end of individual */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
      Death is a valid wave (if date is known).      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        for(mi=1; mi<= wav[i]-1; mi++){
      and mw[mi+1][i]. dh depends on stepm.          for (ii=1;ii<=nlstate+ndeath;ii++)
      */            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, mi, m;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;            }
      double sum=0., jmean=0.;*/          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   int j, k=0,jk, ju, jl;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double sum=0.;            for (kk=1; kk<=cptcovage;kk++) {
   jmin=1e+5;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   jmax=-1;            }
   jmean=0.;          
   for(i=1; i<=imx; i++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     mi=0;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     m=firstpass;            savm=oldm;
     while(s[m][i] <= nlstate){            oldm=newm;
       if(s[m][i]>=1)          } /* end mult */
         mw[++mi][i]=m;        
       if(m >=lastpass)          s1=s[mw[mi][i]][i];
         break;          s2=s[mw[mi+1][i]][i];
       else          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         m++;          ipmx +=1;
     }/* end while */          sw += weight[i];
     if (s[m][i] > nlstate){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       mi++;     /* Death is another wave */          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
       /* if(mi==0)  never been interviewed correctly before death */        } /* end of wave */
          /* Only death is a correct wave */      } /* end of individual */
       mw[mi][i]=m;    } /* End of if */
     }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     wav[i]=mi;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if(mi==0)    return -l;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  }
   }  
   /*************** log-likelihood *************/
   for(i=1; i<=imx; i++){  double funcone( double *x)
     for(mi=1; mi<wav[i];mi++){  {
       if (stepm <=0)    /* Same as likeli but slower because of a lot of printf and if */
         dh[mi][i]=1;    int i, ii, j, k, mi, d, kk;
       else{    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         if (s[mw[mi+1][i]][i] > nlstate) {    double **out;
           if (agedc[i] < 2*AGESUP) {    double lli; /* Individual log likelihood */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    double llt;
           if(j==0) j=1;  /* Survives at least one month after exam */    int s1, s2;
           k=k+1;    double bbh, survp;
           if (j >= jmax) jmax=j;    /*extern weight */
           if (j <= jmin) jmin=j;    /* We are differentiating ll according to initial status */
           sum=sum+j;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    /*for(i=1;i<imx;i++) 
           }      printf(" %d\n",s[4][i]);
         }    */
         else{    cov[1]=1.;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  
           k=k+1;    for(k=1; k<=nlstate; k++) ll[k]=0.;
           if (j >= jmax) jmax=j;  
           else if (j <= jmin)jmin=j;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           sum=sum+j;      for(mi=1; mi<= wav[i]-1; mi++){
         }        for (ii=1;ii<=nlstate+ndeath;ii++)
         jk= j/stepm;          for (j=1;j<=nlstate+ndeath;j++){
         jl= j -jk*stepm;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         ju= j -(jk+1)*stepm;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
         if(jl <= -ju)          }
           dh[mi][i]=jk;        for(d=0; d<dh[mi][i]; d++){
         else          newm=savm;
           dh[mi][i]=jk+1;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         if(dh[mi][i]==0)          for (kk=1; kk<=cptcovage;kk++) {
           dh[mi][i]=1; /* At least one step */            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }          }
     }          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   jmean=sum/k;          savm=oldm;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          oldm=newm;
  }        } /* end mult */
 /*********** Tricode ****************************/        
 void tricode(int *Tvar, int **nbcode, int imx)        s1=s[mw[mi][i]][i];
 {        s2=s[mw[mi+1][i]][i];
   int Ndum[20],ij=1, k, j, i;        bbh=(double)bh[mi][i]/(double)stepm; 
   int cptcode=0;        /* bias is positive if real duration
   cptcoveff=0;         * is higher than the multiple of stepm and negative otherwise.
           */
   for (k=0; k<19; k++) Ndum[k]=0;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   for (k=1; k<=7; k++) ncodemax[k]=0;          lli=log(out[s1][s2] - savm[s1][s2]);
         } else if (mle==1){
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     for (i=1; i<=imx; i++) {        } else if(mle==2){
       ij=(int)(covar[Tvar[j]][i]);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       Ndum[ij]++;        } else if(mle==3){  /* exponential inter-extrapolation */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       if (ij > cptcode) cptcode=ij;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     }          lli=log(out[s1][s2]); /* Original formula */
         } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
     for (i=0; i<=cptcode; i++) {          lli=log(out[s1][s2]); /* Original formula */
       if(Ndum[i]!=0) ncodemax[j]++;        } /* End of if */
     }        ipmx +=1;
     ij=1;        sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     for (i=1; i<=ncodemax[j]; i++) {        if(globpr){
       for (k=0; k<=19; k++) {          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
         if (Ndum[k] != 0) {   %10.6f %10.6f %10.6f ", \
           nbcode[Tvar[j]][ij]=k;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
           ij++;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
         if (ij > ncodemax[j]) break;            llt +=ll[k]*gipmx/gsw;
       }              fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     }          }
   }            fprintf(ficresilk," %10.6f\n", -llt);
         }
  for (k=0; k<19; k++) Ndum[k]=0;      } /* end of wave */
     } /* end of individual */
  for (i=1; i<=ncovmodel-2; i++) {    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       ij=Tvar[i];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       Ndum[ij]++;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     }    if(globpr==0){ /* First time we count the contributions and weights */
       gipmx=ipmx;
  ij=1;      gsw=sw;
  for (i=1; i<=10; i++) {    }
    if((Ndum[i]!=0) && (i<=ncov)){    return -l;
      Tvaraff[ij]=i;  }
      ij++;  
    }  
  }  /*************** function likelione ***********/
    void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     cptcoveff=ij-1;  {
 }    /* This routine should help understanding what is done with 
        the selection of individuals/waves and
 /*********** Health Expectancies ****************/       to check the exact contribution to the likelihood.
        Plotting could be done.
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)     */
 {    int k;
   /* Health expectancies */  
   int i, j, nhstepm, hstepm, h, nstepm, k;    if(*globpri !=0){ /* Just counts and sums, no printings */
   double age, agelim,hf;      strcpy(fileresilk,"ilk"); 
   double ***p3mat;      strcat(fileresilk,fileres);
        if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   fprintf(ficreseij,"# Health expectancies\n");        printf("Problem with resultfile: %s\n", fileresilk);
   fprintf(ficreseij,"# Age");        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   for(i=1; i<=nlstate;i++)      }
     for(j=1; j<=nlstate;j++)      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
       fprintf(ficreseij," %1d-%1d",i,j);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   fprintf(ficreseij,"\n");      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(k=1; k<=nlstate; k++) 
   k=1;             /* For example stepm=6 months */        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   hstepm=1;   /* or (b) We decided to compute the life expectancy with the smallest unit */    }
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.  
      nhstepm is the number of hstepm from age to agelim    *fretone=(*funcone)(p);
      nstepm is the number of stepm from age to agelin.    if(*globpri !=0){
      Look at hpijx to understand the reason of that which relies in memory size      fclose(ficresilk);
      and note for a fixed period like k years */      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      fflush(fichtm); 
      survival function given par stepm (the optimization length). Unfortunately it    } 
      means that if the survival funtion is printed only each two years of age and if    return;
      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 k= 2 years, = 2/6 months = 4 */  /*********** Maximum Likelihood Estimation ***************/
   
   agelim=AGESUP;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  {
     /* nhstepm age range expressed in number of stepm */    int i,j, iter;
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    double **xi;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    double fret;
     if (stepm >= YEARM) hstepm=1;    double fretone; /* Only one call to likelihood */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    /*  char filerespow[FILENAMELENGTH];*/
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    xi=matrix(1,npar,1,npar);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    for (i=1;i<=npar;i++)
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      for (j=1;j<=npar;j++)
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          xi[i][j]=(i==j ? 1.0 : 0.0);
     hf=hstepm/YEARM;  /* Duration of hstepm expressed in year unit. */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     for(i=1; i<=nlstate;i++)    strcpy(filerespow,"pow"); 
       for(j=1; j<=nlstate;j++)    strcat(filerespow,fileres);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    if((ficrespow=fopen(filerespow,"w"))==NULL) {
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      printf("Problem with resultfile: %s\n", filerespow);
           /* 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(ficlog,"Problem with resultfile: %s\n", filerespow);
         }    }
     fprintf(ficreseij,"%3.0f",age );    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for(i=1; i<=nlstate;i++)    for (i=1;i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){      for(j=1;j<=nlstate+ndeath;j++)
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       }    fprintf(ficrespow,"\n");
     fprintf(ficreseij,"\n");  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    powell(p,xi,npar,ftol,&iter,&fret,func);
   }  
 }    fclose(ficrespow);
     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
 /************ Variance ******************/    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
 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)    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
 {  
   /* Variance of health expectancies */  }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;  /**** Computes Hessian and covariance matrix ***/
   double **dnewm,**doldm;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   int i, j, nhstepm, hstepm, h;  {
   int k, cptcode;    double  **a,**y,*x,pd;
   double *xp;    double **hess;
   double **gp, **gm;    int i, j,jk;
   double ***gradg, ***trgradg;    int *indx;
   double ***p3mat;  
   double age,agelim;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   int theta;    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[]) ;
    fprintf(ficresvij,"# Covariances of life expectancies\n");    void ludcmp(double **a, int npar, int *indx, double *d) ;
   fprintf(ficresvij,"# Age");    double gompertz(double p[]);
   for(i=1; i<=nlstate;i++)    hess=matrix(1,npar,1,npar);
     for(j=1; j<=nlstate;j++)  
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    printf("\nCalculation of the hessian matrix. Wait...\n");
   fprintf(ficresvij,"\n");    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
   xp=vector(1,npar);      printf("%d",i);fflush(stdout);
   dnewm=matrix(1,nlstate,1,npar);      fprintf(ficlog,"%d",i);fflush(ficlog);
   doldm=matrix(1,nlstate,1,nlstate);     
         hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   hstepm=1*YEARM; /* Every year of age */      
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      /*  printf(" %f ",p[i]);
   agelim = AGESUP;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    
     if (stepm >= YEARM) hstepm=1;    for (i=1;i<=npar;i++) {
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      for (j=1;j<=npar;j++)  {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if (j>i) { 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          printf(".%d%d",i,j);fflush(stdout);
     gp=matrix(0,nhstepm,1,nlstate);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     gm=matrix(0,nhstepm,1,nlstate);          hess[i][j]=hessij(p,delti,i,j,func,npar);
           
     for(theta=1; theta <=npar; theta++){          hess[j][i]=hess[i][j];    
       for(i=1; i<=npar; i++){ /* Computes gradient */          /*printf(" %lf ",hess[i][j]);*/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        }
       }      }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    printf("\n");
     fprintf(ficlog,"\n");
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
           prlim[i][i]=probs[(int)age][i][ij];    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       }    
      a=matrix(1,npar,1,npar);
       for(j=1; j<= nlstate; j++){    y=matrix(1,npar,1,npar);
         for(h=0; h<=nhstepm; h++){    x=vector(1,npar);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    indx=ivector(1,npar);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    for (i=1;i<=npar;i++)
         }      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       }    ludcmp(a,npar,indx,&pd);
      
       for(i=1; i<=npar; i++) /* Computes gradient */    for (j=1;j<=npar;j++) {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (i=1;i<=npar;i++) x[i]=0;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        x[j]=1;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      lubksb(a,npar,indx,x);
        for (i=1;i<=npar;i++){ 
       if (popbased==1) {        matcov[i][j]=x[i];
         for(i=1; i<=nlstate;i++)      }
           prlim[i][i]=probs[(int)age][i][ij];    }
       }  
     printf("\n#Hessian matrix#\n");
       for(j=1; j<= nlstate; j++){    fprintf(ficlog,"\n#Hessian matrix#\n");
         for(h=0; h<=nhstepm; h++){    for (i=1;i<=npar;i++) { 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      for (j=1;j<=npar;j++) { 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        printf("%.3e ",hess[i][j]);
         }        fprintf(ficlog,"%.3e ",hess[i][j]);
       }      }
       printf("\n");
       for(j=1; j<= nlstate; j++)      fprintf(ficlog,"\n");
         for(h=0; h<=nhstepm; h++){    }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  
         }    /* Recompute Inverse */
     } /* End theta */    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    ludcmp(a,npar,indx,&pd);
   
     for(h=0; h<=nhstepm; h++)    /*  printf("\n#Hessian matrix recomputed#\n");
       for(j=1; j<=nlstate;j++)  
         for(theta=1; theta <=npar; theta++)    for (j=1;j<=npar;j++) {
           trgradg[h][j][theta]=gradg[h][theta][j];      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
     for(i=1;i<=nlstate;i++)      lubksb(a,npar,indx,x);
       for(j=1;j<=nlstate;j++)      for (i=1;i<=npar;i++){ 
         vareij[i][j][(int)age] =0.;        y[i][j]=x[i];
     for(h=0;h<=nhstepm;h++){        printf("%.3e ",y[i][j]);
       for(k=0;k<=nhstepm;k++){        fprintf(ficlog,"%.3e ",y[i][j]);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      }
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      printf("\n");
         for(i=1;i<=nlstate;i++)      fprintf(ficlog,"\n");
           for(j=1;j<=nlstate;j++)    }
             vareij[i][j][(int)age] += doldm[i][j];    */
       }  
     }    free_matrix(a,1,npar,1,npar);
     h=1;    free_matrix(y,1,npar,1,npar);
     if (stepm >= YEARM) h=stepm/YEARM;    free_vector(x,1,npar);
     fprintf(ficresvij,"%.0f ",age );    free_ivector(indx,1,npar);
     for(i=1; i<=nlstate;i++)    free_matrix(hess,1,npar,1,npar);
       for(j=1; j<=nlstate;j++){  
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);  
       }  }
     fprintf(ficresvij,"\n");  
     free_matrix(gp,0,nhstepm,1,nlstate);  /*************** hessian matrix ****************/
     free_matrix(gm,0,nhstepm,1,nlstate);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  {
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    int i;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int l=1, lmax=20;
   } /* End age */    double k1,k2;
      double p2[NPARMAX+1];
   free_vector(xp,1,npar);    double res;
   free_matrix(doldm,1,nlstate,1,npar);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   free_matrix(dnewm,1,nlstate,1,nlstate);    double fx;
     int k=0,kmax=10;
 }    double l1;
   
 /************ Variance of prevlim ******************/    fx=func(x);
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    for (i=1;i<=npar;i++) p2[i]=x[i];
 {    for(l=0 ; l <=lmax; l++){
   /* Variance of prevalence limit */      l1=pow(10,l);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      delts=delt;
   double **newm;      for(k=1 ; k <kmax; k=k+1){
   double **dnewm,**doldm;        delt = delta*(l1*k);
   int i, j, nhstepm, hstepm;        p2[theta]=x[theta] +delt;
   int k, cptcode;        k1=func(p2)-fx;
   double *xp;        p2[theta]=x[theta]-delt;
   double *gp, *gm;        k2=func(p2)-fx;
   double **gradg, **trgradg;        /*res= (k1-2.0*fx+k2)/delt/delt; */
   double age,agelim;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   int theta;        
      #ifdef DEBUG
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   fprintf(ficresvpl,"# Age");        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);
   for(i=1; i<=nlstate;i++)  #endif
       fprintf(ficresvpl," %1d-%1d",i,i);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   fprintf(ficresvpl,"\n");        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k=kmax;
   xp=vector(1,npar);        }
   dnewm=matrix(1,nlstate,1,npar);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   doldm=matrix(1,nlstate,1,nlstate);          k=kmax; l=lmax*10.;
          }
   hstepm=1*YEARM; /* Every year of age */        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          delts=delt;
   agelim = AGESUP;        }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    }
     if (stepm >= YEARM) hstepm=1;    delti[theta]=delts;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    return res; 
     gradg=matrix(1,npar,1,nlstate);    
     gp=vector(1,nlstate);  }
     gm=vector(1,nlstate);  
   double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     for(theta=1; theta <=npar; theta++){  {
       for(i=1; i<=npar; i++){ /* Computes gradient */    int i;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    int l=1, l1, lmax=20;
       }    double k1,k2,k3,k4,res,fx;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double p2[NPARMAX+1];
       for(i=1;i<=nlstate;i++)    int k;
         gp[i] = prlim[i][i];  
        fx=func(x);
       for(i=1; i<=npar; i++) /* Computes gradient */    for (k=1; k<=2; k++) {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (i=1;i<=npar;i++) p2[i]=x[i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      p2[thetai]=x[thetai]+delti[thetai]/k;
       for(i=1;i<=nlstate;i++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         gm[i] = prlim[i][i];      k1=func(p2)-fx;
     
       for(i=1;i<=nlstate;i++)      p2[thetai]=x[thetai]+delti[thetai]/k;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     } /* End theta */      k2=func(p2)-fx;
     
     trgradg =matrix(1,nlstate,1,npar);      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     for(j=1; j<=nlstate;j++)      k3=func(p2)-fx;
       for(theta=1; theta <=npar; theta++)    
         trgradg[j][theta]=gradg[theta][j];      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     for(i=1;i<=nlstate;i++)      k4=func(p2)-fx;
       varpl[i][(int)age] =0.;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  #ifdef DEBUG
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      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<=nlstate;i++)      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);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  #endif
     }
     fprintf(ficresvpl,"%.0f ",age );    return res;
     for(i=1; i<=nlstate;i++)  }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  
     fprintf(ficresvpl,"\n");  /************** Inverse of matrix **************/
     free_vector(gp,1,nlstate);  void ludcmp(double **a, int n, int *indx, double *d) 
     free_vector(gm,1,nlstate);  { 
     free_matrix(gradg,1,npar,1,nlstate);    int i,imax,j,k; 
     free_matrix(trgradg,1,nlstate,1,npar);    double big,dum,sum,temp; 
   } /* End age */    double *vv; 
    
   free_vector(xp,1,npar);    vv=vector(1,n); 
   free_matrix(doldm,1,nlstate,1,npar);    *d=1.0; 
   free_matrix(dnewm,1,nlstate,1,nlstate);    for (i=1;i<=n;i++) { 
       big=0.0; 
 }      for (j=1;j<=n;j++) 
         if ((temp=fabs(a[i][j])) > big) big=temp; 
 /************ Variance of one-step probabilities  ******************/      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)      vv[i]=1.0/big; 
 {    } 
   int i, j;    for (j=1;j<=n;j++) { 
   int k=0, cptcode;      for (i=1;i<j;i++) { 
   double **dnewm,**doldm;        sum=a[i][j]; 
   double *xp;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   double *gp, *gm;        a[i][j]=sum; 
   double **gradg, **trgradg;      } 
   double age,agelim, cov[NCOVMAX];      big=0.0; 
   int theta;      for (i=j;i<=n;i++) { 
   char fileresprob[FILENAMELENGTH];        sum=a[i][j]; 
         for (k=1;k<j;k++) 
   strcpy(fileresprob,"prob");          sum -= a[i][k]*a[k][j]; 
   strcat(fileresprob,fileres);        a[i][j]=sum; 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     printf("Problem with resultfile: %s\n", fileresprob);          big=dum; 
   }          imax=i; 
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        } 
        } 
       if (j != imax) { 
   xp=vector(1,npar);        for (k=1;k<=n;k++) { 
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          dum=a[imax][k]; 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));          a[imax][k]=a[j][k]; 
            a[j][k]=dum; 
   cov[1]=1;        } 
   for (age=bage; age<=fage; age ++){        *d = -(*d); 
     cov[2]=age;        vv[imax]=vv[j]; 
     gradg=matrix(1,npar,1,9);      } 
     trgradg=matrix(1,9,1,npar);      indx[j]=imax; 
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      if (a[j][j] == 0.0) a[j][j]=TINY; 
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      if (j != n) { 
            dum=1.0/(a[j][j]); 
     for(theta=1; theta <=npar; theta++){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       for(i=1; i<=npar; i++)      } 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    } 
          free_vector(vv,1,n);  /* Doesn't work */
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  ;
      } 
       k=0;  
       for(i=1; i<= (nlstate+ndeath); i++){  void lubksb(double **a, int n, int *indx, double b[]) 
         for(j=1; j<=(nlstate+ndeath);j++){  { 
            k=k+1;    int i,ii=0,ip,j; 
           gp[k]=pmmij[i][j];    double sum; 
         }   
       }    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
       for(i=1; i<=npar; i++)      sum=b[ip]; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      b[ip]=b[i]; 
          if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      else if (sum) ii=i; 
       k=0;      b[i]=sum; 
       for(i=1; i<=(nlstate+ndeath); i++){    } 
         for(j=1; j<=(nlstate+ndeath);j++){    for (i=n;i>=1;i--) { 
           k=k+1;      sum=b[i]; 
           gm[k]=pmmij[i][j];      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         }      b[i]=sum/a[i][i]; 
       }    } 
        } 
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    /************ Frequencies ********************/
     }  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)
   {  /* Some frequencies */
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    
       for(theta=1; theta <=npar; theta++)    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       trgradg[j][theta]=gradg[theta][j];    int first;
      double ***freq; /* Frequencies */
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    double *pp, **prop;
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     FILE *ficresp;
      pmij(pmmij,cov,ncovmodel,x,nlstate);    char fileresp[FILENAMELENGTH];
     
      k=0;    pp=vector(1,nlstate);
      for(i=1; i<=(nlstate+ndeath); i++){    prop=matrix(1,nlstate,iagemin,iagemax+3);
        for(j=1; j<=(nlstate+ndeath);j++){    strcpy(fileresp,"p");
          k=k+1;    strcat(fileresp,fileres);
          gm[k]=pmmij[i][j];    if((ficresp=fopen(fileresp,"w"))==NULL) {
         }      printf("Problem with prevalence resultfile: %s\n", fileresp);
      }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
            exit(0);
      /*printf("\n%d ",(int)age);    }
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
            j1=0;
     
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    j=cptcoveff;
      }*/    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
   fprintf(ficresprob,"\n%d ",(int)age);    first=1;
   
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    for(k1=1; k1<=j;k1++){
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      for(i1=1; i1<=ncodemax[k1];i1++){
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        j1++;
   }        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           scanf("%d", i);*/
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        for (i=-1; i<=nlstate+ndeath; i++)  
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          for (jk=-1; jk<=nlstate+ndeath; jk++)  
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            for(m=iagemin; m <= iagemax+3; m++)
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              freq[i][jk][m]=0;
 }  
  free_vector(xp,1,npar);      for (i=1; i<=nlstate; i++)  
 fclose(ficresprob);        for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
 }        
         dateintsum=0;
 /******************* Printing html file ***********/        k2cpt=0;
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){        for (i=1; i<=imx; i++) {
   int jj1, k1, i1, cpt;          bool=1;
   FILE *fichtm;          if  (cptcovn>0) {
   /*char optionfilehtm[FILENAMELENGTH];*/            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   strcpy(optionfilehtm,optionfile);                bool=0;
   strcat(optionfilehtm,".htm");          }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          if (bool==1){
     printf("Problem with %s \n",optionfilehtm), exit(0);            for(m=firstpass; m<=lastpass; m++){
   }              k2=anint[m][i]+(mint[m][i]/12.);
               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71a </font> <hr size=\"2\" color=\"#EC5E5E\">                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
 Total number of observations=%d <br>                if (m<lastpass) {
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
 <hr  size=\"2\" color=\"#EC5E5E\">                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
 <li>Outputs files<br><br>\n                }
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n                
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>                  dateintsum=dateintsum+k2;
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>                  k2cpt++;
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>                }
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>                /*}*/
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>            }
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>          }
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>        }
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>         
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);  
          if  (cptcovn>0) {
 fprintf(fichtm," <li>Graphs</li><p>");          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  m=cptcoveff;          fprintf(ficresp, "**********\n#");
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        }
         for(i=1; i<=nlstate;i++) 
  jj1=0;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
  for(k1=1; k1<=m;k1++){        fprintf(ficresp, "\n");
    for(i1=1; i1<=ncodemax[k1];i1++){        
        jj1++;        for(i=iagemin; i <= iagemax+3; i++){
        if (cptcovn > 0) {          if(i==iagemax+3){
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");            fprintf(ficlog,"Total");
          for (cpt=1; cpt<=cptcoveff;cpt++)          }else{
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);            if(first==1){
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");              first=0;
        }              printf("See log file for details...\n");
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>            }
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                fprintf(ficlog,"Age %d", i);
        for(cpt=1; cpt<nlstate;cpt++){          }
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>          for(jk=1; jk <=nlstate ; jk++){
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
        }              pp[jk] += freq[jk][m][i]; 
     for(cpt=1; cpt<=nlstate;cpt++) {          }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          for(jk=1; jk <=nlstate ; jk++){
 interval) in state (%d): v%s%d%d.gif <br>            for(m=-1, pos=0; m <=0 ; m++)
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                pos += freq[jk][m][i];
      }            if(pp[jk]>=1.e-10){
      for(cpt=1; cpt<=nlstate;cpt++) {              if(first==1){
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              }
      }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            }else{
 health expectancies in states (1) and (2): e%s%d.gif<br>              if(first==1)
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 fprintf(fichtm,"\n</body>");              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
    }            }
    }          }
 fclose(fichtm);  
 }          for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 /******************* Gnuplot file **************/              pp[jk] += freq[jk][m][i];
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){          }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;            pos += pp[jk];
             posprop += prop[jk][i];
   strcpy(optionfilegnuplot,optionfilefiname);          }
   strcat(optionfilegnuplot,".plt");          for(jk=1; jk <=nlstate ; jk++){
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {            if(pos>=1.e-5){
     printf("Problem with file %s",optionfilegnuplot);              if(first==1)
   }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 #ifdef windows            }else{
     fprintf(ficgp,"cd \"%s\" \n",pathc);              if(first==1)
 #endif                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 m=pow(2,cptcoveff);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
              }
  /* 1eme*/            if( i <= iagemax){
   for (cpt=1; cpt<= nlstate ; cpt ++) {              if(pos>=1.e-5){
    for (k1=1; k1<= m ; k1 ++) {                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
 #ifdef windows                /*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,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);              }
 #endif              else
 #ifdef unix                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);            }
 #endif          }
           
 for (i=1; i<= nlstate ; i ++) {          for(jk=-1; jk <=nlstate+ndeath; jk++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            for(m=-1; m <=nlstate+ndeath; m++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");              if(freq[jk][m][i] !=0 ) {
 }              if(first==1)
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     for (i=1; i<= nlstate ; i ++) {                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              }
   else fprintf(ficgp," \%%*lf (\%%*lf)");          if(i <= iagemax)
 }            fprintf(ficresp,"\n");
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          if(first==1)
      for (i=1; i<= nlstate ; i ++) {            printf("Others in log...\n");
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(ficlog,"\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }        }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    }
 #ifdef unix    dateintmean=dateintsum/k2cpt; 
 fprintf(ficgp,"\nset ter gif small size 400,300");   
 #endif    fclose(ficresp);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
    }    free_vector(pp,1,nlstate);
   }    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   /*2 eme*/    /* End of Freq */
   }
   for (k1=1; k1<= m ; k1 ++) {  
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);  /************ Prevalence ********************/
      void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
     for (i=1; i<= nlstate+1 ; i ++) {  {  
       k=2*i;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);       in each health status at the date of interview (if between dateprev1 and dateprev2).
       for (j=1; j<= nlstate+1 ; j ++) {       We still use firstpass and lastpass as another selection.
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    */
   else fprintf(ficgp," \%%*lf (\%%*lf)");   
 }      int i, m, jk, k1, i1, j1, bool, z1,z2,j;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    double ***freq; /* Frequencies */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    double *pp, **prop;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    double pos,posprop; 
       for (j=1; j<= nlstate+1 ; j ++) {    double  y2; /* in fractional years */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    int iagemin, iagemax;
         else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      iagemin= (int) agemin;
       fprintf(ficgp,"\" t\"\" w l 0,");    iagemax= (int) agemax;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    /*pp=vector(1,nlstate);*/
       for (j=1; j<= nlstate+1 ; j ++) {    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");    j1=0;
 }      
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    j=cptcoveff;
       else fprintf(ficgp,"\" t\"\" w l 0,");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     }    
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    for(k1=1; k1<=j;k1++){
   }      for(i1=1; i1<=ncodemax[k1];i1++){
          j1++;
   /*3eme*/        
         for (i=1; i<=nlstate; i++)  
   for (k1=1; k1<= m ; k1 ++) {          for(m=iagemin; m <= iagemax+3; m++)
     for (cpt=1; cpt<= nlstate ; cpt ++) {            prop[i][m]=0.0;
       k=2+nlstate*(cpt-1);       
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);        for (i=1; i<=imx; i++) { /* Each individual */
       for (i=1; i< nlstate ; i ++) {          bool=1;
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);          if  (cptcovn>0) {
       }            for (z1=1; z1<=cptcoveff; z1++) 
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     }                bool=0;
     }          } 
            if (bool==1) { 
   /* CV preval stat */            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     for (k1=1; k1<= m ; k1 ++) {              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     for (cpt=1; cpt<nlstate ; cpt ++) {              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       k=3;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
       for (i=1; i< nlstate ; i ++)                if (s[m][i]>0 && s[m][i]<=nlstate) { 
         fprintf(ficgp,"+$%d",k+i+1);                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                        prop[s[m][i]][iagemax+3] += weight[i]; 
       l=3+(nlstate+ndeath)*cpt;                } 
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);              }
       for (i=1; i< nlstate ; i ++) {            } /* end selection of waves */
         l=3+(nlstate+ndeath)*cpt;          }
         fprintf(ficgp,"+$%d",l+i+1);        }
       }        for(i=iagemin; i <= iagemax+3; i++){  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     }            posprop += prop[jk][i]; 
   }            } 
    
   /* proba elementaires */          for(jk=1; jk <=nlstate ; jk++){     
    for(i=1,jk=1; i <=nlstate; i++){            if( i <=  iagemax){ 
     for(k=1; k <=(nlstate+ndeath); k++){              if(posprop>=1.e-5){ 
       if (k != i) {                probs[i][jk][j1]= prop[jk][i]/posprop;
         for(j=1; j <=ncovmodel; j++){              } 
                    } 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          }/* end jk */ 
           jk++;        }/* end i */ 
           fprintf(ficgp,"\n");      } /* end i1 */
         }    } /* end k1 */
       }    
     }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     }    /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     for(jk=1; jk <=m; jk++) {  }  /* End of prevalence */
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);  
    i=1;  /************* Waves Concatenation ***************/
    for(k2=1; k2<=nlstate; k2++) {  
      k3=i;  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(k=1; k<=(nlstate+ndeath); k++) {  {
        if (k != k2){    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);       Death is a valid wave (if date is known).
 ij=1;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         for(j=3; j <=ncovmodel; j++) {       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {       and mw[mi+1][i]. dh depends on stepm.
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);       */
             ij++;  
           }    int i, mi, m;
           else    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);       double sum=0., jmean=0.;*/
         }    int first;
           fprintf(ficgp,")/(1");    int j, k=0,jk, ju, jl;
            double sum=0.;
         for(k1=1; k1 <=nlstate; k1++){      first=0;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    jmin=1e+5;
 ij=1;    jmax=-1;
           for(j=3; j <=ncovmodel; j++){    jmean=0.;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    for(i=1; i<=imx; i++){
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      mi=0;
             ij++;      m=firstpass;
           }      while(s[m][i] <= nlstate){
           else        if(s[m][i]>=1)
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          mw[++mi][i]=m;
           }        if(m >=lastpass)
           fprintf(ficgp,")");          break;
         }        else
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);          m++;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      }/* end while */
         i=i+ncovmodel;      if (s[m][i] > nlstate){
        }        mi++;     /* Death is another wave */
      }        /* if(mi==0)  never been interviewed correctly before death */
    }           /* Only death is a correct wave */
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        mw[mi][i]=m;
    }      }
      
   fclose(ficgp);      wav[i]=mi;
 }  /* end gnuplot */      if(mi==0){
         nbwarn++;
         if(first==0){
 /*************** Moving average **************/          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){          first=1;
         }
   int i, cpt, cptcod;        if(first==1){
     for (agedeb=agemin; agedeb<=fage; agedeb++)          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
       for (i=1; i<=nlstate;i++)        }
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      } /* end mi==0 */
           mobaverage[(int)agedeb][i][cptcod]=0.;    } /* End individuals */
      
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){    for(i=1; i<=imx; i++){
       for (i=1; i<=nlstate;i++){      for(mi=1; mi<wav[i];mi++){
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        if (stepm <=0)
           for (cpt=0;cpt<=4;cpt++){          dh[mi][i]=1;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        else{
           }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;            if (agedc[i] < 2*AGESUP) {
         }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       }              if(j==0) j=1;  /* Survives at least one month after exam */
     }              else if(j<0){
                    nberr++;
 }                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 j=1; /* Temporary Dangerous patch */
                 printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
 /************** Forecasting ******************/                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]);
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){                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);
                }
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;              k=k+1;
   int *popage;              if (j >= jmax) jmax=j;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;              if (j <= jmin) jmin=j;
   double *popeffectif,*popcount;              sum=sum+j;
   double ***p3mat;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   char fileresf[FILENAMELENGTH];              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
  agelim=AGESUP;          }
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
              k=k+1;
              if (j >= jmax) jmax=j;
   strcpy(fileresf,"f");            else if (j <= jmin)jmin=j;
   strcat(fileresf,fileres);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   if((ficresf=fopen(fileresf,"w"))==NULL) {            /*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]);*/
     printf("Problem with forecast resultfile: %s\n", fileresf);            if(j<0){
   }              nberr++;
   printf("Computing forecasting: result on file '%s' \n", fileresf);              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            }
             sum=sum+j;
   if (mobilav==1) {          }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          jk= j/stepm;
     movingaverage(agedeb, fage, agemin, mobaverage);          jl= j -jk*stepm;
   }          ju= j -(jk+1)*stepm;
           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   stepsize=(int) (stepm+YEARM-1)/YEARM;            if(jl==0){
   if (stepm<=12) stepsize=1;              dh[mi][i]=jk;
                bh[mi][i]=0;
   agelim=AGESUP;            }else{ /* We want a negative bias in order to only have interpolation ie
                      * at the price of an extra matrix product in likelihood */
   hstepm=1;              dh[mi][i]=jk+1;
   hstepm=hstepm/stepm;              bh[mi][i]=ju;
   yp1=modf(dateintmean,&yp);            }
   anprojmean=yp;          }else{
   yp2=modf((yp1*12),&yp);            if(jl <= -ju){
   mprojmean=yp;              dh[mi][i]=jk;
   yp1=modf((yp2*30.5),&yp);              bh[mi][i]=jl;       /* bias is positive if real duration
   jprojmean=yp;                                   * is higher than the multiple of stepm and negative otherwise.
   if(jprojmean==0) jprojmean=1;                                   */
   if(mprojmean==0) jprojmean=1;            }
              else{
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);              dh[mi][i]=jk+1;
                bh[mi][i]=ju;
   for(cptcov=1;cptcov<=i2;cptcov++){            }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            if(dh[mi][i]==0){
       k=k+1;              dh[mi][i]=1; /* At least one step */
       fprintf(ficresf,"\n#******");              bh[mi][i]=ju; /* At least one step */
       for(j=1;j<=cptcoveff;j++) {              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            }
       }          } /* end if mle */
       fprintf(ficresf,"******\n");        }
       fprintf(ficresf,"# StartingAge FinalAge");      } /* end wave */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    }
          jmean=sum/k;
          printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
         fprintf(ficresf,"\n");   }
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    
   /*********** Tricode ****************************/
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){  void tricode(int *Tvar, int **nbcode, int imx)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  {
           nhstepm = nhstepm/hstepm;    
              int Ndum[20],ij=1, k, j, i, maxncov=19;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int cptcode=0;
           oldm=oldms;savm=savms;    cptcoveff=0; 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);     
            for (k=0; k<maxncov; k++) Ndum[k]=0;
           for (h=0; h<=nhstepm; h++){    for (k=1; k<=7; k++) ncodemax[k]=0;
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
             }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
             for(j=1; j<=nlstate+ndeath;j++) {                                 modality*/ 
               kk1=0.;kk2=0;        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
               for(i=1; i<=nlstate;i++) {                      Ndum[ij]++; /*store the modality */
                 if (mobilav==1)        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                 else {                                         Tvar[j]. If V=sex and male is 0 and 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                                         female is 1, then  cptcode=1.*/
                 }      }
                  
               }      for (i=0; i<=cptcode; i++) {
               if (h==(int)(calagedate+12*cpt)){        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 */
                 fprintf(ficresf," %.3f", kk1);      }
                          
               }      ij=1; 
             }      for (i=1; i<=ncodemax[j]; i++) {
           }        for (k=0; k<= maxncov; k++) {
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if (Ndum[k] != 0) {
         }            nbcode[Tvar[j]][ij]=k; 
       }            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
     }            
   }            ij++;
                  }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          if (ij > ncodemax[j]) break; 
         }  
   fclose(ficresf);      } 
 }    }  
 /************** Forecasting ******************/  
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){   for (k=0; k< maxncov; k++) Ndum[k]=0;
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;   for (i=1; i<=ncovmodel-2; i++) { 
   int *popage;     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;     ij=Tvar[i];
   double *popeffectif,*popcount;     Ndum[ij]++;
   double ***p3mat,***tabpop,***tabpopprev;   }
   char filerespop[FILENAMELENGTH];  
    ij=1;
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   for (i=1; i<= maxncov; i++) {
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     if((Ndum[i]!=0) && (i<=ncovcol)){
   agelim=AGESUP;       Tvaraff[ij]=i; /*For printing */
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;       ij++;
       }
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);   }
     
     cptcoveff=ij-1; /*Number of simple covariates*/
   strcpy(filerespop,"pop");  }
   strcat(filerespop,fileres);  
   if((ficrespop=fopen(filerespop,"w"))==NULL) {  /*********** Health Expectancies ****************/
     printf("Problem with forecast resultfile: %s\n", filerespop);  
   }  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 )
   printf("Computing forecasting: result on file '%s' \n", filerespop);  
   {
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    /* Health expectancies */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   if (mobilav==1) {    double age, agelim, hf;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double ***p3mat,***varhe;
     movingaverage(agedeb, fage, agemin, mobaverage);    double **dnewm,**doldm;
   }    double *xp;
     double **gp, **gm;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double ***gradg, ***trgradg;
   if (stepm<=12) stepsize=1;    int theta;
    
   agelim=AGESUP;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
      xp=vector(1,npar);
   hstepm=1;    dnewm=matrix(1,nlstate*nlstate,1,npar);
   hstepm=hstepm/stepm;    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
      
   if (popforecast==1) {    fprintf(ficreseij,"# Health expectancies\n");
     if((ficpop=fopen(popfile,"r"))==NULL) {    fprintf(ficreseij,"# Age");
       printf("Problem with population file : %s\n",popfile);exit(0);    for(i=1; i<=nlstate;i++)
     }      for(j=1; j<=nlstate;j++)
     popage=ivector(0,AGESUP);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     popeffectif=vector(0,AGESUP);    fprintf(ficreseij,"\n");
     popcount=vector(0,AGESUP);  
        if(estepm < stepm){
     i=1;        printf ("Problem %d lower than %d\n",estepm, stepm);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    }
        else  hstepm=estepm;   
     imx=i;    /* We compute the life expectancy from trapezoids spaced every estepm months
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];     * 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
      * we are calculating an estimate of the Life Expectancy assuming a linear 
   for(cptcov=1;cptcov<=i2;cptcov++){     * progression in between and thus overestimating or underestimating according
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){     * to the curvature of the survival function. If, for the same date, we 
       k=k+1;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       fprintf(ficrespop,"\n#******");     * to compare the new estimate of Life expectancy with the same linear 
       for(j=1;j<=cptcoveff;j++) {     * hypothesis. A more precise result, taking into account a more precise
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     * curvature will be obtained if estepm is as small as stepm. */
       }  
       fprintf(ficrespop,"******\n");    /* For example we decided to compute the life expectancy with the smallest unit */
       fprintf(ficrespop,"# Age");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);       nhstepm is the number of hstepm from age to agelim 
       if (popforecast==1)  fprintf(ficrespop," [Population]");       nstepm is the number of stepm from age to agelin. 
             Look at hpijx to understand the reason of that which relies in memory size
       for (cpt=0; cpt<=0;cpt++) {       and note for a fixed period like estepm months */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      /* 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 (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){       means that if the survival funtion is printed only each two years of age and if
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           nhstepm = nhstepm/hstepm;       results. So we changed our mind and took the option of the best precision.
              */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      agelim=AGESUP;
            for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           for (h=0; h<=nhstepm; h++){      /* nhstepm age range expressed in number of stepm */
             if (h==(int) (calagedate+YEARM*cpt)) {      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
             }      /* if (stepm >= YEARM) hstepm=1;*/
             for(j=1; j<=nlstate+ndeath;j++) {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
               kk1=0.;kk2=0;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               for(i=1; i<=nlstate;i++) {                    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
                 if (mobilav==1)      gp=matrix(0,nhstepm,1,nlstate*nlstate);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      gm=matrix(0,nhstepm,1,nlstate*nlstate);
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      /* Computed by stepm unit matrices, product of hstepm matrices, stored
                 }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
               }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
               if (h==(int)(calagedate+12*cpt)){   
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;  
                   /*fprintf(ficrespop," %.3f", kk1);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  
               }      /* Computing  Variances of health expectancies */
             }  
             for(i=1; i<=nlstate;i++){       for(theta=1; theta <=npar; theta++){
               kk1=0.;        for(i=1; i<=npar; i++){ 
                 for(j=1; j<=nlstate;j++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];        }
                 }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    
             }        cptj=0;
         for(j=1; j<= nlstate; j++){
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)          for(i=1; i<=nlstate; i++){
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);            cptj=cptj+1;
           }            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
         }            }
       }          }
          }
   /******/       
        
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {        for(i=1; i<=npar; i++) 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            xp[i] = x[i] - (i==theta ?delti[theta]:0);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        
           nhstepm = nhstepm/hstepm;        cptj=0;
                  for(j=1; j<= nlstate; j++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(i=1;i<=nlstate;i++){
           oldm=oldms;savm=savms;            cptj=cptj+1;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);            }
             }          }
             for(j=1; j<=nlstate+ndeath;j++) {        }
               kk1=0.;kk2=0;        for(j=1; j<= nlstate*nlstate; j++)
               for(i=1; i<=nlstate;i++) {                        for(h=0; h<=nhstepm-1; h++){
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
               }          }
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);       } 
             }     
           }  /* End theta */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }       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++)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            trgradg[h][j][theta]=gradg[h][theta][j];
        
   if (popforecast==1) {  
     free_ivector(popage,0,AGESUP);       for(i=1;i<=nlstate*nlstate;i++)
     free_vector(popeffectif,0,AGESUP);        for(j=1;j<=nlstate*nlstate;j++)
     free_vector(popcount,0,AGESUP);          varhe[i][j][(int)age] =0.;
   }  
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       printf("%d|",(int)age);fflush(stdout);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   fclose(ficrespop);       for(h=0;h<=nhstepm-1;h++){
 }        for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
 /***********************************************/          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
 /**************** Main Program *****************/          for(i=1;i<=nlstate*nlstate;i++)
 /***********************************************/            for(j=1;j<=nlstate*nlstate;j++)
               varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
 int main(int argc, char *argv[])        }
 {      }
       /* Computing expectancies */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      for(i=1; i<=nlstate;i++)
   double agedeb, agefin,hf;        for(j=1; j<=nlstate;j++)
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   double fret;            
   double **xi,tmp,delta;  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
   double dum; /* Dummy variable */          }
   double ***p3mat;  
   int *indx;      fprintf(ficreseij,"%3.0f",age );
   char line[MAXLINE], linepar[MAXLINE];      cptj=0;
   char title[MAXLINE];      for(i=1; i<=nlstate;i++)
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];        for(j=1; j<=nlstate;j++){
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];          cptj++;
            fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];        }
       fprintf(ficreseij,"\n");
   char filerest[FILENAMELENGTH];     
   char fileregp[FILENAMELENGTH];      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   char popfile[FILENAMELENGTH];      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   int firstobs=1, lastobs=10;      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   int sdeb, sfin; /* Status at beginning and end */      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   int c,  h , cpt,l;    }
   int ju,jl, mi;    printf("\n");
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    fprintf(ficlog,"\n");
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  
   int mobilav=0,popforecast=0;    free_vector(xp,1,npar);
   int hstepm, nhstepm;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   double bage, fage, age, agelim, agebase;  }
   double ftolpl=FTOL;  
   double **prlim;  /************ Variance ******************/
   double *severity;  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
   double ***param; /* Matrix of parameters */  {
   double  *p;    /* Variance of health expectancies */
   double **matcov; /* Matrix of covariance */    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   double ***delti3; /* Scale */    /* double **newm;*/
   double *delti; /* Scale */    double **dnewm,**doldm;
   double ***eij, ***vareij;    double **dnewmp,**doldmp;
   double **varpl; /* Variances of prevalence limits by age */    int i, j, nhstepm, hstepm, h, nstepm ;
   double *epj, vepp;    int k, cptcode;
   double kk1, kk2;    double *xp;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    double **gp, **gm;  /* for var eij */
      double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
   char version[80]="Imach version 0.71a, March 2002, INED-EUROREVES ";    double *gpp, *gmp; /* for var p point j */
   char *alph[]={"a","a","b","c","d","e"}, str[4];    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
   char z[1]="c", occ;    double ***mobaverage;
 #include <sys/time.h>    int theta;
 #include <time.h>    char digit[4];
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    char digitp[25];
    
   /* long total_usecs;    char fileresprobmorprev[FILENAMELENGTH];
   struct timeval start_time, end_time;  
      if(popbased==1){
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
   printf("\n%s",version);    }
   if(argc <=1){    else 
     printf("\nEnter the parameter file name: ");      strcpy(digitp,"-stablbased-");
     scanf("%s",pathtot);  
   }    if (mobilav!=0) {
   else{      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     strcpy(pathtot,argv[1]);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   /*cygwin_split_path(pathtot,path,optionfile);      }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    }
   /* cutv(path,optionfile,pathtot,'\\');*/  
     strcpy(fileresprobmorprev,"prmorprev"); 
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    sprintf(digit,"%-d",ij);
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   chdir(path);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   replace(pathc,path);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
 /*-------- arguments in the command line --------*/    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
   strcpy(fileres,"r");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   strcat(fileres, optionfilefiname);    }
   strcat(fileres,".txt");    /* Other files have txt extension */    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   /*---------arguments file --------*/    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);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     printf("Problem with optionfile %s\n",optionfile);      fprintf(ficresprobmorprev," p.%-d SE",j);
     goto end;      for(i=1; i<=nlstate;i++)
   }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
   strcpy(filereso,"o");    fprintf(ficresprobmorprev,"\n");
   strcat(filereso,fileres);    fprintf(ficgp,"\n# Routine varevsij");
   if((ficparo=fopen(filereso,"w"))==NULL) {    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");
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   }  /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    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");
     ungetc(c,ficpar);    fprintf(ficresvij,"# Age");
     fgets(line, MAXLINE, ficpar);    for(i=1; i<=nlstate;i++)
     puts(line);      for(j=1; j<=nlstate;j++)
     fputs(line,ficparo);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   }    fprintf(ficresvij,"\n");
   ungetc(c,ficpar);  
     xp=vector(1,npar);
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    dnewm=matrix(1,nlstate,1,npar);
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    doldm=matrix(1,nlstate,1,nlstate);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
 while((c=getc(ficpar))=='#' && c!= EOF){    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     puts(line);    gpp=vector(nlstate+1,nlstate+ndeath);
     fputs(line,ficparo);    gmp=vector(nlstate+1,nlstate+ndeath);
   }    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   ungetc(c,ficpar);    
      if(estepm < stepm){
          printf ("Problem %d lower than %d\n",estepm, stepm);
   covar=matrix(0,NCOVMAX,1,n);    }
   cptcovn=0;    else  hstepm=estepm;   
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   ncovmodel=2+cptcovn;       nhstepm is the number of hstepm from age to agelim 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */       nstepm is the number of stepm from age to agelin. 
         Look at hpijx to understand the reason of that which relies in memory size
   /* Read guess parameters */       and note for a fixed period like k years */
   /* Reads comments: lines beginning with '#' */    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   while((c=getc(ficpar))=='#' && c!= EOF){       survival function given by stepm (the optimization length). Unfortunately it
     ungetc(c,ficpar);       means that if the survival funtion is printed every two years of age and if
     fgets(line, MAXLINE, ficpar);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     puts(line);       results. So we changed our mind and took the option of the best precision.
     fputs(line,ficparo);    */
   }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   ungetc(c,ficpar);    agelim = AGESUP;
      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     for(i=1; i <=nlstate; i++)      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     for(j=1; j <=nlstate+ndeath-1; j++){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fscanf(ficpar,"%1d%1d",&i1,&j1);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       fprintf(ficparo,"%1d%1d",i1,j1);      gp=matrix(0,nhstepm,1,nlstate);
       printf("%1d%1d",i,j);      gm=matrix(0,nhstepm,1,nlstate);
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);  
         printf(" %lf",param[i][j][k]);      for(theta=1; theta <=npar; theta++){
         fprintf(ficparo," %lf",param[i][j][k]);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fscanf(ficpar,"\n");        }
       printf("\n");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       fprintf(ficparo,"\n");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     }  
          if (popbased==1) {
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
   p=param[1][1];              prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
   /* Reads comments: lines beginning with '#' */            for(i=1; i<=nlstate;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){              prlim[i][i]=mobaverage[(int)age][i][ij];
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);        }
     puts(line);    
     fputs(line,ficparo);        for(j=1; j<= nlstate; j++){
   }          for(h=0; h<=nhstepm; h++){
   ungetc(c,ficpar);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          }
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        }
   for(i=1; i <=nlstate; i++){        /* This for computing probability of death (h=1 means
     for(j=1; j <=nlstate+ndeath-1; j++){           computed over hstepm matrices product = hstepm*stepm months) 
       fscanf(ficpar,"%1d%1d",&i1,&j1);           as a weighted average of prlim.
       printf("%1d%1d",i,j);        */
       fprintf(ficparo,"%1d%1d",i1,j1);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       for(k=1; k<=ncovmodel;k++){          for(i=1,gpp[j]=0.; i<= nlstate; i++)
         fscanf(ficpar,"%le",&delti3[i][j][k]);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         printf(" %le",delti3[i][j][k]);        }    
         fprintf(ficparo," %le",delti3[i][j][k]);        /* end probability of death */
       }  
       fscanf(ficpar,"\n");        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
       printf("\n");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       fprintf(ficparo,"\n");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   }   
   delti=delti3[1][1];        if (popbased==1) {
            if(mobilav ==0){
   /* Reads comments: lines beginning with '#' */            for(i=1; i<=nlstate;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){              prlim[i][i]=probs[(int)age][i][ij];
     ungetc(c,ficpar);          }else{ /* mobilav */ 
     fgets(line, MAXLINE, ficpar);            for(i=1; i<=nlstate;i++)
     puts(line);              prlim[i][i]=mobaverage[(int)age][i][ij];
     fputs(line,ficparo);          }
   }        }
   ungetc(c,ficpar);  
          for(j=1; j<= nlstate; j++){
   matcov=matrix(1,npar,1,npar);          for(h=0; h<=nhstepm; h++){
   for(i=1; i <=npar; i++){            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     fscanf(ficpar,"%s",&str);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     printf("%s",str);          }
     fprintf(ficparo,"%s",str);        }
     for(j=1; j <=i; j++){        /* This for computing probability of death (h=1 means
       fscanf(ficpar," %le",&matcov[i][j]);           computed over hstepm matrices product = hstepm*stepm months) 
       printf(" %.5le",matcov[i][j]);           as a weighted average of prlim.
       fprintf(ficparo," %.5le",matcov[i][j]);        */
     }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     fscanf(ficpar,"\n");          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     printf("\n");           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     fprintf(ficparo,"\n");        }    
   }        /* end probability of death */
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)        for(j=1; j<= nlstate; j++) /* vareij */
       matcov[i][j]=matcov[j][i];          for(h=0; h<=nhstepm; h++){
                gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   printf("\n");          }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     /*-------- Rewriting paramater file ----------*/          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
      strcpy(rfileres,"r");    /* "Rparameterfile */        }
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/  
      strcat(rfileres,".");    /* */      } /* End theta */
      strcat(rfileres,optionfilext);    /* Other files have txt extension */  
     if((ficres =fopen(rfileres,"w"))==NULL) {      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       printf("Problem writing new parameter file: %s\n", fileres);goto end;  
     }      for(h=0; h<=nhstepm; h++) /* veij */
     fprintf(ficres,"#%s\n",version);        for(j=1; j<=nlstate;j++)
              for(theta=1; theta <=npar; theta++)
     /*-------- data file ----------*/            trgradg[h][j][theta]=gradg[h][theta][j];
     if((fic=fopen(datafile,"r"))==NULL)    {  
       printf("Problem with datafile: %s\n", datafile);goto end;      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     }        for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     n= lastobs;    
     severity = vector(1,maxwav);  
     outcome=imatrix(1,maxwav+1,1,n);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     num=ivector(1,n);      for(i=1;i<=nlstate;i++)
     moisnais=vector(1,n);        for(j=1;j<=nlstate;j++)
     annais=vector(1,n);          vareij[i][j][(int)age] =0.;
     moisdc=vector(1,n);  
     andc=vector(1,n);      for(h=0;h<=nhstepm;h++){
     agedc=vector(1,n);        for(k=0;k<=nhstepm;k++){
     cod=ivector(1,n);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     weight=vector(1,n);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          for(i=1;i<=nlstate;i++)
     mint=matrix(1,maxwav,1,n);            for(j=1;j<=nlstate;j++)
     anint=matrix(1,maxwav,1,n);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     s=imatrix(1,maxwav+1,1,n);        }
     adl=imatrix(1,maxwav+1,1,n);          }
     tab=ivector(1,NCOVMAX);    
     ncodemax=ivector(1,8);      /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
     i=1;      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
     while (fgets(line, MAXLINE, fic) != NULL)    {      for(j=nlstate+1;j<=nlstate+ndeath;j++)
       if ((i >= firstobs) && (i <=lastobs)) {        for(i=nlstate+1;i<=nlstate+ndeath;i++)
                  varppt[j][i]=doldmp[j][i];
         for (j=maxwav;j>=1;j--){      /* end ppptj */
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      /*  x centered again */
           strcpy(line,stra);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);   
         }      if (popbased==1) {
                if(mobilav ==0){
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);          for(i=1; i<=nlstate;i++)
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);            prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          for(i=1; i<=nlstate;i++)
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);            prlim[i][i]=mobaverage[(int)age][i][ij];
         }
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      }
         for (j=ncov;j>=1;j--){               
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      /* This for computing probability of death (h=1 means
         }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         num[i]=atol(stra);         as a weighted average of prlim.
              */
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){      for(j=nlstate+1;j<=nlstate+ndeath;j++){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
         i=i+1;      }    
       }      /* end probability of death */
     }  
     /* printf("ii=%d", ij);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
        scanf("%d",i);*/      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   imx=i-1; /* Number of individuals */        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
   /* for (i=1; i<=imx; i++){          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     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;      fprintf(ficresprobmorprev,"\n");
     }  
       fprintf(ficresvij,"%.0f ",age );
     for (i=1; i<=imx; i++)      for(i=1; i<=nlstate;i++)
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/        for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   /* Calculation of the number of parameter from char model*/        }
   Tvar=ivector(1,15);      fprintf(ficresvij,"\n");
   Tprod=ivector(1,15);      free_matrix(gp,0,nhstepm,1,nlstate);
   Tvaraff=ivector(1,15);      free_matrix(gm,0,nhstepm,1,nlstate);
   Tvard=imatrix(1,15,1,2);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   Tage=ivector(1,15);            free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if (strlen(model) >1){    } /* End age */
     j=0, j1=0, k1=1, k2=1;    free_vector(gpp,nlstate+1,nlstate+ndeath);
     j=nbocc(model,'+');    free_vector(gmp,nlstate+1,nlstate+ndeath);
     j1=nbocc(model,'*');    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     cptcovn=j+1;    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     cptcovprod=j1;    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
        /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
        fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     strcpy(modelsav,model);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
       printf("Error. Non available option model=%s ",model);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
       goto end;    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
        fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     for(i=(j+1); i>=1;i--){    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
       cutv(stra,strb,modelsav,'+');    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);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  */
       /*scanf("%d",i);*/  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
       if (strchr(strb,'*')) {    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {    free_vector(xp,1,npar);
           cptcovprod--;    free_matrix(doldm,1,nlstate,1,nlstate);
           cutv(strb,stre,strd,'V');    free_matrix(dnewm,1,nlstate,1,npar);
           Tvar[i]=atoi(stre);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           cptcovage++;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
             Tage[cptcovage]=i;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             /*printf("stre=%s ", stre);*/    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         }    fclose(ficresprobmorprev);
         else if (strcmp(strd,"age")==0) {    fflush(ficgp);
           cptcovprod--;    fflush(fichtm); 
           cutv(strb,stre,strc,'V');  }  /* end varevsij */
           Tvar[i]=atoi(stre);  
           cptcovage++;  /************ Variance of prevlim ******************/
           Tage[cptcovage]=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)
         }  {
         else {    /* Variance of prevalence limit */
           cutv(strb,stre,strc,'V');    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
           Tvar[i]=ncov+k1;    double **newm;
           cutv(strb,strc,strd,'V');    double **dnewm,**doldm;
           Tprod[k1]=i;    int i, j, nhstepm, hstepm;
           Tvard[k1][1]=atoi(strc);    int k, cptcode;
           Tvard[k1][2]=atoi(stre);    double *xp;
           Tvar[cptcovn+k2]=Tvard[k1][1];    double *gp, *gm;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    double **gradg, **trgradg;
           for (k=1; k<=lastobs;k++)    double age,agelim;
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    int theta;
           k1++;     
           k2=k2+2;    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
         }    fprintf(ficresvpl,"# Age");
       }    for(i=1; i<=nlstate;i++)
       else {        fprintf(ficresvpl," %1d-%1d",i,i);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    fprintf(ficresvpl,"\n");
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');    xp=vector(1,npar);
       Tvar[i]=atoi(strc);    dnewm=matrix(1,nlstate,1,npar);
       }    doldm=matrix(1,nlstate,1,nlstate);
       strcpy(modelsav,stra);      
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    hstepm=1*YEARM; /* Every year of age */
         scanf("%d",i);*/    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     }    agelim = AGESUP;
 }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      if (stepm >= YEARM) hstepm=1;
   printf("cptcovprod=%d ", cptcovprod);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   scanf("%d ",i);*/      gradg=matrix(1,npar,1,nlstate);
     fclose(fic);      gp=vector(1,nlstate);
       gm=vector(1,nlstate);
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/      for(theta=1; theta <=npar; theta++){
       for(i=1;i<=n;i++) weight[i]=1.0;        for(i=1; i<=npar; i++){ /* Computes gradient */
     }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     /*-calculation of age at interview from date of interview and age at death -*/        }
     agev=matrix(1,maxwav,1,imx);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
    for (i=1; i<=imx; i++)          gp[i] = prlim[i][i];
      for(m=2; (m<= maxwav); m++)      
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){        for(i=1; i<=npar; i++) /* Computes gradient */
          anint[m][i]=9999;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          s[m][i]=-1;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        }        for(i=1;i<=nlstate;i++)
              gm[i] = prlim[i][i];
     for (i=1; i<=imx; i++)  {  
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        for(i=1;i<=nlstate;i++)
       for(m=1; (m<= maxwav); m++){          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         if(s[m][i] >0){      } /* End theta */
           if (s[m][i] == nlstate+1) {  
             if(agedc[i]>0)      trgradg =matrix(1,nlstate,1,npar);
               if(moisdc[i]!=99 && andc[i]!=9999)  
               agev[m][i]=agedc[i];      for(j=1; j<=nlstate;j++)
             else {        for(theta=1; theta <=npar; theta++)
               if (andc[i]!=9999){          trgradg[j][theta]=gradg[theta][j];
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;      for(i=1;i<=nlstate;i++)
               }        varpl[i][(int)age] =0.;
             }      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
           }      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
           else if(s[m][i] !=9){ /* Should no more exist */      for(i=1;i<=nlstate;i++)
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
             if(mint[m][i]==99 || anint[m][i]==9999)  
               agev[m][i]=1;      fprintf(ficresvpl,"%.0f ",age );
             else if(agev[m][i] <agemin){      for(i=1; i<=nlstate;i++)
               agemin=agev[m][i];        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      fprintf(ficresvpl,"\n");
             }      free_vector(gp,1,nlstate);
             else if(agev[m][i] >agemax){      free_vector(gm,1,nlstate);
               agemax=agev[m][i];      free_matrix(gradg,1,npar,1,nlstate);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      free_matrix(trgradg,1,nlstate,1,npar);
             }    } /* End age */
             /*agev[m][i]=anint[m][i]-annais[i];*/  
             /*   agev[m][i] = age[i]+2*m;*/    free_vector(xp,1,npar);
           }    free_matrix(doldm,1,nlstate,1,npar);
           else { /* =9 */    free_matrix(dnewm,1,nlstate,1,nlstate);
             agev[m][i]=1;  
             s[m][i]=-1;  }
           }  
         }  /************ Variance of one-step probabilities  ******************/
         else /*= 0 Unknown */  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
           agev[m][i]=1;  {
       }    int i, j=0,  i1, k1, l1, t, tj;
        int k2, l2, j1,  z1;
     }    int k=0,l, cptcode;
     for (i=1; i<=imx; i++)  {    int first=1, first1;
       for(m=1; (m<= maxwav); m++){    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
         if (s[m][i] > (nlstate+ndeath)) {    double **dnewm,**doldm;
           printf("Error: Wrong value in nlstate or ndeath\n");      double *xp;
           goto end;    double *gp, *gm;
         }    double **gradg, **trgradg;
       }    double **mu;
     }    double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    int theta;
     char fileresprob[FILENAMELENGTH];
     free_vector(severity,1,maxwav);    char fileresprobcov[FILENAMELENGTH];
     free_imatrix(outcome,1,maxwav+1,1,n);    char fileresprobcor[FILENAMELENGTH];
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);    double ***varpij;
     /* free_matrix(mint,1,maxwav,1,n);  
        free_matrix(anint,1,maxwav,1,n);*/    strcpy(fileresprob,"prob"); 
     free_vector(moisdc,1,n);    strcat(fileresprob,fileres);
     free_vector(andc,1,n);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
          fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     wav=ivector(1,imx);    }
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    strcpy(fileresprobcov,"probcov"); 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    strcat(fileresprobcov,fileres);
        if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     /* Concatenates waves */      printf("Problem with resultfile: %s\n", fileresprobcov);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
       Tcode=ivector(1,100);    strcat(fileresprobcor,fileres);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       ncodemax[1]=1;      printf("Problem with resultfile: %s\n", fileresprobcor);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
          }
    codtab=imatrix(1,100,1,10);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
    h=0;    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
    m=pow(2,cptcoveff);    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);
    for(k=1;k<=cptcoveff; k++){    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      for(i=1; i <=(m/pow(2,k));i++){    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
        for(j=1; j <= ncodemax[k]; j++){    
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
            h++;    fprintf(ficresprob,"# Age");
            if (h>m) h=1;codtab[h][k]=j;    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(i=1; i<=nlstate;i++)
    /*for(i=1; i <=m ;i++){      for(j=1; j<=(nlstate+ndeath);j++){
      for(k=1; k <=cptcovn; k++){        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
      }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
      printf("\n");      }  
    }   /* fprintf(ficresprob,"\n");
    scanf("%d",i);*/    fprintf(ficresprobcov,"\n");
        fprintf(ficresprobcor,"\n");
    /* Calculates basic frequencies. Computes observed prevalence at single age   */
        and prints on file fileres'p'. */   xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
        doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
        mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    first=1;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficgp,"\n# Routine varprob");
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fprintf(fichtm,"\n");
        
     /* For Powell, parameters are in a vector p[] starting at p[1]    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
     if(mle==1){  and drawn. It helps understanding how is the covariance between two incidences.\
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     }    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
      It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
     /*--------- results files --------------*/  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);  standard deviations wide on each axis. <br>\
     Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
    jk=1;  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
    fprintf(ficres,"# Parameters\n");  
    printf("# Parameters\n");    cov[1]=1;
    for(i=1,jk=1; i <=nlstate; i++){    tj=cptcoveff;
      for(k=1; k <=(nlstate+ndeath); k++){    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
        if (k != i)    j1=0;
          {    for(t=1; t<=tj;t++){
            printf("%d%d ",i,k);      for(i1=1; i1<=ncodemax[t];i1++){ 
            fprintf(ficres,"%1d%1d ",i,k);        j1++;
            for(j=1; j <=ncovmodel; j++){        if  (cptcovn>0) {
              printf("%f ",p[jk]);          fprintf(ficresprob, "\n#********** Variable "); 
              fprintf(ficres,"%f ",p[jk]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
              jk++;          fprintf(ficresprob, "**********\n#\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(ficres,"\n");          fprintf(ficresprobcov, "**********\n#\n");
          }          
      }          fprintf(ficgp, "\n#********** Variable "); 
    }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  if(mle==1){          fprintf(ficgp, "**********\n#\n");
     /* Computing hessian and covariance matrix */          
     ftolhess=ftol; /* Usually correct */          
     hesscov(matcov, p, npar, delti, ftolhess, func);          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
  }          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fprintf(ficres,"# Scales\n");          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     printf("# Scales\n");          
      for(i=1,jk=1; i <=nlstate; i++){          fprintf(ficresprobcor, "\n#********** Variable ");    
       for(j=1; j <=nlstate+ndeath; j++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         if (j!=i) {          fprintf(ficresprobcor, "**********\n#");    
           fprintf(ficres,"%1d%1d",i,j);        }
           printf("%1d%1d",i,j);        
           for(k=1; k<=ncovmodel;k++){        for (age=bage; age<=fage; age ++){ 
             printf(" %.5e",delti[jk]);          cov[2]=age;
             fprintf(ficres," %.5e",delti[jk]);          for (k=1; k<=cptcovn;k++) {
             jk++;            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }          }
           printf("\n");          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           fprintf(ficres,"\n");          for (k=1; k<=cptcovprod;k++)
         }            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       }          
      }          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
              trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     k=1;          gp=vector(1,(nlstate)*(nlstate+ndeath));
     fprintf(ficres,"# Covariance\n");          gm=vector(1,(nlstate)*(nlstate+ndeath));
     printf("# Covariance\n");      
     for(i=1;i<=npar;i++){          for(theta=1; theta <=npar; theta++){
       /*  if (k>nlstate) k=1;            for(i=1; i<=npar; i++)
       i1=(i-1)/(ncovmodel*nlstate)+1;              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);            
       printf("%s%d%d",alph[k],i1,tab[i]);*/            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       fprintf(ficres,"%3d",i);            
       printf("%3d",i);            k=0;
       for(j=1; j<=i;j++){            for(i=1; i<= (nlstate); i++){
         fprintf(ficres," %.5e",matcov[i][j]);              for(j=1; j<=(nlstate+ndeath);j++){
         printf(" %.5e",matcov[i][j]);                k=k+1;
       }                gp[k]=pmmij[i][j];
       fprintf(ficres,"\n");              }
       printf("\n");            }
       k++;            
     }            for(i=1; i<=npar; i++)
                  xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     while((c=getc(ficpar))=='#' && c!= EOF){      
       ungetc(c,ficpar);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       fgets(line, MAXLINE, ficpar);            k=0;
       puts(line);            for(i=1; i<=(nlstate); i++){
       fputs(line,ficparo);              for(j=1; j<=(nlstate+ndeath);j++){
     }                k=k+1;
     ungetc(c,ficpar);                gm[k]=pmmij[i][j];
                }
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);            }
           
     if (fage <= 2) {            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       bage = agemin;              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
       fage = agemaxpar;          }
     }  
              for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");            for(theta=1; theta <=npar; theta++)
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);              trgradg[j][theta]=gradg[theta][j];
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);          
            matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     while((c=getc(ficpar))=='#' && c!= EOF){          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     ungetc(c,ficpar);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     fgets(line, MAXLINE, ficpar);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     puts(line);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     fputs(line,ficparo);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   }  
   ungetc(c,ficpar);          pmij(pmmij,cov,ncovmodel,x,nlstate);
            
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);          k=0;
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          for(i=1; i<=(nlstate); i++){
  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+ndeath);j++){
                    k=k+1;
   while((c=getc(ficpar))=='#' && c!= EOF){              mu[k][(int) age]=pmmij[i][j];
     ungetc(c,ficpar);            }
     fgets(line, MAXLINE, ficpar);          }
     puts(line);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     fputs(line,ficparo);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   }              varpij[i][j][(int)age] = doldm[i][j];
   ungetc(c,ficpar);  
            /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
    dateprev1=anprev1+mprev1/12.+jprev1/365.;            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
    dateprev2=anprev2+mprev2/12.+jprev2/365.;            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   fscanf(ficpar,"pop_based=%d\n",&popbased);  
   fprintf(ficparo,"pop_based=%d\n",popbased);            fprintf(ficresprob,"\n%d ",(int)age);
   fprintf(ficres,"pop_based=%d\n",popbased);            fprintf(ficresprobcov,"\n%d ",(int)age);
            fprintf(ficresprobcor,"\n%d ",(int)age);
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     fgets(line, MAXLINE, ficpar);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     puts(line);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     fputs(line,ficparo);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   }            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   ungetc(c,ficpar);          }
           i=0;
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);          for (k=1; k<=(nlstate);k++){
 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);            for (l=1; l<=(nlstate+ndeath);l++){ 
 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);              i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
 while((c=getc(ficpar))=='#' && c!= EOF){              for (j=1; j<=i;j++){
     ungetc(c,ficpar);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     fgets(line, MAXLINE, ficpar);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     puts(line);              }
     fputs(line,ficparo);            }
   }          }/* end of loop for state */
   ungetc(c,ficpar);        } /* end of loop for age */
   
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);        /* Confidence intervalle of pij  */
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        /*
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
 /*------------ gnuplot -------------*/          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
            fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
 /*------------ free_vector  -------------*/        */
  chdir(path);  
          /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
  free_ivector(wav,1,imx);        first1=1;
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        for (k2=1; k2<=(nlstate);k2++){
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            for (l2=1; l2<=(nlstate+ndeath);l2++){ 
  free_ivector(num,1,n);            if(l2==k2) continue;
  free_vector(agedc,1,n);            j=(k2-1)*(nlstate+ndeath)+l2;
  /*free_matrix(covar,1,NCOVMAX,1,n);*/            for (k1=1; k1<=(nlstate);k1++){
  fclose(ficparo);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
  fclose(ficres);                if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
 /*--------- index.htm --------*/                if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);                  if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                      v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   /*--------------- Prevalence limit --------------*/                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                      mu1=mu[i][(int) age]/stepm*YEARM ;
   strcpy(filerespl,"pl");                    mu2=mu[j][(int) age]/stepm*YEARM;
   strcat(filerespl,fileres);                    c12=cv12/sqrt(v1*v2);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {                    /* Computing eigen value of matrix of covariance */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   }                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);                    /* Eigen vectors */
   fprintf(ficrespl,"#Prevalence limit\n");                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   fprintf(ficrespl,"#Age ");                    /*v21=sqrt(1.-v11*v11); *//* error */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);                    v21=(lc1-v1)/cv12*v11;
   fprintf(ficrespl,"\n");                    v12=-v21;
                      v22=v11;
   prlim=matrix(1,nlstate,1,nlstate);                    tnalp=v21/v11;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    if(first1==1){
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                      first1=0;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                      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);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    }
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                    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);
   k=0;                    /*printf(fignu*/
   agebase=agemin;                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   agelim=agemaxpar;                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   ftolpl=1.e-10;                    if(first==1){
   i1=cptcoveff;                      first=0;
   if (cptcovn < 1){i1=1;}                      fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
   for(cptcov=1;cptcov<=i1;cptcov++){                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
         k=k+1;   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
         fprintf(ficrespl,"\n#******");                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
         for(j=1;j<=cptcoveff;j++)                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
         fprintf(ficrespl,"******\n");                      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);
         for (age=agebase; age<=agelim; age++){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
           fprintf(ficrespl,"%.0f",age );                      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",\
           for(i=1; i<=nlstate;i++)                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
           fprintf(ficrespl," %.5f", prlim[i][i]);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
           fprintf(ficrespl,"\n");                    }else{
         }                      first=0;
       }                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
     }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   fclose(ficrespl);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   /*------------- h Pij x at various ages ------------*/                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                                mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);                    }/* if first */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                  } /* age mod 5 */
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                } /* end loop age */
   }                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   printf("Computing pij: result on file '%s' \n", filerespij);                first=1;
                } /*l12 */
   stepsize=(int) (stepm+YEARM-1)/YEARM;            } /* k12 */
   /*if (stepm<=24) stepsize=2;*/          } /*l1 */
         }/* k1 */
   agelim=AGESUP;      } /* loop covariates */
   hstepm=stepsize*YEARM; /* Every year of age */    }
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
      free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   k=0;    free_vector(xp,1,npar);
   for(cptcov=1;cptcov<=i1;cptcov++){    fclose(ficresprob);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fclose(ficresprobcov);
       k=k+1;    fclose(ficresprobcor);
         fprintf(ficrespij,"\n#****** ");    fflush(ficgp);
         for(j=1;j<=cptcoveff;j++)    fflush(fichtmcov);
           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 */  /******************* Printing html file ***********/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                    int lastpass, int stepm, int weightopt, char model[],\
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
           oldm=oldms;savm=savms;                    int popforecast, int estepm ,\
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                      double jprev1, double mprev1,double anprev1, \
           fprintf(ficrespij,"# Age");                    double jprev2, double mprev2,double anprev2){
           for(i=1; i<=nlstate;i++)    int jj1, k1, i1, cpt;
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %1d-%1d",i,j);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
           fprintf(ficrespij,"\n");   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
           for (h=0; h<=nhstepm; h++){             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );     fprintf(fichtm,"\
             for(i=1; i<=nlstate;i++)   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
               for(j=1; j<=nlstate+ndeath;j++)             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);     fprintf(fichtm,"\
             fprintf(ficrespij,"\n");   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
           }             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     fprintf(fichtm,"\
           fprintf(ficrespij,"\n");   - Life expectancies by age and initial health status (estepm=%2d months): \
         }     <a href=\"%s\">%s</a> <br>\n</li>",
     }             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   }  
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/  
    m=cptcoveff;
   fclose(ficrespij);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
   /*---------- Forecasting ------------------*/   for(k1=1; k1<=m;k1++){
   if((stepm == 1) && (model==".")){     for(i1=1; i1<=ncodemax[k1];i1++){
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);       jj1++;
 if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);       if (cptcovn > 0) {
     free_matrix(mint,1,maxwav,1,n);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);         for (cpt=1; cpt<=cptcoveff;cpt++) 
     free_vector(weight,1,n);}           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   else{         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     erreur=108;       }
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);       /* Pij */
   }       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
    <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
   /*---------- Health expectancies and variances ------------*/       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   strcpy(filerest,"t");  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
   strcat(filerest,fileres);         /* Stable prevalence in each health state */
   if((ficrest=fopen(filerest,"w"))==NULL) {         for(cpt=1; cpt<nlstate;cpt++){
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   }  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);         }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   strcpy(filerese,"e");  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
   strcat(filerese,fileres);       }
   if((ficreseij=fopen(filerese,"w"))==NULL) {     } /* end i1 */
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);   }/* End k1 */
   }   fprintf(fichtm,"</ul>");
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
   
  strcpy(fileresv,"v");   fprintf(fichtm,"\
   strcat(fileresv,fileres);  \n<br><li><h4> Result files (second order: variances)</h4>\n\
   if((ficresvij=fopen(fileresv,"w"))==NULL) {   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
   k=0;   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   for(cptcov=1;cptcov<=i1;cptcov++){           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;   fprintf(fichtm,"\
       fprintf(ficrest,"\n#****** ");   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
       for(j=1;j<=cptcoveff;j++)           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   fprintf(fichtm,"\
       fprintf(ficrest,"******\n");   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
       fprintf(ficreseij,"\n#****** ");   fprintf(fichtm,"\
       for(j=1;j<=cptcoveff;j++)   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
       fprintf(ficreseij,"******\n");   fprintf(fichtm,"\
    - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
       fprintf(ficresvij,"\n#****** ");           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  /*  if(popforecast==1) fprintf(fichtm,"\n */
       fprintf(ficresvij,"******\n");  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  /*      <br>",fileres,fileres,fileres,fileres); */
       oldm=oldms;savm=savms;  /*  else  */
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);    /*    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); */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);   fflush(fichtm);
       oldm=oldms;savm=savms;   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
       m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");   jj1=0;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);   for(k1=1; k1<=m;k1++){
       fprintf(ficrest,"\n");     for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
       hf=1;       if (cptcovn > 0) {
       if (stepm >= YEARM) hf=stepm/YEARM;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       epj=vector(1,nlstate+1);         for (cpt=1; cpt<=cptcoveff;cpt++) 
       for(age=bage; age <=fage ;age++){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         if (popbased==1) {       }
           for(i=1; i<=nlstate;i++)       for(cpt=1; cpt<=nlstate;cpt++) {
             prlim[i][i]=probs[(int)age][i][k];         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
         }  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
          <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
         fprintf(ficrest," %.0f",age);       }
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  health expectancies in states (1) and (2): %s%d.png<br>\
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
           }     } /* end i1 */
           epj[nlstate+1] +=epj[j];   }/* End k1 */
         }   fprintf(fichtm,"</ul>");
         for(i=1, vepp=0.;i <=nlstate;i++)   fflush(fichtm);
           for(j=1;j <=nlstate;j++)  }
             vepp += vareij[i][j][(int)age];  
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));  /******************* Gnuplot file **************/
         for(j=1;j <=nlstate;j++){  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));  
         }    char dirfileres[132],optfileres[132];
         fprintf(ficrest,"\n");    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
       }    int ng;
     }  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   }  /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   fclose(ficreseij);  /*   } */
   fclose(ficresvij);  
   fclose(ficrest);    /*#ifdef windows */
   fclose(ficpar);    fprintf(ficgp,"cd \"%s\" \n",pathc);
   free_vector(epj,1,nlstate+1);      /*#endif */
      m=pow(2,cptcoveff);
   /*------- Variance limit prevalence------*/    
     strcpy(dirfileres,optionfilefiname);
   strcpy(fileresvpl,"vpl");    strcpy(optfileres,"vpl");
   strcat(fileresvpl,fileres);   /* 1eme*/
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    for (cpt=1; cpt<= nlstate ; cpt ++) {
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);     for (k1=1; k1<= m ; k1 ++) {
     exit(0);       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
   }       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);       fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   k=0;  set ter png small\n\
   for(cptcov=1;cptcov<=i1;cptcov++){  set size 0.65,0.65\n\
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
       k=k+1;  
       fprintf(ficresvpl,"\n#****** ");       for (i=1; i<= nlstate ; i ++) {
       for(j=1;j<=cptcoveff;j++)         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       fprintf(ficresvpl,"******\n");       }
             fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);       for (i=1; i<= nlstate ; i ++) {
       oldm=oldms;savm=savms;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     }       } 
  }       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
   fclose(ficresvpl);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
   /*---------- End : free ----------------*/       }  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
       }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    }
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    /*2 eme*/
      
      for (k1=1; k1<= m ; k1 ++) { 
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      for (i=1; i<= nlstate+1 ; i ++) {
          k=2*i;
   free_matrix(matcov,1,npar,1,npar);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   free_vector(delti,1,npar);        for (j=1; j<= nlstate+1 ; j ++) {
   free_matrix(agev,1,maxwav,1,imx);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
   if(erreur >0)        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
     printf("End of Imach with error %d\n",erreur);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   else   printf("End of Imach\n");        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        for (j=1; j<= nlstate+1 ; j ++) {
            if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   /* 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);*/          else fprintf(ficgp," \%%*lf (\%%*lf)");
   /*printf("Total time was %d uSec.\n", total_usecs);*/        }   
   /*------ End -----------*/        fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
  end:          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
 #ifdef windows          else fprintf(ficgp," \%%*lf (\%%*lf)");
   /* chdir(pathcd);*/        }   
 #endif        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
  /*system("wgnuplot graph.plt");*/        else fprintf(ficgp,"\" t\"\" w l 0,");
  /*system("../gp37mgw/wgnuplot graph.plt");*/      }
  /*system("cd ../gp37mgw");*/    }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    
  strcpy(plotcmd,GNUPLOTPROGRAM);    /*3eme*/
  strcat(plotcmd," ");    
  strcat(plotcmd,optionfilegnuplot);    for (k1=1; k1<= m ; k1 ++) { 
  system(plotcmd);      for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
 #ifdef windows        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
   while (z[0] != 'q') {        fprintf(ficgp,"set ter png small\n\
     chdir(path);  set size 0.65,0.65\n\
     printf("\nType e to edit output files, c to start again, and q for exiting: ");  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
     scanf("%s",z);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     if (z[0] == 'c') system("./imach");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     else if (z[0] == 'e') {          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       chdir(path);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
       system(optionfilehtm);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     else if (z[0] == 'q') exit(0);          
   }        */
 #endif        for (i=1; i< nlstate ; i ++) {
 }          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       sump=sump+1;
       num=num+1;
     }
    
    
     /* for (i=1; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=0;i<=imx-1 ; i++)
       {
         if (cens[i]==1 & wav[i]>1)
           A=-x[1]/(x[2])*
             (exp(x[2]/YEARM*(agecens[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)));
         
         if (cens[i]==0 & wav[i]>1)
           A=-x[1]/(x[2])*
                (exp(x[2]/YEARM*(agedc[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)))
             +log(x[1]/YEARM)+x[2]/YEARM*(agedc[i]*12-agegomp*12)+log(YEARM);      
         
         if (wav[i]>1 & agecens[i]>15) {
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov){
     int i;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
         for(j=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){
           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.1.31  
changed lines
  Added in v.1.102


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