Diff for /imach/src/imach.c between versions 1.21 and 1.114

version 1.21, 2002/02/21 18:42:24 version 1.114, 2006/02/26 12:57:58
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.114  2006/02/26 12:57:58  brouard
   individuals from different ages are interviewed on their health status    (Module): Some improvements in processing parameter
   or degree of  disability. At least a second wave of interviews    filename with strsep.
   ("longitudinal") should  measure each new individual health status.  
   Health expectancies are computed from the transistions observed between    Revision 1.113  2006/02/24 14:20:24  brouard
   waves and are computed for each degree of severity of disability (number    (Module): Memory leaks checks with valgrind and:
   of life states). More degrees you consider, more time is necessary to    datafile was not closed, some imatrix were not freed and on matrix
   reach the Maximum Likelihood of the parameters involved in the model.    allocation too.
   The simplest model is the multinomial logistic model where pij is  
   the probabibility to be observed in state j at the second wave conditional    Revision 1.112  2006/01/30 09:55:26  brouard
   to be observed in state i at the first wave. Therefore the model is:    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'  
   is a covariate. If you want to have a more complex model than "constant and    Revision 1.111  2006/01/25 20:38:18  brouard
   age", you should modify the program where the markup    (Module): Lots of cleaning and bugs added (Gompertz)
     *Covariates have to be included here again* invites you to do it.    (Module): Comments can be added in data file. Missing date values
   More covariates you add, less is the speed of the convergence.    can be a simple dot '.'.
   
   The advantage that this computer programme claims, comes from that if the    Revision 1.110  2006/01/25 00:51:50  brouard
   delay between waves is not identical for each individual, or if some    (Module): Lots of cleaning and bugs added (Gompertz)
   individual missed an interview, the information is not rounded or lost, but  
   taken into account using an interpolation or extrapolation.    Revision 1.109  2006/01/24 19:37:15  brouard
   hPijx is the probability to be    (Module): Comments (lines starting with a #) are allowed in data.
   observed in state i at age x+h conditional to the observed state i at age  
   x. The delay 'h' can be split into an exact number (nh*stepm) of    Revision 1.108  2006/01/19 18:05:42  lievre
   unobserved intermediate  states. This elementary transition (by month or    Gnuplot problem appeared...
   quarter trimester, semester or year) is model as a multinomial logistic.    To be fixed
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply hPijx.    Revision 1.107  2006/01/19 16:20:37  brouard
     Test existence of gnuplot in imach path
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.106  2006/01/19 13:24:36  brouard
      Some cleaning and links added in html output
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.105  2006/01/05 20:23:19  lievre
   This software have been partly granted by Euro-REVES, a concerted action    *** empty log message ***
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.104  2005/09/30 16:11:43  lievre
   software can be distributed freely for non commercial use. Latest version    (Module): sump fixed, loop imx fixed, and simplifications.
   can be accessed at http://euroreves.ined.fr/imach .    (Module): If the status is missing at the last wave but we know
   **********************************************************************/    that the person is alive, then we can code his/her status as -2
      (instead of missing=-1 in earlier versions) and his/her
 #include <math.h>    contributions to the likelihood is 1 - Prob of dying from last
 #include <stdio.h>    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 #include <stdlib.h>    the healthy state at last known wave). Version is 0.98
 #include <unistd.h>  
     Revision 1.103  2005/09/30 15:54:49  lievre
 #define MAXLINE 256    (Module): sump fixed, loop imx fixed, and simplifications.
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.102  2004/09/15 17:31:30  brouard
 #define windows    Add the possibility to read data file including tab characters.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.101  2004/09/15 10:38:38  brouard
     Fix on curr_time
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.100  2004/07/12 18:29:06  brouard
     Add version for Mac OS X. Just define UNIX in Makefile
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.99  2004/06/05 08:57:40  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    *** empty log message ***
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.98  2004/05/16 15:05:56  brouard
 #define YEARM 12. /* Number of months per year */    New version 0.97 . First attempt to estimate force of mortality
 #define AGESUP 130    directly from the data i.e. without the need of knowing the health
 #define AGEBASE 40    state at each age, but using a Gompertz model: log u =a + b*age .
     This is the basic analysis of mortality and should be done before any
     other analysis, in order to test if the mortality estimated from the
 int erreur; /* Error number */    cross-longitudinal survey is different from the mortality estimated
 int nvar;    from other sources like vital statistic data.
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    The same imach parameter file can be used but the option for mle should be -3.
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Agnès, who wrote this part of the code, tried to keep most of the
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    former routines in order to include the new code within the former code.
 int popbased=0;  
     The output is very simple: only an estimate of the intercept and of
 int *wav; /* Number of waves for this individuual 0 is possible */    the slope with 95% confident intervals.
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Current limitations:
 int mle, weightopt;    A) Even if you enter covariates, i.e. with the
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    B) There is no computation of Life Expectancy nor Life Table.
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.97  2004/02/20 13:25:42  lievre
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Version 0.96d. Population forecasting command line is (temporarily)
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    suppressed.
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;  
 FILE *ficreseij;    Revision 1.96  2003/07/15 15:38:55  brouard
   char filerese[FILENAMELENGTH];    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
  FILE  *ficresvij;    rewritten within the same printf. Workaround: many printfs.
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.95  2003/07/08 07:54:34  brouard
   char fileresvpl[FILENAMELENGTH];    * imach.c (Repository):
     (Repository): Using imachwizard code to output a more meaningful covariance
 #define NR_END 1    matrix (cov(a12,c31) instead of numbers.
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
 #define NRANSI  
 #define ITMAX 200    Revision 1.93  2003/06/25 16:33:55  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 #define TOL 2.0e-4    exist so I changed back to asctime which exists.
     (Module): Version 0.96b
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.92  2003/06/25 16:30:45  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.91  2003/06/25 15:30:29  brouard
 #define TINY 1.0e-20    * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
 static double maxarg1,maxarg2;    helps to forecast when convergence will be reached. Elapsed time
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    is stamped in powell.  We created a new html file for the graphs
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    concerning matrix of covariance. It has extension -cov.htm.
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.90  2003/06/24 12:34:15  brouard
 #define rint(a) floor(a+0.5)    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 static double sqrarg;    of the covariance matrix to be input.
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Revision 1.89  2003/06/24 12:30:52  brouard
     (Module): Some bugs corrected for windows. Also, when
 int imx;    mle=-1 a template is output in file "or"mypar.txt with the design
 int stepm;    of the covariance matrix to be input.
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.88  2003/06/23 17:54:56  brouard
 int m,nb;    * 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 *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.87  2003/06/18 12:26:01  brouard
 double **pmmij, ***probs, ***mobaverage;    Version 0.96
 double dateintmean=0;  
     Revision 1.86  2003/06/17 20:04:08  brouard
 double *weight;    (Module): Change position of html and gnuplot routines and added
 int **s; /* Status */    routine fileappend.
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    current date of interview. It may happen when the death was just
 double ftolhess; /* Tolerance for computing hessian */    prior to the death. In this case, dh was negative and likelihood
     was wrong (infinity). We still send an "Error" but patch by
 /**************** split *************************/    assuming that the date of death was just one stepm after the
 static  int split( char *path, char *dirc, char *name )    interview.
 {    (Repository): Because some people have very long ID (first column)
    char *s;                             /* pointer */    we changed int to long in num[] and we added a new lvector for
    int  l1, l2;                         /* length counters */    memory allocation. But we also truncated to 8 characters (left
     truncation)
    l1 = strlen( path );                 /* length of path */    (Repository): No more line truncation errors.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s = strrchr( path, '\\' );           /* find last / */    Revision 1.84  2003/06/13 21:44:43  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    * imach.c (Repository): Replace "freqsummary" at a correct
 #if     defined(__bsd__)                /* get current working directory */    place. It differs from routine "prevalence" which may be called
       extern char       *getwd( );    many times. Probs is memory consuming and must be used with
     parcimony.
       if ( getwd( dirc ) == NULL ) {    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #else  
       extern char       *getcwd( );    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.82  2003/06/05 15:57:20  brouard
          return( GLOCK_ERROR_GETCWD );    Add log in  imach.c and  fullversion number is now printed.
       }  
       strcpy( name, path );             /* we've got it */  */
    } else {                             /* strip direcotry from path */  /*
       s++;                              /* after this, the filename */     Interpolated Markov Chain
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Short summary of the programme:
       strcpy( name, s );                /* save file name */    
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    This program computes Healthy Life Expectancies from
       dirc[l1-l2] = 0;                  /* add zero */    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
    }    first survey ("cross") where individuals from different ages are
    l1 = strlen( dirc );                 /* length of directory */    interviewed on their health status or degree of disability (in the
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    case of a health survey which is our main interest) -2- at least a
    return( 0 );                         /* we're done */    second wave of interviews ("longitudinal") which measure each change
 }    (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
     model. More health states you consider, more time is necessary to reach the
 /******************************************/    Maximum Likelihood of the parameters involved in the model.  The
     simplest model is the multinomial logistic model where pij is the
 void replace(char *s, char*t)    probability to be observed in state j at the second wave
 {    conditional to be observed in state i at the first wave. Therefore
   int i;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   int lg=20;    'age' is age and 'sex' is a covariate. If you want to have a more
   i=0;    complex model than "constant and age", you should modify the program
   lg=strlen(t);    where the markup *Covariates have to be included here again* invites
   for(i=0; i<= lg; i++) {    you to do it.  More covariates you add, slower the
     (s[i] = t[i]);    convergence.
     if (t[i]== '\\') s[i]='/';  
   }    The advantage of this computer programme, compared to a simple
 }    multinomial logistic model, is clear when the delay between waves is not
     identical for each individual. Also, if a individual missed an
 int nbocc(char *s, char occ)    intermediate interview, the information is lost, but taken into
 {    account using an interpolation or extrapolation.  
   int i,j=0;  
   int lg=20;    hPijx is the probability to be observed in state i at age x+h
   i=0;    conditional to the observed state i at age x. The delay 'h' can be
   lg=strlen(s);    split into an exact number (nh*stepm) of unobserved intermediate
   for(i=0; i<= lg; i++) {    states. This elementary transition (by month, quarter,
   if  (s[i] == occ ) j++;    semester or year) is modelled as a multinomial logistic.  The hPx
   }    matrix is simply the matrix product of nh*stepm elementary matrices
   return j;    and the contribution of each individual to the likelihood is simply
 }    hPijx.
   
 void cutv(char *u,char *v, char*t, char occ)    Also this programme outputs the covariance matrix of the parameters but also
 {    of the life expectancies. It also computes the stable prevalence. 
   int i,lg,j,p=0;    
   i=0;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   for(j=0; j<=strlen(t)-1; j++) {             Institut national d'études démographiques, Paris.
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    This software have been partly granted by Euro-REVES, a concerted action
   }    from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
   lg=strlen(t);    software can be distributed freely for non commercial use. Latest version
   for(j=0; j<p; j++) {    can be accessed at http://euroreves.ined.fr/imach .
     (u[j] = t[j]);  
   }    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
      u[p]='\0';    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     
    for(j=0; j<= lg; j++) {    **********************************************************************/
     if (j>=(p+1))(v[j-p-1] = t[j]);  /*
   }    main
 }    read parameterfile
     read datafile
 /********************** nrerror ********************/    concatwav
     freqsummary
 void nrerror(char error_text[])    if (mle >= 1)
 {      mlikeli
   fprintf(stderr,"ERREUR ...\n");    print results files
   fprintf(stderr,"%s\n",error_text);    if mle==1 
   exit(1);       computes hessian
 }    read end of parameter file: agemin, agemax, bage, fage, estepm
 /*********************** vector *******************/        begin-prev-date,...
 double *vector(int nl, int nh)    open gnuplot file
 {    open html file
   double *v;    stable prevalence
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));     for age prevalim()
   if (!v) nrerror("allocation failure in vector");    h Pij x
   return v-nl+NR_END;    variance of p varprob
 }    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
 /************************ free vector ******************/    Variance-covariance of DFLE
 void free_vector(double*v, int nl, int nh)    prevalence()
 {     movingaverage()
   free((FREE_ARG)(v+nl-NR_END));    varevsij() 
 }    if popbased==1 varevsij(,popbased)
     total life expectancies
 /************************ivector *******************************/    Variance of stable prevalence
 int *ivector(long nl,long nh)   end
 {  */
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;   
 }  #include <math.h>
   #include <stdio.h>
 /******************free ivector **************************/  #include <stdlib.h>
 void free_ivector(int *v, long nl, long nh)  #include <string.h>
 {  #include <unistd.h>
   free((FREE_ARG)(v+nl-NR_END));  
 }  #include <limits.h>
   #include <sys/types.h>
 /******************* imatrix *******************************/  #include <sys/stat.h>
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #include <errno.h>
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  extern int errno;
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  /* #include <sys/time.h> */
   int **m;  #include <time.h>
    #include "timeval.h"
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  /* #include <libintl.h> */
   if (!m) nrerror("allocation failure 1 in matrix()");  /* #define _(String) gettext (String) */
   m += NR_END;  
   m -= nrl;  #define MAXLINE 256
    
    #define GNUPLOTPROGRAM "gnuplot"
   /* allocate rows and set pointers to them */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #define FILENAMELENGTH 132
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   m[nrl] -= ncl;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
    #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   /* return pointer to array of pointers to rows */  
   return m;  #define NINTERVMAX 8
 }  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 /****************** free_imatrix *************************/  #define NCOVMAX 8 /* Maximum number of covariates */
 void free_imatrix(m,nrl,nrh,ncl,nch)  #define MAXN 20000
       int **m;  #define YEARM 12. /* Number of months per year */
       long nch,ncl,nrh,nrl;  #define AGESUP 130
      /* free an int matrix allocated by imatrix() */  #define AGEBASE 40
 {  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #ifdef UNIX
   free((FREE_ARG) (m+nrl-NR_END));  #define DIRSEPARATOR '/'
 }  #define CHARSEPARATOR "/"
   #define ODIRSEPARATOR '\\'
 /******************* matrix *******************************/  #else
 double **matrix(long nrl, long nrh, long ncl, long nch)  #define DIRSEPARATOR '\\'
 {  #define CHARSEPARATOR "\\"
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  #define ODIRSEPARATOR '/'
   double **m;  #endif
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  /* $Id$ */
   if (!m) nrerror("allocation failure 1 in matrix()");  /* $State$ */
   m += NR_END;  
   m -= nrl;  char version[]="Imach version 0.98b, January 2006, INED-EUROREVES ";
   char fullversion[]="$Revision$ $Date$"; 
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int nvar;
   m[nrl] += NR_END;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   m[nrl] -= ncl;  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int ndeath=1; /* Number of dead states */
   return m;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 }  int popbased=0;
   
 /*************************free matrix ************************/  int *wav; /* Number of waves for this individuual 0 is possible */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  int maxwav; /* Maxim number of waves */
 {  int jmin, jmax; /* min, max spacing between 2 waves */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   free((FREE_ARG)(m+nrl-NR_END));  int gipmx, gsw; /* Global variables on the number of contributions 
 }                     to the likelihood and the sum of weights (done by funcone)*/
   int mle, weightopt;
 /******************* ma3x *******************************/  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  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
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double ***m;  double jmean; /* Mean space between 2 waves */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   if (!m) nrerror("allocation failure 1 in matrix()");  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   m += NR_END;  FILE *ficlog, *ficrespow;
   m -= nrl;  int globpr; /* Global variable for printing or not */
   double fretone; /* Only one call to likelihood */
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  long ipmx; /* Number of contributions */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  double sw; /* Sum of weights */
   m[nrl] += NR_END;  char filerespow[FILENAMELENGTH];
   m[nrl] -= ncl;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   FILE *ficresilk;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  FILE *fichtm, *fichtmcov; /* Html File */
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  FILE *ficreseij;
   m[nrl][ncl] += NR_END;  char filerese[FILENAMELENGTH];
   m[nrl][ncl] -= nll;  FILE  *ficresvij;
   for (j=ncl+1; j<=nch; j++)  char fileresv[FILENAMELENGTH];
     m[nrl][j]=m[nrl][j-1]+nlay;  FILE  *ficresvpl;
    char fileresvpl[FILENAMELENGTH];
   for (i=nrl+1; i<=nrh; i++) {  char title[MAXLINE];
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     for (j=ncl+1; j<=nch; j++)  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       m[i][j]=m[i][j-1]+nlay;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   }  char command[FILENAMELENGTH];
   return m;  int  outcmd=0;
 }  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  char filelog[FILENAMELENGTH]; /* Log file */
 {  char filerest[FILENAMELENGTH];
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  char fileregp[FILENAMELENGTH];
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  char popfile[FILENAMELENGTH];
   free((FREE_ARG)(m+nrl-NR_END));  
 }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   
 /***************** f1dim *************************/  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 extern int ncom;  struct timezone tzp;
 extern double *pcom,*xicom;  extern int gettimeofday();
 extern double (*nrfunc)(double []);  struct tm tmg, tm, tmf, *gmtime(), *localtime();
    long time_value;
 double f1dim(double x)  extern long time();
 {  char strcurr[80], strfor[80];
   int j;  
   double f;  char *endptr;
   double *xt;  long lval;
    
   xt=vector(1,ncom);  #define NR_END 1
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #define FREE_ARG char*
   f=(*nrfunc)(xt);  #define FTOL 1.0e-10
   free_vector(xt,1,ncom);  
   return f;  #define NRANSI 
 }  #define ITMAX 200 
   
 /*****************brent *************************/  #define TOL 2.0e-4 
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {  #define CGOLD 0.3819660 
   int iter;  #define ZEPS 1.0e-10 
   double a,b,d,etemp;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   double fu,fv,fw,fx;  
   double ftemp;  #define GOLD 1.618034 
   double p,q,r,tol1,tol2,u,v,w,x,xm;  #define GLIMIT 100.0 
   double e=0.0;  #define TINY 1.0e-20 
    
   a=(ax < cx ? ax : cx);  static double maxarg1,maxarg2;
   b=(ax > cx ? ax : cx);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   x=w=v=bx;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   fw=fv=fx=(*f)(x);    
   for (iter=1;iter<=ITMAX;iter++) {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     xm=0.5*(a+b);  #define rint(a) floor(a+0.5)
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  static double sqrarg;
     printf(".");fflush(stdout);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 #ifdef DEBUG  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  int agegomp= AGEGOMP;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif  int imx; 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  int stepm=1;
       *xmin=x;  /* Stepm, step in month: minimum step interpolation*/
       return fx;  
     }  int estepm;
     ftemp=fu;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);  int m,nb;
       q=(x-v)*(fx-fw);  long *num;
       p=(x-v)*q-(x-w)*r;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       q=2.0*(q-r);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       if (q > 0.0) p = -p;  double **pmmij, ***probs;
       q=fabs(q);  double *ageexmed,*agecens;
       etemp=e;  double dateintmean=0;
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  double *weight;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  int **s; /* Status */
       else {  double *agedc, **covar, idx;
         d=p/q;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
         u=x+d;  double *lsurv, *lpop, *tpop;
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
       }  double ftolhess; /* Tolerance for computing hessian */
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  /**************** split *************************/
     }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  {
     fu=(*f)(u);    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
     if (fu <= fx) {       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       if (u >= x) a=x; else b=x;    */ 
       SHFT(v,w,x,u)    char  *ss;                            /* pointer */
         SHFT(fv,fw,fx,fu)    int   l1, l2;                         /* length counters */
         } else {  
           if (u < x) a=u; else b=u;    l1 = strlen(path );                   /* length of path */
           if (fu <= fw || w == x) {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
             v=w;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
             w=u;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
             fv=fw;      strcpy( name, path );               /* we got the fullname name because no directory */
             fw=fu;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
           } else if (fu <= fv || v == x || v == w) {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
             v=u;      /* get current working directory */
             fv=fu;      /*    extern  char* getcwd ( char *buf , int len);*/
           }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         }        return( GLOCK_ERROR_GETCWD );
   }      }
   nrerror("Too many iterations in brent");      /* got dirc from getcwd*/
   *xmin=x;      printf(" DIRC = %s \n",dirc);
   return fx;    } else {                              /* strip direcotry from path */
 }      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
 /****************** mnbrak ***********************/      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, ss );         /* save file name */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      strncpy( dirc, path, l1 - l2 );     /* now the directory */
             double (*func)(double))      dirc[l1-l2] = 0;                    /* add zero */
 {      printf(" DIRC2 = %s \n",dirc);
   double ulim,u,r,q, dum;    }
   double fu;    /* We add a separator at the end of dirc if not exists */
      l1 = strlen( dirc );                  /* length of directory */
   *fa=(*func)(*ax);    if( dirc[l1-1] != DIRSEPARATOR ){
   *fb=(*func)(*bx);      dirc[l1] =  DIRSEPARATOR;
   if (*fb > *fa) {      dirc[l1+1] = 0; 
     SHFT(dum,*ax,*bx,dum)      printf(" DIRC3 = %s \n",dirc);
       SHFT(dum,*fb,*fa,dum)    }
       }    ss = strrchr( name, '.' );            /* find last / */
   *cx=(*bx)+GOLD*(*bx-*ax);    if (ss >0){
   *fc=(*func)(*cx);      ss++;
   while (*fb > *fc) {      strcpy(ext,ss);                     /* save extension */
     r=(*bx-*ax)*(*fb-*fc);      l1= strlen( name);
     q=(*bx-*cx)*(*fb-*fa);      l2= strlen(ss)+1;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      strncpy( finame, name, l1-l2);
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));      finame[l1-l2]= 0;
     ulim=(*bx)+GLIMIT*(*cx-*bx);    }
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);    return( 0 );                          /* we're done */
     } else if ((*cx-u)*(u-ulim) > 0.0) {  }
       fu=(*func)(u);  
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  /******************************************/
           SHFT(*fb,*fc,fu,(*func)(u))  
           }  void replace_back_to_slash(char *s, char*t)
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  {
       u=ulim;    int i;
       fu=(*func)(u);    int lg=0;
     } else {    i=0;
       u=(*cx)+GOLD*(*cx-*bx);    lg=strlen(t);
       fu=(*func)(u);    for(i=0; i<= lg; i++) {
     }      (s[i] = t[i]);
     SHFT(*ax,*bx,*cx,u)      if (t[i]== '\\') s[i]='/';
       SHFT(*fa,*fb,*fc,fu)    }
       }  }
 }  
   int nbocc(char *s, char occ)
 /*************** linmin ************************/  {
     int i,j=0;
 int ncom;    int lg=20;
 double *pcom,*xicom;    i=0;
 double (*nrfunc)(double []);    lg=strlen(s);
      for(i=0; i<= lg; i++) {
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    if  (s[i] == occ ) j++;
 {    }
   double brent(double ax, double bx, double cx,    return j;
                double (*f)(double), double tol, double *xmin);  }
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  void cutv(char *u,char *v, char*t, char occ)
               double *fc, double (*func)(double));  {
   int j;    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
   double xx,xmin,bx,ax;       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
   double fx,fb,fa;       gives u="abcedf" and v="ghi2j" */
      int i,lg,j,p=0;
   ncom=n;    i=0;
   pcom=vector(1,n);    for(j=0; j<=strlen(t)-1; j++) {
   xicom=vector(1,n);      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   nrfunc=func;    }
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];    lg=strlen(t);
     xicom[j]=xi[j];    for(j=0; j<p; j++) {
   }      (u[j] = t[j]);
   ax=0.0;    }
   xx=1.0;       u[p]='\0';
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);     for(j=0; j<= lg; j++) {
 #ifdef DEBUG      if (j>=(p+1))(v[j-p-1] = t[j]);
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    }
 #endif  }
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;  /********************** nrerror ********************/
     p[j] += xi[j];  
   }  void nrerror(char error_text[])
   free_vector(xicom,1,n);  {
   free_vector(pcom,1,n);    fprintf(stderr,"ERREUR ...\n");
 }    fprintf(stderr,"%s\n",error_text);
     exit(EXIT_FAILURE);
 /*************** powell ************************/  }
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  /*********************** vector *******************/
             double (*func)(double []))  double *vector(int nl, int nh)
 {  {
   void linmin(double p[], double xi[], int n, double *fret,    double *v;
               double (*func)(double []));    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   int i,ibig,j;    if (!v) nrerror("allocation failure in vector");
   double del,t,*pt,*ptt,*xit;    return v-nl+NR_END;
   double fp,fptt;  }
   double *xits;  
   pt=vector(1,n);  /************************ free vector ******************/
   ptt=vector(1,n);  void free_vector(double*v, int nl, int nh)
   xit=vector(1,n);  {
   xits=vector(1,n);    free((FREE_ARG)(v+nl-NR_END));
   *fret=(*func)(p);  }
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  /************************ivector *******************************/
     fp=(*fret);  int *ivector(long nl,long nh)
     ibig=0;  {
     del=0.0;    int *v;
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     for (i=1;i<=n;i++)    if (!v) nrerror("allocation failure in ivector");
       printf(" %d %.12f",i, p[i]);    return v-nl+NR_END;
     printf("\n");  }
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  /******************free ivector **************************/
       fptt=(*fret);  void free_ivector(int *v, long nl, long nh)
 #ifdef DEBUG  {
       printf("fret=%lf \n",*fret);    free((FREE_ARG)(v+nl-NR_END));
 #endif  }
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);  /************************lvector *******************************/
       if (fabs(fptt-(*fret)) > del) {  long *lvector(long nl,long nh)
         del=fabs(fptt-(*fret));  {
         ibig=i;    long *v;
       }    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 #ifdef DEBUG    if (!v) nrerror("allocation failure in ivector");
       printf("%d %.12e",i,(*fret));    return v-nl+NR_END;
       for (j=1;j<=n;j++) {  }
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);  /******************free lvector **************************/
       }  void free_lvector(long *v, long nl, long nh)
       for(j=1;j<=n;j++)  {
         printf(" p=%.12e",p[j]);    free((FREE_ARG)(v+nl-NR_END));
       printf("\n");  }
 #endif  
     }  /******************* imatrix *******************************/
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  int **imatrix(long nrl, long nrh, long ncl, long nch) 
 #ifdef DEBUG       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       int k[2],l;  { 
       k[0]=1;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       k[1]=-1;    int **m; 
       printf("Max: %.12e",(*func)(p));    
       for (j=1;j<=n;j++)    /* allocate pointers to rows */ 
         printf(" %.12e",p[j]);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       printf("\n");    if (!m) nrerror("allocation failure 1 in matrix()"); 
       for(l=0;l<=1;l++) {    m += NR_END; 
         for (j=1;j<=n;j++) {    m -= nrl; 
           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]);    
         }    /* allocate rows and set pointers to them */ 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 #endif    m[nrl] += NR_END; 
     m[nrl] -= ncl; 
     
       free_vector(xit,1,n);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       free_vector(xits,1,n);    
       free_vector(ptt,1,n);    /* return pointer to array of pointers to rows */ 
       free_vector(pt,1,n);    return m; 
       return;  } 
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  /****************** free_imatrix *************************/
     for (j=1;j<=n;j++) {  void free_imatrix(m,nrl,nrh,ncl,nch)
       ptt[j]=2.0*p[j]-pt[j];        int **m;
       xit[j]=p[j]-pt[j];        long nch,ncl,nrh,nrl; 
       pt[j]=p[j];       /* free an int matrix allocated by imatrix() */ 
     }  { 
     fptt=(*func)(ptt);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     if (fptt < fp) {    free((FREE_ARG) (m+nrl-NR_END)); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  } 
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);  /******************* matrix *******************************/
         for (j=1;j<=n;j++) {  double **matrix(long nrl, long nrh, long ncl, long nch)
           xi[j][ibig]=xi[j][n];  {
           xi[j][n]=xit[j];    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
         }    double **m;
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         for(j=1;j<=n;j++)    if (!m) nrerror("allocation failure 1 in matrix()");
           printf(" %.12e",xit[j]);    m += NR_END;
         printf("\n");    m -= nrl;
 #endif  
       }    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   }    m[nrl] += NR_END;
 }    m[nrl] -= ncl;
   
 /**** Prevalence limit ****************/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
 {     */
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  }
      matrix by transitions matrix until convergence is reached */  
   /*************************free matrix ************************/
   int i, ii,j,k;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double min, max, maxmin, maxmax,sumnew=0.;  {
   double **matprod2();    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double **out, cov[NCOVMAX], **pmij();    free((FREE_ARG)(m+nrl-NR_END));
   double **newm;  }
   double agefin, delaymax=50 ; /* Max number of years to converge */  
   /******************* ma3x *******************************/
   for (ii=1;ii<=nlstate+ndeath;ii++)  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     for (j=1;j<=nlstate+ndeath;j++){  {
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     }    double ***m;
   
    cov[1]=1.;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
      if (!m) nrerror("allocation failure 1 in matrix()");
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    m += NR_END;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    m -= nrl;
     newm=savm;  
     /* Covariates have to be included here again */    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
      cov[2]=agefin;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
      m[nrl] += NR_END;
       for (k=1; k<=cptcovn;k++) {    m[nrl] -= ncl;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       }  
       for (k=1; k<=cptcovage;k++)    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       for (k=1; k<=cptcovprod;k++)    m[nrl][ncl] += NR_END;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    m[nrl][ncl] -= nll;
     for (j=ncl+1; j<=nch; j++) 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      m[nrl][j]=m[nrl][j-1]+nlay;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    
     for (i=nrl+1; i<=nrh; i++) {
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       for (j=ncl+1; j<=nch; j++) 
     savm=oldm;        m[i][j]=m[i][j-1]+nlay;
     oldm=newm;    }
     maxmax=0.;    return m; 
     for(j=1;j<=nlstate;j++){    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       min=1.;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       max=0.;    */
       for(i=1; i<=nlstate; i++) {  }
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  /*************************free ma3x ************************/
         prlim[i][j]= newm[i][j]/(1-sumnew);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
         max=FMAX(max,prlim[i][j]);  {
         min=FMIN(min,prlim[i][j]);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       maxmin=max-min;    free((FREE_ARG)(m+nrl-NR_END));
       maxmax=FMAX(maxmax,maxmin);  }
     }  
     if(maxmax < ftolpl){  /*************** function subdirf ***********/
       return prlim;  char *subdirf(char fileres[])
     }  {
   }    /* Caution optionfilefiname is hidden */
 }    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
 /*************** transition probabilities ***************/    strcat(tmpout,fileres);
     return tmpout;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  }
 {  
   double s1, s2;  /*************** function subdirf2 ***********/
   /*double t34;*/  char *subdirf2(char fileres[], char *preop)
   int i,j,j1, nc, ii, jj;  {
     
     for(i=1; i<= nlstate; i++){    /* Caution optionfilefiname is hidden */
     for(j=1; j<i;j++){    strcpy(tmpout,optionfilefiname);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    strcat(tmpout,"/");
         /*s2 += param[i][j][nc]*cov[nc];*/    strcat(tmpout,preop);
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    strcat(tmpout,fileres);
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    return tmpout;
       }  }
       ps[i][j]=s2;  
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  /*************** function subdirf3 ***********/
     }  char *subdirf3(char fileres[], char *preop, char *preop2)
     for(j=i+1; j<=nlstate+ndeath;j++){  {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    /* Caution optionfilefiname is hidden */
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    strcpy(tmpout,optionfilefiname);
       }    strcat(tmpout,"/");
       ps[i][j]=(s2);    strcat(tmpout,preop);
     }    strcat(tmpout,preop2);
   }    strcat(tmpout,fileres);
     /*ps[3][2]=1;*/    return tmpout;
   }
   for(i=1; i<= nlstate; i++){  
      s1=0;  /***************** f1dim *************************/
     for(j=1; j<i; j++)  extern int ncom; 
       s1+=exp(ps[i][j]);  extern double *pcom,*xicom;
     for(j=i+1; j<=nlstate+ndeath; j++)  extern double (*nrfunc)(double []); 
       s1+=exp(ps[i][j]);   
     ps[i][i]=1./(s1+1.);  double f1dim(double x) 
     for(j=1; j<i; j++)  { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    int j; 
     for(j=i+1; j<=nlstate+ndeath; j++)    double f;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    double *xt; 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */   
   } /* end i */    xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    f=(*nrfunc)(xt); 
     for(jj=1; jj<= nlstate+ndeath; jj++){    free_vector(xt,1,ncom); 
       ps[ii][jj]=0;    return f; 
       ps[ii][ii]=1;  } 
     }  
   }  /*****************brent *************************/
   double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   { 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    int iter; 
     for(jj=1; jj<= nlstate+ndeath; jj++){    double a,b,d,etemp;
      printf("%lf ",ps[ii][jj]);    double fu,fv,fw,fx;
    }    double ftemp;
     printf("\n ");    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     }    double e=0.0; 
     printf("\n ");printf("%lf ",cov[2]);*/   
 /*    a=(ax < cx ? ax : cx); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    b=(ax > cx ? ax : cx); 
   goto end;*/    x=w=v=bx; 
     return ps;    fw=fv=fx=(*f)(x); 
 }    for (iter=1;iter<=ITMAX;iter++) { 
       xm=0.5*(a+b); 
 /**************** Product of 2 matrices ******************/      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      printf(".");fflush(stdout);
 {      fprintf(ficlog,".");fflush(ficlog);
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  #ifdef DEBUG
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      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);
   /* in, b, out are matrice of pointers which should have been initialized      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);
      before: only the contents of out is modified. The function returns      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
      a pointer to pointers identical to out */  #endif
   long i, j, k;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   for(i=nrl; i<= nrh; i++)        *xmin=x; 
     for(k=ncolol; k<=ncoloh; k++)        return fx; 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      } 
         out[i][k] +=in[i][j]*b[j][k];      ftemp=fu;
       if (fabs(e) > tol1) { 
   return out;        r=(x-w)*(fx-fv); 
 }        q=(x-v)*(fx-fw); 
         p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
 /************* Higher Matrix Product ***************/        if (q > 0.0) p = -p; 
         q=fabs(q); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        etemp=e; 
 {        e=d; 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
      duration (i.e. until          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        else { 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step          d=p/q; 
      (typically every 2 years instead of every month which is too big).          u=x+d; 
      Model is determined by parameters x and covariates have to be          if (u-a < tol2 || b-u < tol2) 
      included manually here.            d=SIGN(tol1,xm-x); 
         } 
      */      } else { 
         d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   int i, j, d, h, k;      } 
   double **out, cov[NCOVMAX];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   double **newm;      fu=(*f)(u); 
       if (fu <= fx) { 
   /* Hstepm could be zero and should return the unit matrix */        if (u >= x) a=x; else b=x; 
   for (i=1;i<=nlstate+ndeath;i++)        SHFT(v,w,x,u) 
     for (j=1;j<=nlstate+ndeath;j++){          SHFT(fv,fw,fx,fu) 
       oldm[i][j]=(i==j ? 1.0 : 0.0);          } else { 
       po[i][j][0]=(i==j ? 1.0 : 0.0);            if (u < x) a=u; else b=u; 
     }            if (fu <= fw || w == x) { 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */              v=w; 
   for(h=1; h <=nhstepm; h++){              w=u; 
     for(d=1; d <=hstepm; d++){              fv=fw; 
       newm=savm;              fw=fu; 
       /* Covariates have to be included here again */            } else if (fu <= fv || v == x || v == w) { 
       cov[1]=1.;              v=u; 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;              fv=fu; 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];            } 
       for (k=1; k<=cptcovage;k++)          } 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    } 
       for (k=1; k<=cptcovprod;k++)    nrerror("Too many iterations in brent"); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    *xmin=x; 
     return fx; 
   } 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  /****************** mnbrak ***********************/
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       savm=oldm;              double (*func)(double)) 
       oldm=newm;  { 
     }    double ulim,u,r,q, dum;
     for(i=1; i<=nlstate+ndeath; i++)    double fu; 
       for(j=1;j<=nlstate+ndeath;j++) {   
         po[i][j][h]=newm[i][j];    *fa=(*func)(*ax); 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    *fb=(*func)(*bx); 
          */    if (*fb > *fa) { 
       }      SHFT(dum,*ax,*bx,dum) 
   } /* end h */        SHFT(dum,*fb,*fa,dum) 
   return po;        } 
 }    *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
     while (*fb > *fc) { 
 /*************** log-likelihood *************/      r=(*bx-*ax)*(*fb-*fc); 
 double func( double *x)      q=(*bx-*cx)*(*fb-*fa); 
 {      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   int i, ii, j, k, mi, d, kk;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   double **out;      if ((*bx-u)*(u-*cx) > 0.0) { 
   double sw; /* Sum of weights */        fu=(*func)(u); 
   double lli; /* Individual log likelihood */      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   long ipmx;        fu=(*func)(u); 
   /*extern weight */        if (fu < *fc) { 
   /* We are differentiating ll according to initial status */          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/            SHFT(*fb,*fc,fu,(*func)(u)) 
   /*for(i=1;i<imx;i++)            } 
     printf(" %d\n",s[4][i]);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   */        u=ulim; 
   cov[1]=1.;        fu=(*func)(u); 
       } else { 
   for(k=1; k<=nlstate; k++) ll[k]=0.;        u=(*cx)+GOLD*(*cx-*bx); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        fu=(*func)(u); 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      } 
     for(mi=1; mi<= wav[i]-1; mi++){      SHFT(*ax,*bx,*cx,u) 
       for (ii=1;ii<=nlstate+ndeath;ii++)        SHFT(*fa,*fb,*fc,fu) 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        } 
       for(d=0; d<dh[mi][i]; d++){  } 
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  /*************** linmin ************************/
         for (kk=1; kk<=cptcovage;kk++) {  
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  int ncom; 
         }  double *pcom,*xicom;
          double (*nrfunc)(double []); 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,   
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         savm=oldm;  { 
         oldm=newm;    double brent(double ax, double bx, double cx, 
                         double (*f)(double), double tol, double *xmin); 
            double f1dim(double x); 
       } /* end mult */    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                      double *fc, double (*func)(double)); 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    int j; 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    double xx,xmin,bx,ax; 
       ipmx +=1;    double fx,fb,fa;
       sw += weight[i];   
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    ncom=n; 
     } /* end of wave */    pcom=vector(1,n); 
   } /* end of individual */    xicom=vector(1,n); 
     nrfunc=func; 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    for (j=1;j<=n;j++) { 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      pcom[j]=p[j]; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      xicom[j]=xi[j]; 
   return -l;    } 
 }    ax=0.0; 
     xx=1.0; 
     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
 /*********** Maximum Likelihood Estimation ***************/    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   #ifdef DEBUG
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 {    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   int i,j, iter;  #endif
   double **xi,*delti;    for (j=1;j<=n;j++) { 
   double fret;      xi[j] *= xmin; 
   xi=matrix(1,npar,1,npar);      p[j] += xi[j]; 
   for (i=1;i<=npar;i++)    } 
     for (j=1;j<=npar;j++)    free_vector(xicom,1,n); 
       xi[i][j]=(i==j ? 1.0 : 0.0);    free_vector(pcom,1,n); 
   printf("Powell\n");  } 
   powell(p,xi,npar,ftol,&iter,&fret,func);  
   char *asc_diff_time(long time_sec, char ascdiff[])
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  {
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    long sec_left, days, hours, minutes;
     days = (time_sec) / (60*60*24);
 }    sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
 /**** Computes Hessian and covariance matrix ***/    sec_left = (sec_left) %(60*60);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    minutes = (sec_left) /60;
 {    sec_left = (sec_left) % (60);
   double  **a,**y,*x,pd;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   double **hess;    return ascdiff;
   int i, j,jk;  }
   int *indx;  
   /*************** powell ************************/
   double hessii(double p[], double delta, int theta, double delti[]);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   double hessij(double p[], double delti[], int i, int j);              double (*func)(double [])) 
   void lubksb(double **a, int npar, int *indx, double b[]) ;  { 
   void ludcmp(double **a, int npar, int *indx, double *d) ;    void linmin(double p[], double xi[], int n, double *fret, 
                 double (*func)(double [])); 
   hess=matrix(1,npar,1,npar);    int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
   printf("\nCalculation of the hessian matrix. Wait...\n");    double fp,fptt;
   for (i=1;i<=npar;i++){    double *xits;
     printf("%d",i);fflush(stdout);    int niterf, itmp;
     hess[i][i]=hessii(p,ftolhess,i,delti);  
     /*printf(" %f ",p[i]);*/    pt=vector(1,n); 
     /*printf(" %lf ",hess[i][i]);*/    ptt=vector(1,n); 
   }    xit=vector(1,n); 
      xits=vector(1,n); 
   for (i=1;i<=npar;i++) {    *fret=(*func)(p); 
     for (j=1;j<=npar;j++)  {    for (j=1;j<=n;j++) pt[j]=p[j]; 
       if (j>i) {    for (*iter=1;;++(*iter)) { 
         printf(".%d%d",i,j);fflush(stdout);      fp=(*fret); 
         hess[i][j]=hessij(p,delti,i,j);      ibig=0; 
         hess[j][i]=hess[i][j];          del=0.0; 
         /*printf(" %lf ",hess[i][j]);*/      last_time=curr_time;
       }      (void) gettimeofday(&curr_time,&tzp);
     }      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);
   printf("\n");      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       */
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");     for (i=1;i<=n;i++) {
          printf(" %d %.12f",i, p[i]);
   a=matrix(1,npar,1,npar);        fprintf(ficlog," %d %.12lf",i, p[i]);
   y=matrix(1,npar,1,npar);        fprintf(ficrespow," %.12lf", p[i]);
   x=vector(1,npar);      }
   indx=ivector(1,npar);      printf("\n");
   for (i=1;i<=npar;i++)      fprintf(ficlog,"\n");
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];      fprintf(ficrespow,"\n");fflush(ficrespow);
   ludcmp(a,npar,indx,&pd);      if(*iter <=3){
         tm = *localtime(&curr_time.tv_sec);
   for (j=1;j<=npar;j++) {        strcpy(strcurr,asctime(&tm));
     for (i=1;i<=npar;i++) x[i]=0;  /*       asctime_r(&tm,strcurr); */
     x[j]=1;        forecast_time=curr_time; 
     lubksb(a,npar,indx,x);        itmp = strlen(strcurr);
     for (i=1;i<=npar;i++){        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
       matcov[i][j]=x[i];          strcurr[itmp-1]='\0';
     }        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   }        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         for(niterf=10;niterf<=30;niterf+=10){
   printf("\n#Hessian matrix#\n");          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   for (i=1;i<=npar;i++) {          tmf = *localtime(&forecast_time.tv_sec);
     for (j=1;j<=npar;j++) {  /*      asctime_r(&tmf,strfor); */
       printf("%.3e ",hess[i][j]);          strcpy(strfor,asctime(&tmf));
     }          itmp = strlen(strfor);
     printf("\n");          if(strfor[itmp-1]=='\n')
   }          strfor[itmp-1]='\0';
           printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
   /* Recompute Inverse */          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 (i=1;i<=npar;i++)        }
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      }
   ludcmp(a,npar,indx,&pd);      for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   /*  printf("\n#Hessian matrix recomputed#\n");        fptt=(*fret); 
   #ifdef DEBUG
   for (j=1;j<=npar;j++) {        printf("fret=%lf \n",*fret);
     for (i=1;i<=npar;i++) x[i]=0;        fprintf(ficlog,"fret=%lf \n",*fret);
     x[j]=1;  #endif
     lubksb(a,npar,indx,x);        printf("%d",i);fflush(stdout);
     for (i=1;i<=npar;i++){        fprintf(ficlog,"%d",i);fflush(ficlog);
       y[i][j]=x[i];        linmin(p,xit,n,fret,func); 
       printf("%.3e ",y[i][j]);        if (fabs(fptt-(*fret)) > del) { 
     }          del=fabs(fptt-(*fret)); 
     printf("\n");          ibig=i; 
   }        } 
   */  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
   free_matrix(a,1,npar,1,npar);        fprintf(ficlog,"%d %.12e",i,(*fret));
   free_matrix(y,1,npar,1,npar);        for (j=1;j<=n;j++) {
   free_vector(x,1,npar);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   free_ivector(indx,1,npar);          printf(" x(%d)=%.12e",j,xit[j]);
   free_matrix(hess,1,npar,1,npar);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         }
         for(j=1;j<=n;j++) {
 }          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
 /*************** hessian matrix ****************/        }
 double hessii( double x[], double delta, int theta, double delti[])        printf("\n");
 {        fprintf(ficlog,"\n");
   int i;  #endif
   int l=1, lmax=20;      } 
   double k1,k2;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   double p2[NPARMAX+1];  #ifdef DEBUG
   double res;        int k[2],l;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        k[0]=1;
   double fx;        k[1]=-1;
   int k=0,kmax=10;        printf("Max: %.12e",(*func)(p));
   double l1;        fprintf(ficlog,"Max: %.12e",(*func)(p));
         for (j=1;j<=n;j++) {
   fx=func(x);          printf(" %.12e",p[j]);
   for (i=1;i<=npar;i++) p2[i]=x[i];          fprintf(ficlog," %.12e",p[j]);
   for(l=0 ; l <=lmax; l++){        }
     l1=pow(10,l);        printf("\n");
     delts=delt;        fprintf(ficlog,"\n");
     for(k=1 ; k <kmax; k=k+1){        for(l=0;l<=1;l++) {
       delt = delta*(l1*k);          for (j=1;j<=n;j++) {
       p2[theta]=x[theta] +delt;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       k1=func(p2)-fx;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       p2[theta]=x[theta]-delt;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       k2=func(p2)-fx;          }
       /*res= (k1-2.0*fx+k2)/delt/delt; */          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
              }
 #ifdef DEBUG  #endif
       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  
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        free_vector(xit,1,n); 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        free_vector(xits,1,n); 
         k=kmax;        free_vector(ptt,1,n); 
       }        free_vector(pt,1,n); 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        return; 
         k=kmax; l=lmax*10.;      } 
       }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      for (j=1;j<=n;j++) { 
         delts=delt;        ptt[j]=2.0*p[j]-pt[j]; 
       }        xit[j]=p[j]-pt[j]; 
     }        pt[j]=p[j]; 
   }      } 
   delti[theta]=delts;      fptt=(*func)(ptt); 
   return res;      if (fptt < fp) { 
          t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
 }        if (t < 0.0) { 
           linmin(p,xit,n,fret,func); 
 double hessij( double x[], double delti[], int thetai,int thetaj)          for (j=1;j<=n;j++) { 
 {            xi[j][ibig]=xi[j][n]; 
   int i;            xi[j][n]=xit[j]; 
   int l=1, l1, lmax=20;          }
   double k1,k2,k3,k4,res,fx;  #ifdef DEBUG
   double p2[NPARMAX+1];          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   int k;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           for(j=1;j<=n;j++){
   fx=func(x);            printf(" %.12e",xit[j]);
   for (k=1; k<=2; k++) {            fprintf(ficlog," %.12e",xit[j]);
     for (i=1;i<=npar;i++) p2[i]=x[i];          }
     p2[thetai]=x[thetai]+delti[thetai]/k;          printf("\n");
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          fprintf(ficlog,"\n");
     k1=func(p2)-fx;  #endif
          }
     p2[thetai]=x[thetai]+delti[thetai]/k;      } 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    } 
     k2=func(p2)-fx;  } 
    
     p2[thetai]=x[thetai]-delti[thetai]/k;  /**** Prevalence limit (stable prevalence)  ****************/
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k3=func(p2)-fx;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
    {
     p2[thetai]=x[thetai]-delti[thetai]/k;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;       matrix by transitions matrix until convergence is reached */
     k4=func(p2)-fx;  
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    int i, ii,j,k;
 #ifdef DEBUG    double min, max, maxmin, maxmax,sumnew=0.;
     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);    double **matprod2();
 #endif    double **out, cov[NCOVMAX], **pmij();
   }    double **newm;
   return res;    double agefin, delaymax=50 ; /* Max number of years to converge */
 }  
     for (ii=1;ii<=nlstate+ndeath;ii++)
 /************** Inverse of matrix **************/      for (j=1;j<=nlstate+ndeath;j++){
 void ludcmp(double **a, int n, int *indx, double *d)        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 {      }
   int i,imax,j,k;  
   double big,dum,sum,temp;     cov[1]=1.;
   double *vv;   
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   vv=vector(1,n);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   *d=1.0;      newm=savm;
   for (i=1;i<=n;i++) {      /* Covariates have to be included here again */
     big=0.0;       cov[2]=agefin;
     for (j=1;j<=n;j++)    
       if ((temp=fabs(a[i][j])) > big) big=temp;        for (k=1; k<=cptcovn;k++) {
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     vv[i]=1.0/big;          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
   }        }
   for (j=1;j<=n;j++) {        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for (i=1;i<j;i++) {        for (k=1; k<=cptcovprod;k++)
       sum=a[i][j];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;        /*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]);*/
     big=0.0;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     for (i=j;i<=n;i++) {      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       sum=a[i][j];  
       for (k=1;k<j;k++)      savm=oldm;
         sum -= a[i][k]*a[k][j];      oldm=newm;
       a[i][j]=sum;      maxmax=0.;
       if ( (dum=vv[i]*fabs(sum)) >= big) {      for(j=1;j<=nlstate;j++){
         big=dum;        min=1.;
         imax=i;        max=0.;
       }        for(i=1; i<=nlstate; i++) {
     }          sumnew=0;
     if (j != imax) {          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       for (k=1;k<=n;k++) {          prlim[i][j]= newm[i][j]/(1-sumnew);
         dum=a[imax][k];          max=FMAX(max,prlim[i][j]);
         a[imax][k]=a[j][k];          min=FMIN(min,prlim[i][j]);
         a[j][k]=dum;        }
       }        maxmin=max-min;
       *d = -(*d);        maxmax=FMAX(maxmax,maxmin);
       vv[imax]=vv[j];      }
     }      if(maxmax < ftolpl){
     indx[j]=imax;        return prlim;
     if (a[j][j] == 0.0) a[j][j]=TINY;      }
     if (j != n) {    }
       dum=1.0/(a[j][j]);  }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }  /*************** transition probabilities ***************/ 
   }  
   free_vector(vv,1,n);  /* Doesn't work */  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 ;  {
 }    double s1, s2;
     /*double t34;*/
 void lubksb(double **a, int n, int *indx, double b[])    int i,j,j1, nc, ii, jj;
 {  
   int i,ii=0,ip,j;      for(i=1; i<= nlstate; i++){
   double sum;        for(j=1; j<i;j++){
            for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   for (i=1;i<=n;i++) {            /*s2 += param[i][j][nc]*cov[nc];*/
     ip=indx[i];            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     sum=b[ip];  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
     b[ip]=b[i];          }
     if (ii)          ps[i][j]=s2;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
     else if (sum) ii=i;        }
     b[i]=sum;        for(j=i+1; j<=nlstate+ndeath;j++){
   }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   for (i=n;i>=1;i--) {            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     sum=b[i];  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          }
     b[i]=sum/a[i][i];          ps[i][j]=s2;
   }        }
 }      }
       /*ps[3][2]=1;*/
 /************ Frequencies ********************/      
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2)      for(i=1; i<= nlstate; i++){
 {  /* Some frequencies */        s1=0;
          for(j=1; j<i; j++)
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          s1+=exp(ps[i][j]);
   double ***freq; /* Frequencies */        for(j=i+1; j<=nlstate+ndeath; j++)
   double *pp;          s1+=exp(ps[i][j]);
   double pos, k2, dateintsum=0,k2cpt=0;        ps[i][i]=1./(s1+1.);
   FILE *ficresp;        for(j=1; j<i; j++)
   char fileresp[FILENAMELENGTH];          ps[i][j]= exp(ps[i][j])*ps[i][i];
         for(j=i+1; j<=nlstate+ndeath; j++)
   pp=vector(1,nlstate);          ps[i][j]= exp(ps[i][j])*ps[i][i];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   strcpy(fileresp,"p");      } /* end i */
   strcat(fileresp,fileres);      
   if((ficresp=fopen(fileresp,"w"))==NULL) {      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     printf("Problem with prevalence resultfile: %s\n", fileresp);        for(jj=1; jj<= nlstate+ndeath; jj++){
     exit(0);          ps[ii][jj]=0;
   }          ps[ii][ii]=1;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        }
   j1=0;      }
       
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   for(k1=1; k1<=j;k1++){  /*         printf("ddd %lf ",ps[ii][jj]); */
    for(i1=1; i1<=ncodemax[k1];i1++){  /*       } */
        j1++;  /*       printf("\n "); */
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  /*        } */
          scanf("%d", i);*/  /*        printf("\n ");printf("%lf ",cov[2]); */
         for (i=-1; i<=nlstate+ndeath; i++)           /*
          for (jk=-1; jk<=nlstate+ndeath; jk++)          for(i=1; i<= npar; i++) printf("%f ",x[i]);
            for(m=agemin; m <= agemax+3; m++)        goto end;*/
              freq[i][jk][m]=0;      return ps;
   }
         dateintsum=0;  
         k2cpt=0;  /**************** Product of 2 matrices ******************/
        for (i=1; i<=imx; i++) {  
          bool=1;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
          if  (cptcovn>0) {  {
            for (z1=1; z1<=cptcoveff; z1++)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
                bool=0;    /* in, b, out are matrice of pointers which should have been initialized 
          }       before: only the contents of out is modified. The function returns
          if (bool==1) {       a pointer to pointers identical to out */
            for(m=firstpass; m<=lastpass; m++){    long i, j, k;
              k2=anint[m][i]+(mint[m][i]/12.);    for(i=nrl; i<= nrh; i++)
              if ((k2>=dateprev1) && (k2<=dateprev2)) {      for(k=ncolol; k<=ncoloh; k++)
                if(agev[m][i]==0) agev[m][i]=agemax+1;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
                if(agev[m][i]==1) agev[m][i]=agemax+2;          out[i][k] +=in[i][j]*b[j][k];
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    return out;
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  }
                  dateintsum=dateintsum+k2;  
                  k2cpt++;  
                }  /************* Higher Matrix Product ***************/
   
              }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
            }  {
          }    /* Computes the transition matrix starting at age 'age' over 
        }       'nhstepm*hstepm*stepm' months (i.e. until
         if  (cptcovn>0) {       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
          fprintf(ficresp, "\n#********** Variable ");       nhstepm*hstepm matrices. 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        fprintf(ficresp, "**********\n#");       (typically every 2 years instead of every month which is too big 
         }       for the memory).
        for(i=1; i<=nlstate;i++)       Model is determined by parameters x and covariates have to be 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);       included manually here. 
        fprintf(ficresp, "\n");  
               */
   for(i=(int)agemin; i <= (int)agemax+3; i++){  
     if(i==(int)agemax+3)    int i, j, d, h, k;
       printf("Total");    double **out, cov[NCOVMAX];
     else    double **newm;
       printf("Age %d", i);  
     for(jk=1; jk <=nlstate ; jk++){    /* Hstepm could be zero and should return the unit matrix */
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    for (i=1;i<=nlstate+ndeath;i++)
         pp[jk] += freq[jk][m][i];      for (j=1;j<=nlstate+ndeath;j++){
     }        oldm[i][j]=(i==j ? 1.0 : 0.0);
     for(jk=1; jk <=nlstate ; jk++){        po[i][j][0]=(i==j ? 1.0 : 0.0);
       for(m=-1, pos=0; m <=0 ; m++)      }
         pos += freq[jk][m][i];    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       if(pp[jk]>=1.e-10)    for(h=1; h <=nhstepm; h++){
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      for(d=1; d <=hstepm; d++){
       else        newm=savm;
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        /* Covariates have to be included here again */
     }        cov[1]=1.;
         cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
      for(jk=1; jk <=nlstate ; jk++){        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        for (k=1; k<=cptcovage;k++)
         pp[jk] += freq[jk][m][i];          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
      }        for (k=1; k<=cptcovprod;k++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     for(jk=1,pos=0; jk <=nlstate ; jk++)  
       pos += pp[jk];  
     for(jk=1; jk <=nlstate ; jk++){        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       if(pos>=1.e-5)        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       else                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        savm=oldm;
       if( i <= (int) agemax){        oldm=newm;
         if(pos>=1.e-5){      }
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      for(i=1; i<=nlstate+ndeath; i++)
           probs[i][jk][j1]= pp[jk]/pos;        for(j=1;j<=nlstate+ndeath;j++) {
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          po[i][j][h]=newm[i][j];
         }          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       else           */
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        }
       }    } /* end h */
     }    return po;
     for(jk=-1; jk <=nlstate+ndeath; jk++)  }
       for(m=-1; m <=nlstate+ndeath; m++)  
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  
     if(i <= (int) agemax)  /*************** log-likelihood *************/
       fprintf(ficresp,"\n");  double func( double *x)
     printf("\n");  {
     }    int i, ii, j, k, mi, d, kk;
     }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
  }    double **out;
   dateintmean=dateintsum/k2cpt;    double sw; /* Sum of weights */
      double lli; /* Individual log likelihood */
   fclose(ficresp);    int s1, s2;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    double bbh, survp;
   free_vector(pp,1,nlstate);    long ipmx;
     /*extern weight */
   /* End of Freq */    /* We are differentiating ll according to initial status */
 }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
 /************ Prevalence ********************/      printf(" %d\n",s[4][i]);
 void prevalence(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 calagedate)    */
 {  /* Some frequencies */    cov[1]=1.;
    
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   double ***freq; /* Frequencies */  
   double *pp;    if(mle==1){
   double pos, k2;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   pp=vector(1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   j1=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
   j=cptcoveff;          for(d=0; d<dh[mi][i]; d++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
  for(k1=1; k1<=j;k1++){            for (kk=1; kk<=cptcovage;kk++) {
     for(i1=1; i1<=ncodemax[k1];i1++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       j1++;            }
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for (i=-1; i<=nlstate+ndeath; i++)                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         for (jk=-1; jk<=nlstate+ndeath; jk++)              savm=oldm;
           for(m=agemin; m <= agemax+3; m++)            oldm=newm;
             freq[i][jk][m]=0;          } /* end mult */
              
       for (i=1; i<=imx; i++) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         bool=1;          /* But now since version 0.9 we anticipate for bias at large stepm.
         if  (cptcovn>0) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
           for (z1=1; z1<=cptcoveff; z1++)           * (in months) between two waves is not a multiple of stepm, we rounded to 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])           * the nearest (and in case of equal distance, to the lowest) interval but now
               bool=0;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         }           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         if (bool==1) {           * probability in order to take into account the bias as a fraction of the way
           for(m=firstpass; m<=lastpass; m++){           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
             k2=anint[m][i]+(mint[m][i]/12.);           * -stepm/2 to stepm/2 .
             if ((k2>=dateprev1) && (k2<=dateprev2)) {           * For stepm=1 the results are the same as for previous versions of Imach.
               if(agev[m][i]==0) agev[m][i]=agemax+1;           * For stepm > 1 the results are less biased than in previous versions. 
               if(agev[m][i]==1) agev[m][i]=agemax+2;           */
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          s1=s[mw[mi][i]][i];
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];            s2=s[mw[mi+1][i]][i];
             }          bbh=(double)bh[mi][i]/(double)stepm; 
           }          /* bias bh is positive if real duration
         }           * is higher than the multiple of stepm and negative otherwise.
       }           */
                /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         for(i=(int)agemin; i <= (int)agemax+3; i++){          if( s2 > nlstate){ 
           for(jk=1; jk <=nlstate ; jk++){            /* i.e. if s2 is a death state and if the date of death is known 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)               then the contribution to the likelihood is the probability to 
               pp[jk] += freq[jk][m][i];               die between last step unit time and current  step unit time, 
           }               which is also equal to probability to die before dh 
           for(jk=1; jk <=nlstate ; jk++){               minus probability to die before dh-stepm . 
             for(m=-1, pos=0; m <=0 ; m++)               In version up to 0.92 likelihood was computed
             pos += freq[jk][m][i];          as if date of death was unknown. Death was treated as any other
         }          health state: the date of the interview describes the actual state
                  and not the date of a change in health state. The former idea was
          for(jk=1; jk <=nlstate ; jk++){          to consider that at each interview the state was recorded
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          (healthy, disable or death) and IMaCh was corrected; but when we
              pp[jk] += freq[jk][m][i];          introduced the exact date of death then we should have modified
          }          the contribution of an exact death to the likelihood. This new
                    contribution is smaller and very dependent of the step unit
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          stepm. It is no more the probability to die between last interview
           and month of death but the probability to survive from last
          for(jk=1; jk <=nlstate ; jk++){                    interview up to one month before death multiplied by the
            if( i <= (int) agemax){          probability to die within a month. Thanks to Chris
              if(pos>=1.e-5){          Jackson for correcting this bug.  Former versions increased
                probs[i][jk][j1]= pp[jk]/pos;          mortality artificially. The bad side is that we add another loop
              }          which slows down the processing. The difference can be up to 10%
            }          lower mortality.
          }            */
                      lli=log(out[s1][s2] - savm[s1][s2]);
         }  
     }  
   }          } else if  (s2==-2) {
              for (j=1,survp=0. ; j<=nlstate; j++) 
                survp += out[s1][j];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            lli= survp;
   free_vector(pp,1,nlstate);          }
            
 }  /* End of Freq */          else if  (s2==-4) {
             for (j=3,survp=0. ; j<=nlstate; j++) 
 /************* Waves Concatenation ***************/              survp += out[s1][j];
             lli= survp;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          }
 {          
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          else if  (s2==-5) {
      Death is a valid wave (if date is known).            for (j=1,survp=0. ; j<=2; j++) 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i              survp += out[s1][j];
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            lli= survp;
      and mw[mi+1][i]. dh depends on stepm.          }
      */  
   
   int i, mi, m;          else{
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
      double sum=0., jmean=0.;*/            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
           } 
   int j, k=0,jk, ju, jl;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double sum=0.;          /*if(lli ==000.0)*/
   jmin=1e+5;          /*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); */
   jmax=-1;          ipmx +=1;
   jmean=0.;          sw += weight[i];
   for(i=1; i<=imx; i++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     mi=0;        } /* end of wave */
     m=firstpass;      } /* end of individual */
     while(s[m][i] <= nlstate){    }  else if(mle==2){
       if(s[m][i]>=1)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         mw[++mi][i]=m;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       if(m >=lastpass)        for(mi=1; mi<= wav[i]-1; mi++){
         break;          for (ii=1;ii<=nlstate+ndeath;ii++)
       else            for (j=1;j<=nlstate+ndeath;j++){
         m++;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }/* end while */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (s[m][i] > nlstate){            }
       mi++;     /* Death is another wave */          for(d=0; d<=dh[mi][i]; d++){
       /* if(mi==0)  never been interviewed correctly before death */            newm=savm;
          /* Only death is a correct wave */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       mw[mi][i]=m;            for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
     wav[i]=mi;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     if(mi==0)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            savm=oldm;
   }            oldm=newm;
           } /* end mult */
   for(i=1; i<=imx; i++){        
     for(mi=1; mi<wav[i];mi++){          s1=s[mw[mi][i]][i];
       if (stepm <=0)          s2=s[mw[mi+1][i]][i];
         dh[mi][i]=1;          bbh=(double)bh[mi][i]/(double)stepm; 
       else{          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         if (s[mw[mi+1][i]][i] > nlstate) {          ipmx +=1;
           if (agedc[i] < 2*AGESUP) {          sw += weight[i];
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           if(j==0) j=1;  /* Survives at least one month after exam */        } /* end of wave */
           k=k+1;      } /* end of individual */
           if (j >= jmax) jmax=j;    }  else if(mle==3){  /* exponential inter-extrapolation */
           if (j <= jmin) jmin=j;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           sum=sum+j;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           /* if (j<10) printf("j=%d num=%d ",j,i); */        for(mi=1; mi<= wav[i]-1; mi++){
           }          for (ii=1;ii<=nlstate+ndeath;ii++)
         }            for (j=1;j<=nlstate+ndeath;j++){
         else{              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           k=k+1;            }
           if (j >= jmax) jmax=j;          for(d=0; d<dh[mi][i]; d++){
           else if (j <= jmin)jmin=j;            newm=savm;
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           sum=sum+j;            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         jk= j/stepm;            }
         jl= j -jk*stepm;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         ju= j -(jk+1)*stepm;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if(jl <= -ju)            savm=oldm;
           dh[mi][i]=jk;            oldm=newm;
         else          } /* end mult */
           dh[mi][i]=jk+1;        
         if(dh[mi][i]==0)          s1=s[mw[mi][i]][i];
           dh[mi][i]=1; /* At least one step */          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;
   jmean=sum/k;          sw += weight[i];
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
  }        } /* end of wave */
 /*********** Tricode ****************************/      } /* end of individual */
 void tricode(int *Tvar, int **nbcode, int imx)    }else if (mle==4){  /* ml=4 no inter-extrapolation */
 {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int Ndum[20],ij=1, k, j, i;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int cptcode=0;        for(mi=1; mi<= wav[i]-1; mi++){
   cptcoveff=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   for (k=0; k<19; k++) Ndum[k]=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (k=1; k<=7; k++) ncodemax[k]=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          for(d=0; d<dh[mi][i]; d++){
     for (i=1; i<=imx; i++) {            newm=savm;
       ij=(int)(covar[Tvar[j]][i]);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       Ndum[ij]++;            for (kk=1; kk<=cptcovage;kk++) {
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       if (ij > cptcode) cptcode=ij;            }
     }          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for (i=0; i<=cptcode; i++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       if(Ndum[i]!=0) ncodemax[j]++;            savm=oldm;
     }            oldm=newm;
     ij=1;          } /* end mult */
         
           s1=s[mw[mi][i]][i];
     for (i=1; i<=ncodemax[j]; i++) {          s2=s[mw[mi+1][i]][i];
       for (k=0; k<=19; k++) {          if( s2 > nlstate){ 
         if (Ndum[k] != 0) {            lli=log(out[s1][s2] - savm[s1][s2]);
           nbcode[Tvar[j]][ij]=k;          }else{
           ij++;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         }          }
         if (ij > ncodemax[j]) break;          ipmx +=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]); */
         } /* end of wave */
  for (k=0; k<19; k++) Ndum[k]=0;      } /* end of individual */
     }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
  for (i=1; i<=ncovmodel-2; i++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       ij=Tvar[i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       Ndum[ij]++;        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
  ij=1;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  for (i=1; i<=10; i++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
    if((Ndum[i]!=0) && (i<=ncov)){            }
      Tvaraff[ij]=i;          for(d=0; d<dh[mi][i]; d++){
      ij++;            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];
     cptcoveff=ij-1;            }
 }          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 /*********** Health Expectancies ****************/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)            oldm=newm;
 {          } /* end mult */
   /* Health expectancies */        
   int i, j, nhstepm, hstepm, h;          s1=s[mw[mi][i]][i];
   double age, agelim,hf;          s2=s[mw[mi+1][i]][i];
   double ***p3mat;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
            ipmx +=1;
   fprintf(ficreseij,"# Health expectancies\n");          sw += weight[i];
   fprintf(ficreseij,"# Age");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for(i=1; i<=nlstate;i++)          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
     for(j=1; j<=nlstate;j++)        } /* end of wave */
       fprintf(ficreseij," %1d-%1d",i,j);      } /* end of individual */
   fprintf(ficreseij,"\n");    } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   hstepm=1*YEARM; /*  Every j years of age (in month) */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     return -l;
   agelim=AGESUP;  }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     /* nhstepm age range expressed in number of stepm */  /*************** log-likelihood *************/
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);  double funcone( double *x)
     /* Typically if 20 years = 20*12/6=40 stepm */  {
     if (stepm >= YEARM) hstepm=1;    /* Same as likeli but slower because of a lot of printf and if */
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */    int i, ii, j, k, mi, d, kk;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    double **out;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    double lli; /* Individual log likelihood */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      double llt;
     int s1, s2;
     double bbh, survp;
     for(i=1; i<=nlstate;i++)    /*extern weight */
       for(j=1; j<=nlstate;j++)    /* We are differentiating ll according to initial status */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           eij[i][j][(int)age] +=p3mat[i][j][h];    /*for(i=1;i<imx;i++) 
         }      printf(" %d\n",s[4][i]);
        */
     hf=1;    cov[1]=1.;
     if (stepm >= YEARM) hf=stepm/YEARM;  
     fprintf(ficreseij,"%.0f",age );    for(k=1; k<=nlstate; k++) ll[k]=0.;
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       }      for(mi=1; mi<= wav[i]-1; mi++){
     fprintf(ficreseij,"\n");        for (ii=1;ii<=nlstate+ndeath;ii++)
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (j=1;j<=nlstate+ndeath;j++){
   }            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
 /************ Variance ******************/        for(d=0; d<dh[mi][i]; d++){
 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)          newm=savm;
 {          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /* Variance of health expectancies */          for (kk=1; kk<=cptcovage;kk++) {
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double **newm;          }
   double **dnewm,**doldm;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int i, j, nhstepm, hstepm, h;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int k, cptcode;          savm=oldm;
   double *xp;          oldm=newm;
   double **gp, **gm;        } /* end mult */
   double ***gradg, ***trgradg;        
   double ***p3mat;        s1=s[mw[mi][i]][i];
   double age,agelim;        s2=s[mw[mi+1][i]][i];
   int theta;        bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
    fprintf(ficresvij,"# Covariances of life expectancies\n");         * is higher than the multiple of stepm and negative otherwise.
   fprintf(ficresvij,"# Age");         */
   for(i=1; i<=nlstate;i++)        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     for(j=1; j<=nlstate;j++)          lli=log(out[s1][s2] - savm[s1][s2]);
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        } else if (mle==1){
   fprintf(ficresvij,"\n");          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
   xp=vector(1,npar);          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 */
   dnewm=matrix(1,nlstate,1,npar);        } else if(mle==3){  /* exponential inter-extrapolation */
   doldm=matrix(1,nlstate,1,nlstate);          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
          } else if (mle==4){  /* mle=4 no inter-extrapolation */
   hstepm=1*YEARM; /* Every year of age */          lli=log(out[s1][s2]); /* Original formula */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   agelim = AGESUP;          lli=log(out[s1][s2]); /* Original formula */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        } /* End of if */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        ipmx +=1;
     if (stepm >= YEARM) hstepm=1;        sw += weight[i];
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*       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]); */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        if(globpr){
     gp=matrix(0,nhstepm,1,nlstate);          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
     gm=matrix(0,nhstepm,1,nlstate);   %10.6f %10.6f %10.6f ", \
                   num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     for(theta=1; theta <=npar; theta++){                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
       for(i=1; i<=npar; i++){ /* Computes gradient */          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            llt +=ll[k]*gipmx/gsw;
       }            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          fprintf(ficresilk," %10.6f\n", -llt);
         }
       if (popbased==1) {      } /* end of wave */
         for(i=1; i<=nlstate;i++)    } /* end of individual */
           prlim[i][i]=probs[(int)age][i][ij];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
          l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       for(j=1; j<= nlstate; j++){    if(globpr==0){ /* First time we count the contributions and weights */
         for(h=0; h<=nhstepm; h++){      gipmx=ipmx;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      gsw=sw;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    }
         }    return -l;
       }  }
      
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  /*************** function likelione ***********/
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  {
     /* This routine should help understanding what is done with 
       if (popbased==1) {       the selection of individuals/waves and
         for(i=1; i<=nlstate;i++)       to check the exact contribution to the likelihood.
           prlim[i][i]=probs[(int)age][i][ij];       Plotting could be done.
       }     */
     int k;
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){    if(*globpri !=0){ /* Just counts and sums, no printings */
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      strcpy(fileresilk,"ilk"); 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      strcat(fileresilk,fileres);
         }      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       }        printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       for(j=1; j<= nlstate; j++)      }
         for(h=0; h<=nhstepm; h++){      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");
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
         }      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     } /* End theta */      for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
     for(h=0; h<=nhstepm; h++)  
       for(j=1; j<=nlstate;j++)    *fretone=(*funcone)(p);
         for(theta=1; theta <=npar; theta++)    if(*globpri !=0){
           trgradg[h][j][theta]=gradg[h][theta][j];      fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     for(i=1;i<=nlstate;i++)      fflush(fichtm); 
       for(j=1;j<=nlstate;j++)    } 
         vareij[i][j][(int)age] =0.;    return;
     for(h=0;h<=nhstepm;h++){  }
       for(k=0;k<=nhstepm;k++){  
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);  
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  /*********** Maximum Likelihood Estimation ***************/
         for(i=1;i<=nlstate;i++)  
           for(j=1;j<=nlstate;j++)  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
             vareij[i][j][(int)age] += doldm[i][j];  {
       }    int i,j, iter;
     }    double **xi;
     h=1;    double fret;
     if (stepm >= YEARM) h=stepm/YEARM;    double fretone; /* Only one call to likelihood */
     fprintf(ficresvij,"%.0f ",age );    /*  char filerespow[FILENAMELENGTH];*/
     for(i=1; i<=nlstate;i++)    xi=matrix(1,npar,1,npar);
       for(j=1; j<=nlstate;j++){    for (i=1;i<=npar;i++)
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);      for (j=1;j<=npar;j++)
       }        xi[i][j]=(i==j ? 1.0 : 0.0);
     fprintf(ficresvij,"\n");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     free_matrix(gp,0,nhstepm,1,nlstate);    strcpy(filerespow,"pow"); 
     free_matrix(gm,0,nhstepm,1,nlstate);    strcat(filerespow,fileres);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      printf("Problem with resultfile: %s\n", filerespow);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   } /* End age */    }
      fprintf(ficrespow,"# Powell\n# iter -2*LL");
   free_vector(xp,1,npar);    for (i=1;i<=nlstate;i++)
   free_matrix(doldm,1,nlstate,1,npar);      for(j=1;j<=nlstate+ndeath;j++)
   free_matrix(dnewm,1,nlstate,1,nlstate);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     fprintf(ficrespow,"\n");
 }  
     powell(p,xi,npar,ftol,&iter,&fret,func);
 /************ Variance of prevlim ******************/  
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    fclose(ficrespow);
 {    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   /* Variance of prevalence limit */    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double **newm;  
   double **dnewm,**doldm;  }
   int i, j, nhstepm, hstepm;  
   int k, cptcode;  /**** Computes Hessian and covariance matrix ***/
   double *xp;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   double *gp, *gm;  {
   double **gradg, **trgradg;    double  **a,**y,*x,pd;
   double age,agelim;    double **hess;
   int theta;    int i, j,jk;
        int *indx;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");  
   fprintf(ficresvpl,"# Age");    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   for(i=1; i<=nlstate;i++)    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
       fprintf(ficresvpl," %1d-%1d",i,i);    void lubksb(double **a, int npar, int *indx, double b[]) ;
   fprintf(ficresvpl,"\n");    void ludcmp(double **a, int npar, int *indx, double *d) ;
     double gompertz(double p[]);
   xp=vector(1,npar);    hess=matrix(1,npar,1,npar);
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);    printf("\nCalculation of the hessian matrix. Wait...\n");
      fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   hstepm=1*YEARM; /* Every year of age */    for (i=1;i<=npar;i++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      printf("%d",i);fflush(stdout);
   agelim = AGESUP;      fprintf(ficlog,"%d",i);fflush(ficlog);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */     
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     if (stepm >= YEARM) hstepm=1;      
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      /*  printf(" %f ",p[i]);
     gradg=matrix(1,npar,1,nlstate);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     gp=vector(1,nlstate);    }
     gm=vector(1,nlstate);    
     for (i=1;i<=npar;i++) {
     for(theta=1; theta <=npar; theta++){      for (j=1;j<=npar;j++)  {
       for(i=1; i<=npar; i++){ /* Computes gradient */        if (j>i) { 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          printf(".%d%d",i,j);fflush(stdout);
       }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          hess[i][j]=hessij(p,delti,i,j,func,npar);
       for(i=1;i<=nlstate;i++)          
         gp[i] = prlim[i][i];          hess[j][i]=hess[i][j];    
              /*printf(" %lf ",hess[i][j]);*/
       for(i=1; i<=npar; i++) /* Computes gradient */        }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    }
       for(i=1;i<=nlstate;i++)    printf("\n");
         gm[i] = prlim[i][i];    fprintf(ficlog,"\n");
   
       for(i=1;i<=nlstate;i++)    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     } /* End theta */    
     a=matrix(1,npar,1,npar);
     trgradg =matrix(1,nlstate,1,npar);    y=matrix(1,npar,1,npar);
     x=vector(1,npar);
     for(j=1; j<=nlstate;j++)    indx=ivector(1,npar);
       for(theta=1; theta <=npar; theta++)    for (i=1;i<=npar;i++)
         trgradg[j][theta]=gradg[theta][j];      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     ludcmp(a,npar,indx,&pd);
     for(i=1;i<=nlstate;i++)  
       varpl[i][(int)age] =0.;    for (j=1;j<=npar;j++) {
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      for (i=1;i<=npar;i++) x[i]=0;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      x[j]=1;
     for(i=1;i<=nlstate;i++)      lubksb(a,npar,indx,x);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
     fprintf(ficresvpl,"%.0f ",age );      }
     for(i=1; i<=nlstate;i++)    }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  
     fprintf(ficresvpl,"\n");    printf("\n#Hessian matrix#\n");
     free_vector(gp,1,nlstate);    fprintf(ficlog,"\n#Hessian matrix#\n");
     free_vector(gm,1,nlstate);    for (i=1;i<=npar;i++) { 
     free_matrix(gradg,1,npar,1,nlstate);      for (j=1;j<=npar;j++) { 
     free_matrix(trgradg,1,nlstate,1,npar);        printf("%.3e ",hess[i][j]);
   } /* End age */        fprintf(ficlog,"%.3e ",hess[i][j]);
       }
   free_vector(xp,1,npar);      printf("\n");
   free_matrix(doldm,1,nlstate,1,npar);      fprintf(ficlog,"\n");
   free_matrix(dnewm,1,nlstate,1,nlstate);    }
   
 }    /* Recompute Inverse */
     for (i=1;i<=npar;i++)
 /************ Variance of one-step probabilities  ******************/      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    ludcmp(a,npar,indx,&pd);
 {  
   int i, j;    /*  printf("\n#Hessian matrix recomputed#\n");
   int k=0, cptcode;  
   double **dnewm,**doldm;    for (j=1;j<=npar;j++) {
   double *xp;      for (i=1;i<=npar;i++) x[i]=0;
   double *gp, *gm;      x[j]=1;
   double **gradg, **trgradg;      lubksb(a,npar,indx,x);
   double age,agelim, cov[NCOVMAX];      for (i=1;i<=npar;i++){ 
   int theta;        y[i][j]=x[i];
   char fileresprob[FILENAMELENGTH];        printf("%.3e ",y[i][j]);
         fprintf(ficlog,"%.3e ",y[i][j]);
   strcpy(fileresprob,"prob");      }
   strcat(fileresprob,fileres);      printf("\n");
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      fprintf(ficlog,"\n");
     printf("Problem with resultfile: %s\n", fileresprob);    }
   }    */
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);  
      free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
   xp=vector(1,npar);    free_vector(x,1,npar);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    free_ivector(indx,1,npar);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    free_matrix(hess,1,npar,1,npar);
    
   cov[1]=1;  
   for (age=bage; age<=fage; age ++){  }
     cov[2]=age;  
     gradg=matrix(1,npar,1,9);  /*************** hessian matrix ****************/
     trgradg=matrix(1,9,1,npar);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  {
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    int i;
        int l=1, lmax=20;
     for(theta=1; theta <=npar; theta++){    double k1,k2;
       for(i=1; i<=npar; i++)    double p2[NPARMAX+1];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double res;
          double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    double fx;
        int k=0,kmax=10;
       k=0;    double l1;
       for(i=1; i<= (nlstate+ndeath); i++){  
         for(j=1; j<=(nlstate+ndeath);j++){    fx=func(x);
            k=k+1;    for (i=1;i<=npar;i++) p2[i]=x[i];
           gp[k]=pmmij[i][j];    for(l=0 ; l <=lmax; l++){
         }      l1=pow(10,l);
       }      delts=delt;
       for(k=1 ; k <kmax; k=k+1){
       for(i=1; i<=npar; i++)        delt = delta*(l1*k);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        p2[theta]=x[theta] +delt;
            k1=func(p2)-fx;
         p2[theta]=x[theta]-delt;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        k2=func(p2)-fx;
       k=0;        /*res= (k1-2.0*fx+k2)/delt/delt; */
       for(i=1; i<=(nlstate+ndeath); i++){        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         for(j=1; j<=(nlstate+ndeath);j++){        
           k=k+1;  #ifdef DEBUG
           gm[k]=pmmij[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);
         }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       }  #endif
              /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            k=kmax;
     }        }
         else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          k=kmax; l=lmax*10.;
       for(theta=1; theta <=npar; theta++)        }
       trgradg[j][theta]=gradg[theta][j];        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
            delts=delt;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        }
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);      }
     }
      pmij(pmmij,cov,ncovmodel,x,nlstate);    delti[theta]=delts;
     return res; 
      k=0;    
      for(i=1; i<=(nlstate+ndeath); i++){  }
        for(j=1; j<=(nlstate+ndeath);j++){  
          k=k+1;  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
          gm[k]=pmmij[i][j];  {
         }    int i;
      }    int l=1, l1, lmax=20;
          double k1,k2,k3,k4,res,fx;
      /*printf("\n%d ",(int)age);    double p2[NPARMAX+1];
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    int k;
          
     fx=func(x);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    for (k=1; k<=2; k++) {
      }*/      for (i=1;i<=npar;i++) p2[i]=x[i];
       p2[thetai]=x[thetai]+delti[thetai]/k;
   fprintf(ficresprob,"\n%d ",(int)age);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k1=func(p2)-fx;
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      p2[thetai]=x[thetai]+delti[thetai]/k;
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   }      k2=func(p2)-fx;
     
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      p2[thetai]=x[thetai]-delti[thetai]/k;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      k3=func(p2)-fx;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    
 }      p2[thetai]=x[thetai]-delti[thetai]/k;
  free_vector(xp,1,npar);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 fclose(ficresprob);      k4=func(p2)-fx;
  exit(0);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
 }  #ifdef DEBUG
       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
 /***********************************************/      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);
 /**************** Main Program *****************/  #endif
 /***********************************************/    }
     return res;
 /*int main(int argc, char *argv[])*/  }
 int main()  
 {  /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;  { 
   double agedeb, agefin,hf;    int i,imax,j,k; 
   double agemin=1.e20, agemax=-1.e20;    double big,dum,sum,temp; 
     double *vv; 
   double fret;   
   double **xi,tmp,delta;    vv=vector(1,n); 
     *d=1.0; 
   double dum; /* Dummy variable */    for (i=1;i<=n;i++) { 
   double ***p3mat;      big=0.0; 
   int *indx;      for (j=1;j<=n;j++) 
   char line[MAXLINE], linepar[MAXLINE];        if ((temp=fabs(a[i][j])) > big) big=temp; 
   char title[MAXLINE];      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];      vv[i]=1.0/big; 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];    } 
   char filerest[FILENAMELENGTH];    for (j=1;j<=n;j++) { 
   char fileregp[FILENAMELENGTH];      for (i=1;i<j;i++) { 
   char popfile[FILENAMELENGTH];        sum=a[i][j]; 
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   int firstobs=1, lastobs=10;        a[i][j]=sum; 
   int sdeb, sfin; /* Status at beginning and end */      } 
   int c,  h , cpt,l;      big=0.0; 
   int ju,jl, mi;      for (i=j;i<=n;i++) { 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;        sum=a[i][j]; 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        for (k=1;k<j;k++) 
   int mobilav=0,popforecast=0;          sum -= a[i][k]*a[k][j]; 
   int hstepm, nhstepm;        a[i][j]=sum; 
   int *popage;/*boolprev=0 if date and zero if wave*/        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;          big=dum; 
           imax=i; 
   double bage, fage, age, agelim, agebase;        } 
   double ftolpl=FTOL;      } 
   double **prlim;      if (j != imax) { 
   double *severity;        for (k=1;k<=n;k++) { 
   double ***param; /* Matrix of parameters */          dum=a[imax][k]; 
   double  *p;          a[imax][k]=a[j][k]; 
   double **matcov; /* Matrix of covariance */          a[j][k]=dum; 
   double ***delti3; /* Scale */        } 
   double *delti; /* Scale */        *d = -(*d); 
   double ***eij, ***vareij;        vv[imax]=vv[j]; 
   double **varpl; /* Variances of prevalence limits by age */      } 
   double *epj, vepp;      indx[j]=imax; 
   double kk1, kk2;      if (a[j][j] == 0.0) a[j][j]=TINY; 
   double *popeffectif,*popcount;      if (j != n) { 
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;        dum=1.0/(a[j][j]); 
   double yp,yp1,yp2;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       } 
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";    } 
   char *alph[]={"a","a","b","c","d","e"}, str[4];    free_vector(vv,1,n);  /* Doesn't work */
   ;
   } 
   char z[1]="c", occ;  
 #include <sys/time.h>  void lubksb(double **a, int n, int *indx, double b[]) 
 #include <time.h>  { 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    int i,ii=0,ip,j; 
      double sum; 
   /* long total_usecs;   
   struct timeval start_time, end_time;    for (i=1;i<=n;i++) { 
        ip=indx[i]; 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      sum=b[ip]; 
       b[ip]=b[i]; 
       if (ii) 
   printf("\nIMACH, Version 0.7");        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   printf("\nEnter the parameter file name: ");      else if (sum) ii=i; 
       b[i]=sum; 
 #ifdef windows    } 
   scanf("%s",pathtot);    for (i=n;i>=1;i--) { 
   getcwd(pathcd, size);      sum=b[i]; 
   /*cygwin_split_path(pathtot,path,optionfile);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      b[i]=sum/a[i][i]; 
   /* cutv(path,optionfile,pathtot,'\\');*/    } 
   } 
 split(pathtot, path,optionfile);  
   chdir(path);  /************ Frequencies ********************/
   replace(pathc,path);  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
 #endif  {  /* Some frequencies */
 #ifdef unix    
   scanf("%s",optionfile);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
 #endif    int first;
     double ***freq; /* Frequencies */
 /*-------- arguments in the command line --------*/    double *pp, **prop;
     double pos,posprop, k2, dateintsum=0,k2cpt=0;
   strcpy(fileres,"r");    FILE *ficresp;
   strcat(fileres, optionfile);    char fileresp[FILENAMELENGTH];
     
   /*---------arguments file --------*/    pp=vector(1,nlstate);
     prop=matrix(1,nlstate,iagemin,iagemax+3);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    strcpy(fileresp,"p");
     printf("Problem with optionfile %s\n",optionfile);    strcat(fileresp,fileres);
     goto end;    if((ficresp=fopen(fileresp,"w"))==NULL) {
   }      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   strcpy(filereso,"o");      exit(0);
   strcat(filereso,fileres);    }
   if((ficparo=fopen(filereso,"w"))==NULL) {    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    j1=0;
   }    
     j=cptcoveff;
   /* Reads comments: lines beginning with '#' */    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    first=1;
     fgets(line, MAXLINE, ficpar);  
     puts(line);    for(k1=1; k1<=j;k1++){
     fputs(line,ficparo);      for(i1=1; i1<=ncodemax[k1];i1++){
   }        j1++;
   ungetc(c,ficpar);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           scanf("%d", i);*/
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);        for (i=-5; i<=nlstate+ndeath; i++)  
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
   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);            for(m=iagemin; m <= iagemax+3; m++)
 while((c=getc(ficpar))=='#' && c!= EOF){              freq[i][jk][m]=0;
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      for (i=1; i<=nlstate; i++)  
     puts(line);        for(m=iagemin; m <= iagemax+3; m++)
     fputs(line,ficparo);          prop[i][m]=0;
   }        
   ungetc(c,ficpar);        dateintsum=0;
          k2cpt=0;
            for (i=1; i<=imx; i++) {
   covar=matrix(0,NCOVMAX,1,n);          bool=1;
   cptcovn=0;          if  (cptcovn>0) {
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   ncovmodel=2+cptcovn;                bool=0;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */          }
            if (bool==1){
   /* Read guess parameters */            for(m=firstpass; m<=lastpass; m++){
   /* Reads comments: lines beginning with '#' */              k2=anint[m][i]+(mint[m][i]/12.);
   while((c=getc(ficpar))=='#' && c!= EOF){              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     ungetc(c,ficpar);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     fgets(line, MAXLINE, ficpar);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     puts(line);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     fputs(line,ficparo);                if (m<lastpass) {
   }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   ungetc(c,ficpar);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                  }
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                
     for(i=1; i <=nlstate; i++)                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     for(j=1; j <=nlstate+ndeath-1; j++){                  dateintsum=dateintsum+k2;
       fscanf(ficpar,"%1d%1d",&i1,&j1);                  k2cpt++;
       fprintf(ficparo,"%1d%1d",i1,j1);                }
       printf("%1d%1d",i,j);                /*}*/
       for(k=1; k<=ncovmodel;k++){            }
         fscanf(ficpar," %lf",&param[i][j][k]);          }
         printf(" %lf",param[i][j][k]);        }
         fprintf(ficparo," %lf",param[i][j][k]);         
       }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       fscanf(ficpar,"\n");  fprintf(ficresp, "#Local time at start: %s", strstart);
       printf("\n");        if  (cptcovn>0) {
       fprintf(ficparo,"\n");          fprintf(ficresp, "\n#********** Variable "); 
     }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresp, "**********\n#");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;        }
         for(i=1; i<=nlstate;i++) 
   p=param[1][1];          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
          fprintf(ficresp, "\n");
   /* Reads comments: lines beginning with '#' */        
   while((c=getc(ficpar))=='#' && c!= EOF){        for(i=iagemin; i <= iagemax+3; i++){
     ungetc(c,ficpar);          if(i==iagemax+3){
     fgets(line, MAXLINE, ficpar);            fprintf(ficlog,"Total");
     puts(line);          }else{
     fputs(line,ficparo);            if(first==1){
   }              first=0;
   ungetc(c,ficpar);              printf("See log file for details...\n");
             }
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            fprintf(ficlog,"Age %d", i);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          }
   for(i=1; i <=nlstate; i++){          for(jk=1; jk <=nlstate ; jk++){
     for(j=1; j <=nlstate+ndeath-1; j++){            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       fscanf(ficpar,"%1d%1d",&i1,&j1);              pp[jk] += freq[jk][m][i]; 
       printf("%1d%1d",i,j);          }
       fprintf(ficparo,"%1d%1d",i1,j1);          for(jk=1; jk <=nlstate ; jk++){
       for(k=1; k<=ncovmodel;k++){            for(m=-1, pos=0; m <=0 ; m++)
         fscanf(ficpar,"%le",&delti3[i][j][k]);              pos += freq[jk][m][i];
         printf(" %le",delti3[i][j][k]);            if(pp[jk]>=1.e-10){
         fprintf(ficparo," %le",delti3[i][j][k]);              if(first==1){
       }              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       fscanf(ficpar,"\n");              }
       printf("\n");              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       fprintf(ficparo,"\n");            }else{
     }              if(first==1)
   }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   delti=delti3[1][1];              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
              }
   /* Reads comments: lines beginning with '#' */          }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);          for(jk=1; jk <=nlstate ; jk++){
     fgets(line, MAXLINE, ficpar);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     puts(line);              pp[jk] += freq[jk][m][i];
     fputs(line,ficparo);          }       
   }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   ungetc(c,ficpar);            pos += pp[jk];
              posprop += prop[jk][i];
   matcov=matrix(1,npar,1,npar);          }
   for(i=1; i <=npar; i++){          for(jk=1; jk <=nlstate ; jk++){
     fscanf(ficpar,"%s",&str);            if(pos>=1.e-5){
     printf("%s",str);              if(first==1)
     fprintf(ficparo,"%s",str);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for(j=1; j <=i; j++){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       fscanf(ficpar," %le",&matcov[i][j]);            }else{
       printf(" %.5le",matcov[i][j]);              if(first==1)
       fprintf(ficparo," %.5le",matcov[i][j]);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     fscanf(ficpar,"\n");            }
     printf("\n");            if( i <= iagemax){
     fprintf(ficparo,"\n");              if(pos>=1.e-5){
   }                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   for(i=1; i <=npar; i++)                /*probs[i][jk][j1]= pp[jk]/pos;*/
     for(j=i+1;j<=npar;j++)                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       matcov[i][j]=matcov[j][i];              }
                  else
   printf("\n");                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
           }
     /*-------- data file ----------*/          
     if((ficres =fopen(fileres,"w"))==NULL) {          for(jk=-1; jk <=nlstate+ndeath; jk++)
       printf("Problem with resultfile: %s\n", fileres);goto end;            for(m=-1; m <=nlstate+ndeath; m++)
     }              if(freq[jk][m][i] !=0 ) {
     fprintf(ficres,"#%s\n",version);              if(first==1)
                    printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     if((fic=fopen(datafile,"r"))==NULL)    {                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       printf("Problem with datafile: %s\n", datafile);goto end;              }
     }          if(i <= iagemax)
             fprintf(ficresp,"\n");
     n= lastobs;          if(first==1)
     severity = vector(1,maxwav);            printf("Others in log...\n");
     outcome=imatrix(1,maxwav+1,1,n);          fprintf(ficlog,"\n");
     num=ivector(1,n);        }
     moisnais=vector(1,n);      }
     annais=vector(1,n);    }
     moisdc=vector(1,n);    dateintmean=dateintsum/k2cpt; 
     andc=vector(1,n);   
     agedc=vector(1,n);    fclose(ficresp);
     cod=ivector(1,n);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     weight=vector(1,n);    free_vector(pp,1,nlstate);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     mint=matrix(1,maxwav,1,n);    /* End of Freq */
     anint=matrix(1,maxwav,1,n);  }
     s=imatrix(1,maxwav+1,1,n);  
     adl=imatrix(1,maxwav+1,1,n);      /************ Prevalence ********************/
     tab=ivector(1,NCOVMAX);  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)
     ncodemax=ivector(1,8);  {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     i=1;       in each health status at the date of interview (if between dateprev1 and dateprev2).
     while (fgets(line, MAXLINE, fic) != NULL)    {       We still use firstpass and lastpass as another selection.
       if ((i >= firstobs) && (i <=lastobs)) {    */
           
         for (j=maxwav;j>=1;j--){    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    double ***freq; /* Frequencies */
           strcpy(line,stra);    double *pp, **prop;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double pos,posprop; 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double  y2; /* in fractional years */
         }    int iagemin, iagemax;
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    iagemin= (int) agemin;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    iagemax= (int) agemax;
     /*pp=vector(1,nlstate);*/
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j1=0;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    
         for (j=ncov;j>=1;j--){    j=cptcoveff;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         }    
         num[i]=atol(stra);    for(k1=1; k1<=j;k1++){
              for(i1=1; i1<=ncodemax[k1];i1++){
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        j1++;
           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; i<=nlstate; i++)  
         i=i+1;          for(m=iagemin; m <= iagemax+3; m++)
       }            prop[i][m]=0.0;
     }       
     /* printf("ii=%d", ij);        for (i=1; i<=imx; i++) { /* Each individual */
        scanf("%d",i);*/          bool=1;
   imx=i-1; /* Number of individuals */          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
   /* for (i=1; i<=imx; i++){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;                bool=0;
     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;          if (bool==1) { 
     }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     for (i=1; i<=imx; i++)              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     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]));*/                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
   /* Calculation of the number of parameter from char model*/                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); 
   Tvar=ivector(1,15);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   Tprod=ivector(1,15);                  /*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]]);*/
   Tvaraff=ivector(1,15);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   Tvard=imatrix(1,15,1,2);                  prop[s[m][i]][iagemax+3] += weight[i]; 
   Tage=ivector(1,15);                      } 
                  }
   if (strlen(model) >1){            } /* end selection of waves */
     j=0, j1=0, k1=1, k2=1;          }
     j=nbocc(model,'+');        }
     j1=nbocc(model,'*');        for(i=iagemin; i <= iagemax+3; i++){  
     cptcovn=j+1;          
     cptcovprod=j1;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                posprop += prop[jk][i]; 
              } 
     strcpy(modelsav,model);  
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          for(jk=1; jk <=nlstate ; jk++){     
       printf("Error. Non available option model=%s ",model);            if( i <=  iagemax){ 
       goto end;              if(posprop>=1.e-5){ 
     }                probs[i][jk][j1]= prop[jk][i]/posprop;
                  } 
     for(i=(j+1); i>=1;i--){            } 
       cutv(stra,strb,modelsav,'+');          }/* end jk */ 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        }/* end i */ 
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      } /* end i1 */
       /*scanf("%d",i);*/    } /* end k1 */
       if (strchr(strb,'*')) {    
         cutv(strd,strc,strb,'*');    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
         if (strcmp(strc,"age")==0) {    /*free_vector(pp,1,nlstate);*/
           cptcovprod--;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
           cutv(strb,stre,strd,'V');  }  /* End of prevalence */
           Tvar[i]=atoi(stre);  
           cptcovage++;  /************* Waves Concatenation ***************/
             Tage[cptcovage]=i;  
             /*printf("stre=%s ", stre);*/  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)
         }  {
         else if (strcmp(strd,"age")==0) {    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
           cptcovprod--;       Death is a valid wave (if date is known).
           cutv(strb,stre,strc,'V');       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
           Tvar[i]=atoi(stre);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
           cptcovage++;       and mw[mi+1][i]. dh depends on stepm.
           Tage[cptcovage]=i;       */
         }  
         else {    int i, mi, m;
           cutv(strb,stre,strc,'V');    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           Tvar[i]=ncov+k1;       double sum=0., jmean=0.;*/
           cutv(strb,strc,strd,'V');    int first;
           Tprod[k1]=i;    int j, k=0,jk, ju, jl;
           Tvard[k1][1]=atoi(strc);    double sum=0.;
           Tvard[k1][2]=atoi(stre);    first=0;
           Tvar[cptcovn+k2]=Tvard[k1][1];    jmin=1e+5;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    jmax=-1;
           for (k=1; k<=lastobs;k++)    jmean=0.;
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    for(i=1; i<=imx; i++){
           k1++;      mi=0;
           k2=k2+2;      m=firstpass;
         }      while(s[m][i] <= nlstate){
       }        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
       else {          mw[++mi][i]=m;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        if(m >=lastpass)
        /*  scanf("%d",i);*/          break;
       cutv(strd,strc,strb,'V');        else
       Tvar[i]=atoi(strc);          m++;
       }      }/* end while */
       strcpy(modelsav,stra);        if (s[m][i] > nlstate){
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        mi++;     /* Death is another wave */
         scanf("%d",i);*/        /* if(mi==0)  never been interviewed correctly before death */
     }           /* Only death is a correct wave */
 }        mw[mi][i]=m;
        }
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);  
   printf("cptcovprod=%d ", cptcovprod);      wav[i]=mi;
   scanf("%d ",i);*/      if(mi==0){
     fclose(fic);        nbwarn++;
         if(first==0){
     /*  if(mle==1){*/          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     if (weightopt != 1) { /* Maximisation without weights*/          first=1;
       for(i=1;i<=n;i++) weight[i]=1.0;        }
     }        if(first==1){
     /*-calculation of age at interview from date of interview and age at death -*/          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
     agev=matrix(1,maxwav,1,imx);        }
       } /* end mi==0 */
    for (i=1; i<=imx; i++)    } /* End individuals */
      for(m=2; (m<= maxwav); m++)  
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    for(i=1; i<=imx; i++){
          anint[m][i]=9999;      for(mi=1; mi<wav[i];mi++){
          s[m][i]=-1;        if (stepm <=0)
        }          dh[mi][i]=1;
            else{
     for (i=1; i<=imx; i++)  {          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);            if (agedc[i] < 2*AGESUP) {
       for(m=1; (m<= maxwav); m++){              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
         if(s[m][i] >0){              if(j==0) j=1;  /* Survives at least one month after exam */
           if (s[m][i] == nlstate+1) {              else if(j<0){
             if(agedc[i]>0)                nberr++;
               if(moisdc[i]!=99 && andc[i]!=9999)                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]);
               agev[m][i]=agedc[i];                j=1; /* Temporary Dangerous patch */
             else {                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               if (andc[i]!=9999){                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]);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               agev[m][i]=-1;              }
               }              k=k+1;
             }              if (j >= jmax){
           }                jmax=j;
           else if(s[m][i] !=9){ /* Should no more exist */                ijmax=i;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);              }
             if(mint[m][i]==99 || anint[m][i]==9999)              if (j <= jmin){
               agev[m][i]=1;                jmin=j;
             else if(agev[m][i] <agemin){                ijmin=i;
               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);*/              sum=sum+j;
             }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
             else if(agev[m][i] >agemax){              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
               agemax=agev[m][i];            }
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/          }
             }          else{
             /*agev[m][i]=anint[m][i]-annais[i];*/            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
             /*   agev[m][i] = age[i]+2*m;*/  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
           }  
           else { /* =9 */            k=k+1;
             agev[m][i]=1;            if (j >= jmax) {
             s[m][i]=-1;              jmax=j;
           }              ijmax=i;
         }            }
         else /*= 0 Unknown */            else if (j <= jmin){
           agev[m][i]=1;              jmin=j;
       }              ijmin=i;
                }
     }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     for (i=1; i<=imx; i++)  {            /*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]);*/
       for(m=1; (m<= maxwav); m++){            if(j<0){
         if (s[m][i] > (nlstate+ndeath)) {              nberr++;
           printf("Error: Wrong value in nlstate or ndeath\n");                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]);
           goto end;              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]);
         }            }
       }            sum=sum+j;
     }          }
           jk= j/stepm;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
     free_vector(severity,1,maxwav);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     free_imatrix(outcome,1,maxwav+1,1,n);            if(jl==0){
     free_vector(moisnais,1,n);              dh[mi][i]=jk;
     free_vector(annais,1,n);              bh[mi][i]=0;
     /* free_matrix(mint,1,maxwav,1,n);            }else{ /* We want a negative bias in order to only have interpolation ie
        free_matrix(anint,1,maxwav,1,n);*/                    * at the price of an extra matrix product in likelihood */
     free_vector(moisdc,1,n);              dh[mi][i]=jk+1;
     free_vector(andc,1,n);              bh[mi][i]=ju;
             }
              }else{
     wav=ivector(1,imx);            if(jl <= -ju){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);              dh[mi][i]=jk;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);              bh[mi][i]=jl;       /* bias is positive if real duration
                                       * is higher than the multiple of stepm and negative otherwise.
     /* Concatenates waves */                                   */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);            }
             else{
               dh[mi][i]=jk+1;
       Tcode=ivector(1,100);              bh[mi][i]=ju;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);            }
       ncodemax[1]=1;            if(dh[mi][i]==0){
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);              dh[mi][i]=1; /* At least one step */
                    bh[mi][i]=ju; /* At least one step */
    codtab=imatrix(1,100,1,10);              /*  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);*/
    h=0;            }
    m=pow(2,cptcoveff);          } /* end if mle */
          }
    for(k=1;k<=cptcoveff; k++){      } /* end wave */
      for(i=1; i <=(m/pow(2,k));i++){    }
        for(j=1; j <= ncodemax[k]; j++){    jmean=sum/k;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
            h++;    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
            if (h>m) h=1;codtab[h][k]=j;   }
          }  
        }  /*********** Tricode ****************************/
      }  void tricode(int *Tvar, int **nbcode, int imx)
    }  {
        
    /* Calculates basic frequencies. Computes observed prevalence at single age    int Ndum[20],ij=1, k, j, i, maxncov=19;
        and prints on file fileres'p'. */    int cptcode=0;
     cptcoveff=0; 
       
        for (k=0; k<maxncov; k++) Ndum[k]=0;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    for (k=1; k<=7; k++) ncodemax[k]=0;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                                 modality*/ 
              ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     /* For Powell, parameters are in a vector p[] starting at p[1]        Ndum[ij]++; /*store the modality */
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                                          Tvar[j]. If V=sex and male is 0 and 
     if(mle==1){                                         female is 1, then  cptcode=1.*/
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      }
     }  
          for (i=0; i<=cptcode; i++) {
     /*--------- results files --------------*/        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(ficres,"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);      }
    
       ij=1; 
    jk=1;      for (i=1; i<=ncodemax[j]; i++) {
    fprintf(ficres,"# Parameters\n");        for (k=0; k<= maxncov; k++) {
    printf("# Parameters\n");          if (Ndum[k] != 0) {
    for(i=1,jk=1; i <=nlstate; i++){            nbcode[Tvar[j]][ij]=k; 
      for(k=1; k <=(nlstate+ndeath); 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; */
        if (k != i)            
          {            ij++;
            printf("%d%d ",i,k);          }
            fprintf(ficres,"%1d%1d ",i,k);          if (ij > ncodemax[j]) break; 
            for(j=1; j <=ncovmodel; j++){        }  
              printf("%f ",p[jk]);      } 
              fprintf(ficres,"%f ",p[jk]);    }  
              jk++;  
            }   for (k=0; k< maxncov; k++) Ndum[k]=0;
            printf("\n");  
            fprintf(ficres,"\n");   for (i=1; i<=ncovmodel-2; i++) { 
          }     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
      }     ij=Tvar[i];
    }     Ndum[ij]++;
  if(mle==1){   }
     /* Computing hessian and covariance matrix */  
     ftolhess=ftol; /* Usually correct */   ij=1;
     hesscov(matcov, p, npar, delti, ftolhess, func);   for (i=1; i<= maxncov; i++) {
  }     if((Ndum[i]!=0) && (i<=ncovcol)){
     fprintf(ficres,"# Scales\n");       Tvaraff[ij]=i; /*For printing */
     printf("# Scales\n");       ij++;
      for(i=1,jk=1; i <=nlstate; i++){     }
       for(j=1; j <=nlstate+ndeath; j++){   }
         if (j!=i) {   
           fprintf(ficres,"%1d%1d",i,j);   cptcoveff=ij-1; /*Number of simple covariates*/
           printf("%1d%1d",i,j);  }
           for(k=1; k<=ncovmodel;k++){  
             printf(" %.5e",delti[jk]);  /*********** Health Expectancies ****************/
             fprintf(ficres," %.5e",delti[jk]);  
             jk++;  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov,char strstart[] )
           }  
           printf("\n");  {
           fprintf(ficres,"\n");    /* Health expectancies */
         }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
       }    double age, agelim, hf;
      }    double ***p3mat,***varhe;
        double **dnewm,**doldm;
     k=1;    double *xp;
     fprintf(ficres,"# Covariance\n");    double **gp, **gm;
     printf("# Covariance\n");    double ***gradg, ***trgradg;
     for(i=1;i<=npar;i++){    int theta;
       /*  if (k>nlstate) k=1;  
       i1=(i-1)/(ncovmodel*nlstate)+1;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    xp=vector(1,npar);
       printf("%s%d%d",alph[k],i1,tab[i]);*/    dnewm=matrix(1,nlstate*nlstate,1,npar);
       fprintf(ficres,"%3d",i);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       printf("%3d",i);    
       for(j=1; j<=i;j++){    fprintf(ficreseij,"# Local time at start: %s", strstart);
         fprintf(ficres," %.5e",matcov[i][j]);    fprintf(ficreseij,"# Health expectancies\n");
         printf(" %.5e",matcov[i][j]);    fprintf(ficreseij,"# Age");
       }    for(i=1; i<=nlstate;i++)
       fprintf(ficres,"\n");      for(j=1; j<=nlstate;j++)
       printf("\n");        fprintf(ficreseij," %1d-%1d (SE)",i,j);
       k++;    fprintf(ficreseij,"\n");
     }  
        if(estepm < stepm){
     while((c=getc(ficpar))=='#' && c!= EOF){      printf ("Problem %d lower than %d\n",estepm, stepm);
       ungetc(c,ficpar);    }
       fgets(line, MAXLINE, ficpar);    else  hstepm=estepm;   
       puts(line);    /* We compute the life expectancy from trapezoids spaced every estepm months
       fputs(line,ficparo);     * 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
     ungetc(c,ficpar);     * we are calculating an estimate of the Life Expectancy assuming a linear 
       * progression in between and thus overestimating or underestimating according
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);     * to the curvature of the survival function. If, for the same date, we 
         * estimate the model with stepm=1 month, we can keep estepm to 24 months
     if (fage <= 2) {     * to compare the new estimate of Life expectancy with the same linear 
       bage = agemin;     * hypothesis. A more precise result, taking into account a more precise
       fage = agemax;     * curvature will be obtained if estepm is as small as stepm. */
     }  
     /* For example we decided to compute the life expectancy with the smallest unit */
     fprintf(ficres,"# agemin agemax for life expectancy.\n");    /* 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 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);       nstepm is the number of stepm from age to agelin. 
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);       Look at hpijx to understand the reason of that which relies in memory size
         and note for a fixed period like estepm months */
     while((c=getc(ficpar))=='#' && c!= EOF){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     ungetc(c,ficpar);       survival function given by stepm (the optimization length). Unfortunately it
     fgets(line, MAXLINE, ficpar);       means that if the survival funtion is printed only each two years of age and if
     puts(line);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     fputs(line,ficparo);       results. So we changed our mind and took the option of the best precision.
   }    */
   ungetc(c,ficpar);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
    
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);    agelim=AGESUP;
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);      /* nhstepm age range expressed in number of stepm */
            nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   while((c=getc(ficpar))=='#' && c!= EOF){      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     ungetc(c,ficpar);      /* if (stepm >= YEARM) hstepm=1;*/
     fgets(line, MAXLINE, ficpar);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     puts(line);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fputs(line,ficparo);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   }      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   ungetc(c,ficpar);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
    
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
    dateprev1=anprev1+mprev1/12.+jprev1/365.;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
    
   fscanf(ficpar,"pop_based=%d\n",&popbased);  
    fprintf(ficparo,"pop_based=%d\n",popbased);        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    fprintf(ficres,"pop_based=%d\n",popbased);    
       /* Computing  Variances of health expectancies */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);       for(theta=1; theta <=npar; theta++){
     fgets(line, MAXLINE, ficpar);        for(i=1; i<=npar; i++){ 
     puts(line);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     fputs(line,ficparo);        }
   }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   ungetc(c,ficpar);    
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);        cptj=0;
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);        for(j=1; j<= nlstate; j++){
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);          for(i=1; i<=nlstate; i++){
             cptj=cptj+1;
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
               gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
  /*------------ gnuplot -------------*/            }
 chdir(pathcd);          }
   if((ficgp=fopen("graph.plt","w"))==NULL) {        }
     printf("Problem with file graph.gp");goto end;       
   }       
 #ifdef windows        for(i=1; i<=npar; i++) 
   fprintf(ficgp,"cd \"%s\" \n",pathc);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 #endif        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 m=pow(2,cptcoveff);        
          cptj=0;
  /* 1eme*/        for(j=1; j<= nlstate; j++){
   for (cpt=1; cpt<= nlstate ; cpt ++) {          for(i=1;i<=nlstate;i++){
    for (k1=1; k1<= m ; k1 ++) {            cptj=cptj+1;
             for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
 #ifdef windows  
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
 #endif            }
 #ifdef unix          }
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);        }
 #endif        for(j=1; j<= nlstate*nlstate; j++)
           for(h=0; h<=nhstepm-1; h++){
 for (i=1; i<= nlstate ; i ++) {            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");       } 
 }     
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  /* End theta */
     for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }       for(h=0; h<=nhstepm-1; h++)
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        for(j=1; j<=nlstate*nlstate;j++)
      for (i=1; i<= nlstate ; i ++) {          for(theta=1; theta <=npar; theta++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            trgradg[h][j][theta]=gradg[h][theta][j];
   else fprintf(ficgp," \%%*lf (\%%*lf)");       
 }    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));       for(i=1;i<=nlstate*nlstate;i++)
 #ifdef unix        for(j=1;j<=nlstate*nlstate;j++)
 fprintf(ficgp,"\nset ter gif small size 400,300");          varhe[i][j][(int)age] =0.;
 #endif  
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);       printf("%d|",(int)age);fflush(stdout);
    }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   }       for(h=0;h<=nhstepm-1;h++){
   /*2 eme*/        for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   for (k1=1; k1<= m ; k1 ++) {          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);          for(i=1;i<=nlstate*nlstate;i++)
                for(j=1;j<=nlstate*nlstate;j++)
     for (i=1; i<= nlstate+1 ; i ++) {              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       k=2*i;        }
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      }
       for (j=1; j<= nlstate+1 ; j ++) {      /* Computing expectancies */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      for(i=1; i<=nlstate;i++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=1; j<=nlstate;j++)
 }            for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);            
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
       for (j=1; j<= nlstate+1 ; j ++) {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          }
         else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }        fprintf(ficreseij,"%3.0f",age );
       fprintf(ficgp,"\" t\"\" w l 0,");      cptj=0;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      for(i=1; i<=nlstate;i++)
       for (j=1; j<= nlstate+1 ; j ++) {        for(j=1; j<=nlstate;j++){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          cptj++;
   else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
 }          }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      fprintf(ficreseij,"\n");
       else fprintf(ficgp,"\" t\"\" w l 0,");     
     }      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
        free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   /*3eme*/      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }
   for (k1=1; k1<= m ; k1 ++) {    printf("\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {    fprintf(ficlog,"\n");
       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);    free_vector(xp,1,npar);
       for (i=1; i< nlstate ; i ++) {    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
         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);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  }
     }  
   }  /************ Variance ******************/
    void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   /* CV preval stat */  {
   for (k1=1; k1<= m ; k1 ++) {    /* Variance of health expectancies */
     for (cpt=1; cpt<nlstate ; cpt ++) {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       k=3;    /* double **newm;*/
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);    double **dnewm,**doldm;
       for (i=1; i< nlstate ; i ++)    double **dnewmp,**doldmp;
         fprintf(ficgp,"+$%d",k+i+1);    int i, j, nhstepm, hstepm, h, nstepm ;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    int k, cptcode;
          double *xp;
       l=3+(nlstate+ndeath)*cpt;    double **gp, **gm;  /* for var eij */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    double ***gradg, ***trgradg; /*for var eij */
       for (i=1; i< nlstate ; i ++) {    double **gradgp, **trgradgp; /* for var p point j */
         l=3+(nlstate+ndeath)*cpt;    double *gpp, *gmp; /* for var p point j */
         fprintf(ficgp,"+$%d",l+i+1);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       }    double ***p3mat;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      double age,agelim, hf;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    double ***mobaverage;
     }    int theta;
   }      char digit[4];
     char digitp[25];
   /* proba elementaires */  
    for(i=1,jk=1; i <=nlstate; i++){    char fileresprobmorprev[FILENAMELENGTH];
     for(k=1; k <=(nlstate+ndeath); k++){  
       if (k != i) {    if(popbased==1){
         for(j=1; j <=ncovmodel; j++){      if(mobilav!=0)
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/        strcpy(digitp,"-populbased-mobilav-");
           /*fprintf(ficgp,"%s",alph[1]);*/      else strcpy(digitp,"-populbased-nomobil-");
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    }
           jk++;    else 
           fprintf(ficgp,"\n");      strcpy(digitp,"-stablbased-");
         }  
       }    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);
   for(jk=1; jk <=m; jk++) {        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);      }
    i=1;    }
    for(k2=1; k2<=nlstate; k2++) {  
      k3=i;    strcpy(fileresprobmorprev,"prmorprev"); 
      for(k=1; k<=(nlstate+ndeath); k++) {    sprintf(digit,"%-d",ij);
        if (k != k2){    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
 ij=1;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         for(j=3; j <=ncovmodel; j++) {    strcat(fileresprobmorprev,fileres);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
             ij++;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
           }    }
           else    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);   
         }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           fprintf(ficgp,")/(1");    fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
            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);
         for(k1=1; k1 <=nlstate; k1++){      fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
 ij=1;      fprintf(ficresprobmorprev," p.%-d SE",j);
           for(j=3; j <=ncovmodel; j++){      for(i=1; i<=nlstate;i++)
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    }  
             ij++;    fprintf(ficresprobmorprev,"\n");
           }    fprintf(ficgp,"\n# Routine varevsij");
           else    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
           }    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
           fprintf(ficgp,")");  /*   } */
         }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);   fprintf(ficresvij, "#Local time at start: %s", strstart);
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    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");
         i=i+ncovmodel;    fprintf(ficresvij,"# Age");
        }    for(i=1; i<=nlstate;i++)
      }      for(j=1; j<=nlstate;j++)
    }        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    fprintf(ficresvij,"\n");
   }  
        xp=vector(1,npar);
   fclose(ficgp);    dnewm=matrix(1,nlstate,1,npar);
   /* end gnuplot */    doldm=matrix(1,nlstate,1,nlstate);
        dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
 chdir(path);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      
     free_ivector(wav,1,imx);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    gpp=vector(nlstate+1,nlstate+ndeath);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      gmp=vector(nlstate+1,nlstate+ndeath);
     free_ivector(num,1,n);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     free_vector(agedc,1,n);    
     /*free_matrix(covar,1,NCOVMAX,1,n);*/    if(estepm < stepm){
     fclose(ficparo);      printf ("Problem %d lower than %d\n",estepm, stepm);
     fclose(ficres);    }
     /*  }*/    else  hstepm=estepm;   
        /* For example we decided to compute the life expectancy with the smallest unit */
    /*________fin mle=1_________*/    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
         Look at hpijx to understand the reason of that which relies in memory size
     /* No more information from the sample is required now */       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 */
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 /*--------- index.htm --------*/      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
   strcpy(optionfilehtm,optionfile);      gm=matrix(0,nhstepm,1,nlstate);
   strcat(optionfilehtm,".htm");  
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm);goto end;      for(theta=1; theta <=npar; theta++){
   }        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">        }
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 Total number of observations=%d <br>        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>  
 <hr  size=\"2\" color=\"#EC5E5E\">        if (popbased==1) {
 <li>Outputs files<br><br>\n          if(mobilav ==0){
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n            for(i=1; i<=nlstate;i++)
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>              prlim[i][i]=probs[(int)age][i][ij];
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>          }else{ /* mobilav */ 
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>            for(i=1; i<=nlstate;i++)
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>              prlim[i][i]=mobaverage[(int)age][i][ij];
         - 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>        for(j=1; j<= nlstate; j++){
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>          for(h=0; h<=nhstepm; h++){
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
  fprintf(fichtm," <li>Graphs</li><p>");          }
         }
  m=cptcoveff;        /* This for computing probability of death (h=1 means
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
  j1=0;        */
  for(k1=1; k1<=m;k1++){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
    for(i1=1; i1<=ncodemax[k1];i1++){          for(i=1,gpp[j]=0.; i<= nlstate; i++)
        j1++;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
        if (cptcovn > 0) {        }    
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        /* end probability of death */
          for (cpt=1; cpt<=cptcoveff;cpt++)  
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
        }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);       
        for(cpt=1; cpt<nlstate;cpt++){        if (popbased==1) {
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>          if(mobilav ==0){
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);            for(i=1; i<=nlstate;i++)
        }              prlim[i][i]=probs[(int)age][i][ij];
     for(cpt=1; cpt<=nlstate;cpt++) {          }else{ /* mobilav */ 
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident            for(i=1; i<=nlstate;i++)
 interval) in state (%d): v%s%d%d.gif <br>              prlim[i][i]=mobaverage[(int)age][i][ij];
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);            }
      }        }
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        for(j=1; j<= nlstate; j++){
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          for(h=0; h<=nhstepm; h++){
      }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
      fprintf(fichtm,"\n<br>- Total life expectancy by age and              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
 health expectancies in states (1) and (2): e%s%d.gif<br>          }
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        }
 fprintf(fichtm,"\n</body>");        /* This for computing probability of death (h=1 means
    }           computed over hstepm matrices product = hstepm*stepm months) 
  }           as a weighted average of prlim.
 fclose(fichtm);        */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
   /*--------------- Prevalence limit --------------*/          for(i=1,gmp[j]=0.; i<= nlstate; i++)
             gmp[j] += prlim[i][i]*p3mat[i][j][1];
   strcpy(filerespl,"pl");        }    
   strcat(filerespl,fileres);        /* end probability of death */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        for(j=1; j<= nlstate; j++) /* vareij */
   }          for(h=0; h<=nhstepm; h++){
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   fprintf(ficrespl,"#Prevalence limit\n");          }
   fprintf(ficrespl,"#Age ");  
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   fprintf(ficrespl,"\n");          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
          }
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      } /* End theta */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      for(h=0; h<=nhstepm; h++) /* veij */
   k=0;        for(j=1; j<=nlstate;j++)
   agebase=agemin;          for(theta=1; theta <=npar; theta++)
   agelim=agemax;            trgradg[h][j][theta]=gradg[h][theta][j];
   ftolpl=1.e-10;  
   i1=cptcoveff;      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   if (cptcovn < 1){i1=1;}        for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
   for(cptcov=1;cptcov<=i1;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
         k=k+1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      for(i=1;i<=nlstate;i++)
         fprintf(ficrespl,"\n#******");        for(j=1;j<=nlstate;j++)
         for(j=1;j<=cptcoveff;j++)          vareij[i][j][(int)age] =0.;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespl,"******\n");      for(h=0;h<=nhstepm;h++){
                for(k=0;k<=nhstepm;k++){
         for (age=agebase; age<=agelim; age++){          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           fprintf(ficrespl,"%.0f",age );          for(i=1;i<=nlstate;i++)
           for(i=1; i<=nlstate;i++)            for(j=1;j<=nlstate;j++)
           fprintf(ficrespl," %.5f", prlim[i][i]);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
           fprintf(ficrespl,"\n");        }
         }      }
       }    
     }      /* pptj */
   fclose(ficrespl);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   /*------------- h Pij x at various ages ------------*/      for(j=nlstate+1;j<=nlstate+ndeath;j++)
          for(i=nlstate+1;i<=nlstate+ndeath;i++)
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          varppt[j][i]=doldmp[j][i];
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      /* end ppptj */
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      /*  x centered again */
   }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   printf("Computing pij: result on file '%s' \n", filerespij);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     
   stepsize=(int) (stepm+YEARM-1)/YEARM;      if (popbased==1) {
   /*if (stepm<=24) stepsize=2;*/        if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
   agelim=AGESUP;            prlim[i][i]=probs[(int)age][i][ij];
   hstepm=stepsize*YEARM; /* Every year of age */        }else{ /* mobilav */ 
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          for(i=1; i<=nlstate;i++)
              prlim[i][i]=mobaverage[(int)age][i][ij];
   k=0;        }
   for(cptcov=1;cptcov<=i1;cptcov++){      }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){               
       k=k+1;      /* This for computing probability of death (h=1 means
         fprintf(ficrespij,"\n#****** ");         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         for(j=1;j<=cptcoveff;j++)         as a weighted average of prlim.
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      */
         fprintf(ficrespij,"******\n");      for(j=nlstate+1;j<=nlstate+ndeath;j++){
                for(i=1,gmp[j]=0.;i<= nlstate; i++) 
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      }    
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      /* end probability of death */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           fprintf(ficrespij,"# Age");        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
           for(i=1; i<=nlstate;i++)        for(i=1; i<=nlstate;i++){
             for(j=1; j<=nlstate+ndeath;j++)          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
               fprintf(ficrespij," %1d-%1d",i,j);        }
           fprintf(ficrespij,"\n");      } 
           for (h=0; h<=nhstepm; h++){      fprintf(ficresprobmorprev,"\n");
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)      fprintf(ficresvij,"%.0f ",age );
               for(j=1; j<=nlstate+ndeath;j++)      for(i=1; i<=nlstate;i++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);        for(j=1; j<=nlstate;j++){
             fprintf(ficrespij,"\n");          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
           }        }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficresvij,"\n");
           fprintf(ficrespij,"\n");      free_matrix(gp,0,nhstepm,1,nlstate);
         }      free_matrix(gm,0,nhstepm,1,nlstate);
     }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   }      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
   fclose(ficrespij);    free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   if(stepm == 1) {    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   /*---------- Forecasting ------------------*/    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    /* 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)\";");
   /*printf("calage= %f", calagedate);*/  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
   strcpy(fileresf,"f");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
   strcat(fileresf,fileres);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   if((ficresf=fopen(fileresf,"w"))==NULL) {    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;    /*  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("Computing forecasting: result on file '%s' \n", fileresf);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   free_matrix(mint,1,maxwav,1,n);  
   free_matrix(anint,1,maxwav,1,n);    free_vector(xp,1,npar);
   free_matrix(agev,1,maxwav,1,imx);    free_matrix(doldm,1,nlstate,1,nlstate);
   /* Mobile average */    free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if (mobilav==1) {    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fclose(ficresprobmorprev);
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)    fflush(ficgp);
       for (i=1; i<=nlstate;i++)    fflush(fichtm); 
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)  }  /* end varevsij */
           mobaverage[(int)agedeb][i][cptcod]=0.;  
      /************ Variance of prevlim ******************/
     for (agedeb=bage+4; agedeb<=fage; agedeb++){  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
       for (i=1; i<=nlstate;i++){  {
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    /* Variance of prevalence limit */
           for (cpt=0;cpt<=4;cpt++){    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    double **newm;
           }    double **dnewm,**doldm;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    int i, j, nhstepm, hstepm;
         }    int k, cptcode;
       }    double *xp;
     }      double *gp, *gm;
   }    double **gradg, **trgradg;
     double age,agelim;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    int theta;
   if (stepm<=12) stepsize=1;    fprintf(ficresvpl, "#Local time at start: %s", strstart); 
     fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   agelim=AGESUP;    fprintf(ficresvpl,"# Age");
   /*hstepm=stepsize*YEARM; *//* Every year of age */    for(i=1; i<=nlstate;i++)
   hstepm=1;        fprintf(ficresvpl," %1d-%1d",i,i);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */    fprintf(ficresvpl,"\n");
   yp1=modf(dateintmean,&yp);  
   anprojmean=yp;    xp=vector(1,npar);
   yp2=modf((yp1*12),&yp);    dnewm=matrix(1,nlstate,1,npar);
   mprojmean=yp;    doldm=matrix(1,nlstate,1,nlstate);
   yp1=modf((yp2*30.5),&yp);    
   jprojmean=yp;    hstepm=1*YEARM; /* Every year of age */
   if(jprojmean==0) jprojmean=1;    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   if(mprojmean==0) jprojmean=1;    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
   if (popforecast==1) {      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     if((ficpop=fopen(popfile,"r"))==NULL)    {      gradg=matrix(1,npar,1,nlstate);
       printf("Problem with population file : %s\n",popfile);goto end;      gp=vector(1,nlstate);
     }      gm=vector(1,nlstate);
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);      for(theta=1; theta <=npar; theta++){
     popcount=vector(0,AGESUP);        for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
     i=1;          }
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       {        for(i=1;i<=nlstate;i++)
         i=i+1;          gp[i] = prlim[i][i];
       }      
     imx=i;        for(i=1; i<=npar; i++) /* Computes gradient */
              xp[i] = x[i] - (i==theta ?delti[theta]:0);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   }        for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        for(i=1;i<=nlstate;i++)
       k=k+1;          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       fprintf(ficresf,"\n#******");      } /* End theta */
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      trgradg =matrix(1,nlstate,1,npar);
       }  
       fprintf(ficresf,"******\n");      for(j=1; j<=nlstate;j++)
       fprintf(ficresf,"# StartingAge FinalAge");        for(theta=1; theta <=npar; theta++)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);          trgradg[j][theta]=gradg[theta][j];
       if (popforecast==1)  fprintf(ficresf," [Population]");  
          for(i=1;i<=nlstate;i++)
       for (cpt=0; cpt<4;cpt++) {        varpl[i][(int)age] =0.;
         fprintf(ficresf,"\n");      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
         nhstepm = nhstepm/hstepm;      fprintf(ficresvpl,"%.0f ",age );
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/      for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficresvpl,"\n");
         oldm=oldms;savm=savms;      free_vector(gp,1,nlstate);
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        free_vector(gm,1,nlstate);
              free_matrix(gradg,1,npar,1,nlstate);
         for (h=0; h<=nhstepm; h++){      free_matrix(trgradg,1,nlstate,1,npar);
           if (h==(int) (calagedate+YEARM*cpt)) {    } /* End age */
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);  
           }    free_vector(xp,1,npar);
           for(j=1; j<=nlstate+ndeath;j++) {    free_matrix(doldm,1,nlstate,1,npar);
             kk1=0.;kk2=0;    free_matrix(dnewm,1,nlstate,1,nlstate);
             for(i=1; i<=nlstate;i++) {          
               if (mobilav==1)  }
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
               else {  /************ Variance of one-step probabilities  ******************/
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/  {
               }    int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];    int k=0,l, cptcode;
             }    int first=1, first1;
              double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
             if (h==(int)(calagedate+12*cpt)){    double **dnewm,**doldm;
               fprintf(ficresf," %.3f", kk1);    double *xp;
                  double *gp, *gm;
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);    double **gradg, **trgradg;
             }    double **mu;
           }    double age,agelim, cov[NCOVMAX];
         }    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int theta;
       }    char fileresprob[FILENAMELENGTH];
       }    char fileresprobcov[FILENAMELENGTH];
     }    char fileresprobcor[FILENAMELENGTH];
   }  
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double ***varpij;
   if (popforecast==1) {  
     free_ivector(popage,0,AGESUP);    strcpy(fileresprob,"prob"); 
     free_vector(popeffectif,0,AGESUP);    strcat(fileresprob,fileres);
     free_vector(popcount,0,AGESUP);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprob);
   free_imatrix(s,1,maxwav+1,1,n);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   free_vector(weight,1,n);    }
   fclose(ficresf);    strcpy(fileresprobcov,"probcov"); 
   }/* End forecasting */    strcat(fileresprobcov,fileres);
   else{    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     erreur=108;      printf("Problem with resultfile: %s\n", fileresprobcov);
     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);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   }    }
     strcpy(fileresprobcor,"probcor"); 
   /*---------- Health expectancies and variances ------------*/    strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   strcpy(filerest,"t");      printf("Problem with resultfile: %s\n", fileresprobcor);
   strcat(filerest,fileres);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   if((ficrest=fopen(filerest,"w"))==NULL) {    }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   }    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   strcpy(filerese,"e");    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   strcat(filerese,fileres);    fprintf(ficresprob, "#Local time at start: %s", strstart);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    fprintf(ficresprob,"# Age");
   }    fprintf(ficresprobcov, "#Local time at start: %s", strstart);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
  strcpy(fileresv,"v");    fprintf(ficresprobcor, "#Local time at start: %s", strstart);
   strcat(fileresv,fileres);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    fprintf(ficresprobcov,"# Age");
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }  
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
   k=0;        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   for(cptcov=1;cptcov<=i1;cptcov++){        fprintf(ficresprobcov," p%1d-%1d ",i,j);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       k=k+1;      }  
       fprintf(ficrest,"\n#****** ");   /* fprintf(ficresprob,"\n");
       for(j=1;j<=cptcoveff;j++)    fprintf(ficresprobcov,"\n");
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresprobcor,"\n");
       fprintf(ficrest,"******\n");   */
    xp=vector(1,npar);
       fprintf(ficreseij,"\n#****** ");    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       for(j=1;j<=cptcoveff;j++)    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
       fprintf(ficreseij,"******\n");    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
       fprintf(ficresvij,"\n#****** ");    fprintf(ficgp,"\n# Routine varprob");
       for(j=1;j<=cptcoveff;j++)    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    fprintf(fichtm,"\n");
       fprintf(ficresvij,"******\n");  
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
       oldm=oldms;savm=savms;    file %s<br>\n",optionfilehtmcov);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  and drawn. It helps understanding how is the covariance between two incidences.\
       oldm=oldms;savm=savms;   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    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 \
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  standard deviations wide on each axis. <br>\
       fprintf(ficrest,"\n");   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>\
       hf=1;  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
       if (stepm >= YEARM) hf=stepm/YEARM;  
       epj=vector(1,nlstate+1);    cov[1]=1;
       for(age=bage; age <=fage ;age++){    tj=cptcoveff;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
         if (popbased==1) {    j1=0;
           for(i=1; i<=nlstate;i++)    for(t=1; t<=tj;t++){
             prlim[i][i]=probs[(int)age][i][k];      for(i1=1; i1<=ncodemax[t];i1++){ 
         }        j1++;
                if  (cptcovn>0) {
         fprintf(ficrest," %.0f",age);          fprintf(ficresprob, "\n#********** Variable "); 
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          fprintf(ficresprob, "**********\n#\n");
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];          fprintf(ficresprobcov, "\n#********** Variable "); 
           }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           epj[nlstate+1] +=epj[j];          fprintf(ficresprobcov, "**********\n#\n");
         }          
         for(i=1, vepp=0.;i <=nlstate;i++)          fprintf(ficgp, "\n#********** Variable "); 
           for(j=1;j <=nlstate;j++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             vepp += vareij[i][j][(int)age];          fprintf(ficgp, "**********\n#\n");
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));          
         for(j=1;j <=nlstate;j++){          
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));          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(ficrest,"\n");          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
       }          
     }          fprintf(ficresprobcor, "\n#********** Variable ");    
   }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                  fprintf(ficresprobcor, "**********\n#");    
                }
         
         for (age=bage; age<=fage; age ++){ 
  fclose(ficreseij);          cov[2]=age;
  fclose(ficresvij);          for (k=1; k<=cptcovn;k++) {
   fclose(ficrest);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   fclose(ficpar);          }
   free_vector(epj,1,nlstate+1);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   /*  scanf("%d ",i); */          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]]];
   /*------- Variance limit prevalence------*/            
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
 strcpy(fileresvpl,"vpl");          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   strcat(fileresvpl,fileres);          gp=vector(1,(nlstate)*(nlstate+ndeath));
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          gm=vector(1,(nlstate)*(nlstate+ndeath));
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      
     exit(0);          for(theta=1; theta <=npar; theta++){
   }            for(i=1; i<=npar; i++)
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
  k=0;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
  for(cptcov=1;cptcov<=i1;cptcov++){            
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            k=0;
      k=k+1;            for(i=1; i<= (nlstate); i++){
      fprintf(ficresvpl,"\n#****** ");              for(j=1; j<=(nlstate+ndeath);j++){
      for(j=1;j<=cptcoveff;j++)                k=k+1;
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                gp[k]=pmmij[i][j];
      fprintf(ficresvpl,"******\n");              }
                  }
      varpl=matrix(1,nlstate,(int) bage, (int) fage);            
      oldm=oldms;savm=savms;            for(i=1; i<=npar; i++)
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
    }      
  }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
   fclose(ficresvpl);            for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
   /*---------- End : free ----------------*/                k=k+1;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);                gm[k]=pmmij[i][j];
                }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);            }
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);       
              for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
                gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
   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);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);            for(theta=1; theta <=npar; theta++)
                trgradg[j][theta]=gradg[theta][j];
   free_matrix(matcov,1,npar,1,npar);          
   free_vector(delti,1,npar);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
            matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   if(erreur >0)          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     printf("End of Imach with error %d\n",erreur);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   else   printf("End of Imach\n");  
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          pmij(pmmij,cov,ncovmodel,x,nlstate);
            
   /* 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);*/          k=0;
   /*printf("Total time was %d uSec.\n", total_usecs);*/          for(i=1; i<=(nlstate); i++){
   /*------ End -----------*/            for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
  end:            }
 #ifdef windows          }
  chdir(pathcd);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
 #endif            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                varpij[i][j][(int)age] = doldm[i][j];
  system("..\\gp37mgw\\wgnuplot graph.plt");  
           /*printf("\n%d ",(int)age);
 #ifdef windows            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   while (z[0] != 'q') {            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     chdir(pathcd);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     printf("\nType e to edit output files, c to start again, and q for exiting: ");            }*/
     scanf("%s",z);  
     if (z[0] == 'c') system("./imach");          fprintf(ficresprob,"\n%d ",(int)age);
     else if (z[0] == 'e') {          fprintf(ficresprobcov,"\n%d ",(int)age);
       chdir(path);          fprintf(ficresprobcor,"\n%d ",(int)age);
       system(optionfilehtm);  
     }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     else if (z[0] == 'q') exit(0);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
 #endif            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
 }            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - Life expectancies by age and initial health status (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     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];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     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]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Un peu sale */
       }
     }
     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], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",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;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
           exit(1);
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           exit(1);
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         exit(1);
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         exit(1);
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       lval=strtol(strb,&endptr,10); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight.  Exiting.\n",lval, i,line,linei);
         exit(1);
       }
       weight[i]=(double)(lval); 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self).  Exiting.\n",lval,linei, i,line,j);
           exit(1);
         }
         covar[j][i]=(double)(lval);
         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;
     } /* End loop reading  data */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    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;
           }else 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]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficrespl, "#Local time at start: %s", strstart);
       fprintf(ficrespl,"#Stable prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       fprintf(ficrespij, "#Local time at start: %s", strstart);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /*---------- Health expectancies and variances ------------*/
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total LEs with variances: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficreseij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
           }
   
           fprintf(ficrest, "#Local time at start: %s", strstart);
           fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficreseij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of stable prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
     free_matrix(prlim,1,nlstate,1,nlstate);
       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);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n 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.1.21  
changed lines
  Added in v.1.114


FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>