Diff for /imach/src/imach.c between versions 1.16 and 1.124

version 1.16, 2002/02/20 17:12:32 version 1.124, 2006/03/22 17:13:53
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 1.124  2006/03/22 17:13:53  lievre
   individuals from different ages are interviewed on their health status    Parameters are printed with %lf instead of %f (more numbers after the comma).
   or degree of  disability. At least a second wave of interviews    The log-likelihood is printed in the log file
   ("longitudinal") should  measure each new individual health status.  
   Health expectancies are computed from the transistions observed between    Revision 1.123  2006/03/20 10:52:43  brouard
   waves and are computed for each degree of severity of disability (number    * imach.c (Module): <title> changed, corresponds to .htm file
   of life states). More degrees you consider, more time is necessary to    name. <head> headers where missing.
   reach the Maximum Likelihood of the parameters involved in the model.  
   The simplest model is the multinomial logistic model where pij is    * imach.c (Module): Weights can have a decimal point as for
   the probabibility to be observed in state j at the second wave conditional    English (a comma might work with a correct LC_NUMERIC environment,
   to be observed in state i at the first wave. Therefore the model is:    otherwise the weight is truncated).
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Modification of warning when the covariates values are not 0 or
   is a covariate. If you want to have a more complex model than "constant and    1.
   age", you should modify the program where the markup    Version 0.98g
     *Covariates have to be included here again* invites you to do it.  
   More covariates you add, less is the speed of the convergence.    Revision 1.122  2006/03/20 09:45:41  brouard
     (Module): Weights can have a decimal point as for
   The advantage that this computer programme claims, comes from that if the    English (a comma might work with a correct LC_NUMERIC environment,
   delay between waves is not identical for each individual, or if some    otherwise the weight is truncated).
   individual missed an interview, the information is not rounded or lost, but    Modification of warning when the covariates values are not 0 or
   taken into account using an interpolation or extrapolation.    1.
   hPijx is the probability to be    Version 0.98g
   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 1.121  2006/03/16 17:45:01  lievre
   unobserved intermediate  states. This elementary transition (by month or    * imach.c (Module): Comments concerning covariates added
   quarter trimester, semester or year) is model as a multinomial logistic.  
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    * imach.c (Module): refinements in the computation of lli if
   and the contribution of each individual to the likelihood is simply hPijx.    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.120  2006/03/16 15:10:38  lievre
      (Module): refinements in the computation of lli if
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    status=-2 in order to have more reliable computation if stepm is
            Institut national d'études démographiques, Paris.    not 1 month. Version 0.98f
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.119  2006/03/15 17:42:26  brouard
   It is copyrighted identically to a GNU software product, ie programme and    (Module): Bug if status = -2, the loglikelihood was
   software can be distributed freely for non commercial use. Latest version    computed as likelihood omitting the logarithm. Version O.98e
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.118  2006/03/14 18:20:07  brouard
      (Module): varevsij Comments added explaining the second
 #include <math.h>    table of variances if popbased=1 .
 #include <stdio.h>    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #include <stdlib.h>    (Module): Function pstamp added
 #include <unistd.h>    (Module): Version 0.98d
   
 #define MAXLINE 256    Revision 1.117  2006/03/14 17:16:22  brouard
 #define FILENAMELENGTH 80    (Module): varevsij Comments added explaining the second
 /*#define DEBUG*/    table of variances if popbased=1 .
 #define windows    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    (Module): Function pstamp added
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    (Module): Version 0.98d
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.116  2006/03/06 10:29:27  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (Module): Variance-covariance wrong links and
     varian-covariance of ej. is needed (Saito).
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.115  2006/02/27 12:17:45  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    (Module): One freematrix added in mlikeli! 0.98c
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.114  2006/02/26 12:57:58  brouard
 #define YEARM 12. /* Number of months per year */    (Module): Some improvements in processing parameter
 #define AGESUP 130    filename with strsep.
 #define AGEBASE 40  
     Revision 1.113  2006/02/24 14:20:24  brouard
     (Module): Memory leaks checks with valgrind and:
 int nvar;    datafile was not closed, some imatrix were not freed and on matrix
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    allocation too.
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Revision 1.112  2006/01/30 09:55:26  brouard
 int ndeath=1; /* Number of dead states */    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.111  2006/01/25 20:38:18  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 int *wav; /* Number of waves for this individuual 0 is possible */    (Module): Comments can be added in data file. Missing date values
 int maxwav; /* Maxim number of waves */    can be a simple dot '.'.
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.110  2006/01/25 00:51:50  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Module): Lots of cleaning and bugs added (Gompertz)
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Revision 1.109  2006/01/24 19:37:15  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    (Module): Comments (lines starting with a #) are allowed in data.
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    Revision 1.108  2006/01/19 18:05:42  lievre
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    Gnuplot problem appeared...
 FILE *ficreseij;    To be fixed
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.107  2006/01/19 16:20:37  brouard
   char fileresv[FILENAMELENGTH];    Test existence of gnuplot in imach path
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    Revision 1.106  2006/01/19 13:24:36  brouard
     Some cleaning and links added in html output
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.105  2006/01/05 20:23:19  lievre
 #define FTOL 1.0e-10    *** empty log message ***
   
 #define NRANSI    Revision 1.104  2005/09/30 16:11:43  lievre
 #define ITMAX 200    (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
 #define TOL 2.0e-4    that the person is alive, then we can code his/her status as -2
     (instead of missing=-1 in earlier versions) and his/her
 #define CGOLD 0.3819660    contributions to the likelihood is 1 - Prob of dying from last
 #define ZEPS 1.0e-10    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    the healthy state at last known wave). Version is 0.98
   
 #define GOLD 1.618034    Revision 1.103  2005/09/30 15:54:49  lievre
 #define GLIMIT 100.0    (Module): sump fixed, loop imx fixed, and simplifications.
 #define TINY 1.0e-20  
     Revision 1.102  2004/09/15 17:31:30  brouard
 static double maxarg1,maxarg2;    Add the possibility to read data file including tab characters.
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.101  2004/09/15 10:38:38  brouard
      Fix on curr_time
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.100  2004/07/12 18:29:06  brouard
     Add version for Mac OS X. Just define UNIX in Makefile
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.99  2004/06/05 08:57:40  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    *** empty log message ***
   
 int imx;    Revision 1.98  2004/05/16 15:05:56  brouard
 int stepm;    New version 0.97 . First attempt to estimate force of mortality
 /* Stepm, step in month: minimum step interpolation*/    directly from the data i.e. without the need of knowing the health
     state at each age, but using a Gompertz model: log u =a + b*age .
 int m,nb;    This is the basic analysis of mortality and should be done before any
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    other analysis, in order to test if the mortality estimated from the
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    cross-longitudinal survey is different from the mortality estimated
 double **pmmij, ***probs, ***mobaverage;    from other sources like vital statistic data.
   
 double *weight;    The same imach parameter file can be used but the option for mle should be -3.
 int **s; /* Status */  
 double *agedc, **covar, idx;    Agnès, who wrote this part of the code, tried to keep most of the
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    former routines in order to include the new code within the former code.
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    The output is very simple: only an estimate of the intercept and of
 double ftolhess; /* Tolerance for computing hessian */    the slope with 95% confident intervals.
   
 /**************** split *************************/    Current limitations:
 static  int split( char *path, char *dirc, char *name )    A) Even if you enter covariates, i.e. with the
 {    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
    char *s;                             /* pointer */    B) There is no computation of Life Expectancy nor Life Table.
    int  l1, l2;                         /* length counters */  
     Revision 1.97  2004/02/20 13:25:42  lievre
    l1 = strlen( path );                 /* length of path */    Version 0.96d. Population forecasting command line is (temporarily)
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    suppressed.
    s = strrchr( path, '\\' );           /* find last / */  
    if ( s == NULL ) {                   /* no directory, so use current */    Revision 1.96  2003/07/15 15:38:55  brouard
 #if     defined(__bsd__)                /* get current working directory */    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
       extern char       *getwd( );    rewritten within the same printf. Workaround: many printfs.
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.95  2003/07/08 07:54:34  brouard
 #else    * imach.c (Repository):
       extern char       *getcwd( );    (Repository): Using imachwizard code to output a more meaningful covariance
     matrix (cov(a12,c31) instead of numbers.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.94  2003/06/27 13:00:02  brouard
          return( GLOCK_ERROR_GETCWD );    Just cleaning
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.93  2003/06/25 16:33:55  brouard
    } else {                             /* strip direcotry from path */    (Module): On windows (cygwin) function asctime_r doesn't
       s++;                              /* after this, the filename */    exist so I changed back to asctime which exists.
       l2 = strlen( s );                 /* length of filename */    (Module): Version 0.96b
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Revision 1.92  2003/06/25 16:30:45  brouard
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    (Module): On windows (cygwin) function asctime_r doesn't
       dirc[l1-l2] = 0;                  /* add zero */    exist so I changed back to asctime which exists.
    }  
    l1 = strlen( dirc );                 /* length of directory */    Revision 1.91  2003/06/25 15:30:29  brouard
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    * imach.c (Repository): Duplicated warning errors corrected.
    return( 0 );                         /* we're done */    (Repository): Elapsed time after each iteration is now output. It
 }    helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
     concerning matrix of covariance. It has extension -cov.htm.
 /******************************************/  
     Revision 1.90  2003/06/24 12:34:15  brouard
 void replace(char *s, char*t)    (Module): Some bugs corrected for windows. Also, when
 {    mle=-1 a template is output in file "or"mypar.txt with the design
   int i;    of the covariance matrix to be input.
   int lg=20;  
   i=0;    Revision 1.89  2003/06/24 12:30:52  brouard
   lg=strlen(t);    (Module): Some bugs corrected for windows. Also, when
   for(i=0; i<= lg; i++) {    mle=-1 a template is output in file "or"mypar.txt with the design
     (s[i] = t[i]);    of the covariance matrix to be input.
     if (t[i]== '\\') s[i]='/';  
   }    Revision 1.88  2003/06/23 17:54:56  brouard
 }    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   
 int nbocc(char *s, char occ)    Revision 1.87  2003/06/18 12:26:01  brouard
 {    Version 0.96
   int i,j=0;  
   int lg=20;    Revision 1.86  2003/06/17 20:04:08  brouard
   i=0;    (Module): Change position of html and gnuplot routines and added
   lg=strlen(s);    routine fileappend.
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;    Revision 1.85  2003/06/17 13:12:43  brouard
   }    * imach.c (Repository): Check when date of death was earlier that
   return j;    current date of interview. It may happen when the death was just
 }    prior to the death. In this case, dh was negative and likelihood
     was wrong (infinity). We still send an "Error" but patch by
 void cutv(char *u,char *v, char*t, char occ)    assuming that the date of death was just one stepm after the
 {    interview.
   int i,lg,j,p=0;    (Repository): Because some people have very long ID (first column)
   i=0;    we changed int to long in num[] and we added a new lvector for
   for(j=0; j<=strlen(t)-1; j++) {    memory allocation. But we also truncated to 8 characters (left
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    truncation)
   }    (Repository): No more line truncation errors.
   
   lg=strlen(t);    Revision 1.84  2003/06/13 21:44:43  brouard
   for(j=0; j<p; j++) {    * imach.c (Repository): Replace "freqsummary" at a correct
     (u[j] = t[j]);    place. It differs from routine "prevalence" which may be called
   }    many times. Probs is memory consuming and must be used with
      u[p]='\0';    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    Revision 1.83  2003/06/10 13:39:11  lievre
   }    *** empty log message ***
 }  
     Revision 1.82  2003/06/05 15:57:20  brouard
 /********************** nrerror ********************/    Add log in  imach.c and  fullversion number is now printed.
   
 void nrerror(char error_text[])  */
 {  /*
   fprintf(stderr,"ERREUR ...\n");     Interpolated Markov Chain
   fprintf(stderr,"%s\n",error_text);  
   exit(1);    Short summary of the programme:
 }    
 /*********************** vector *******************/    This program computes Healthy Life Expectancies from
 double *vector(int nl, int nh)    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 {    first survey ("cross") where individuals from different ages are
   double *v;    interviewed on their health status or degree of disability (in the
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    case of a health survey which is our main interest) -2- at least a
   if (!v) nrerror("allocation failure in vector");    second wave of interviews ("longitudinal") which measure each change
   return v-nl+NR_END;    (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
 /************************ free vector ******************/    Maximum Likelihood of the parameters involved in the model.  The
 void free_vector(double*v, int nl, int nh)    simplest model is the multinomial logistic model where pij is the
 {    probability to be observed in state j at the second wave
   free((FREE_ARG)(v+nl-NR_END));    conditional to be observed in state i at the first wave. Therefore
 }    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     'age' is age and 'sex' is a covariate. If you want to have a more
 /************************ivector *******************************/    complex model than "constant and age", you should modify the program
 int *ivector(long nl,long nh)    where the markup *Covariates have to be included here again* invites
 {    you to do it.  More covariates you add, slower the
   int *v;    convergence.
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");    The advantage of this computer programme, compared to a simple
   return v-nl+NR_END;    multinomial logistic model, is clear when the delay between waves is not
 }    identical for each individual. Also, if a individual missed an
     intermediate interview, the information is lost, but taken into
 /******************free ivector **************************/    account using an interpolation or extrapolation.  
 void free_ivector(int *v, long nl, long nh)  
 {    hPijx is the probability to be observed in state i at age x+h
   free((FREE_ARG)(v+nl-NR_END));    conditional to the observed state i at age x. The delay 'h' can be
 }    split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
 /******************* imatrix *******************************/    semester or year) is modelled as a multinomial logistic.  The hPx
 int **imatrix(long nrl, long nrh, long ncl, long nch)    matrix is simply the matrix product of nh*stepm elementary matrices
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    and the contribution of each individual to the likelihood is simply
 {    hPijx.
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;    Also this programme outputs the covariance matrix of the parameters but also
      of the life expectancies. It also computes the period (stable) prevalence. 
   /* allocate pointers to rows */    
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   if (!m) nrerror("allocation failure 1 in matrix()");             Institut national d'études démographiques, Paris.
   m += NR_END;    This software have been partly granted by Euro-REVES, a concerted action
   m -= nrl;    from the European Union.
      It is copyrighted identically to a GNU software product, ie programme and
      software can be distributed freely for non commercial use. Latest version
   /* allocate rows and set pointers to them */    can be accessed at http://euroreves.ined.fr/imach .
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   m[nrl] += NR_END;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   m[nrl] -= ncl;    
      **********************************************************************/
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  /*
      main
   /* return pointer to array of pointers to rows */    read parameterfile
   return m;    read datafile
 }    concatwav
     freqsummary
 /****************** free_imatrix *************************/    if (mle >= 1)
 void free_imatrix(m,nrl,nrh,ncl,nch)      mlikeli
       int **m;    print results files
       long nch,ncl,nrh,nrl;    if mle==1 
      /* free an int matrix allocated by imatrix() */       computes hessian
 {    read end of parameter file: agemin, agemax, bage, fage, estepm
   free((FREE_ARG) (m[nrl]+ncl-NR_END));        begin-prev-date,...
   free((FREE_ARG) (m+nrl-NR_END));    open gnuplot file
 }    open html file
     period (stable) prevalence
 /******************* matrix *******************************/     for age prevalim()
 double **matrix(long nrl, long nrh, long ncl, long nch)    h Pij x
 {    variance of p varprob
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    forecasting if prevfcast==1 prevforecast call prevalence()
   double **m;    health expectancies
     Variance-covariance of DFLE
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    prevalence()
   if (!m) nrerror("allocation failure 1 in matrix()");     movingaverage()
   m += NR_END;    varevsij() 
   m -= nrl;    if popbased==1 varevsij(,popbased)
     total life expectancies
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Variance of period (stable) prevalence
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");   end
   m[nrl] += NR_END;  */
   m[nrl] -= ncl;  
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;   
 }  #include <math.h>
   #include <stdio.h>
 /*************************free matrix ************************/  #include <stdlib.h>
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  #include <string.h>
 {  #include <unistd.h>
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  #include <limits.h>
 }  #include <sys/types.h>
   #include <sys/stat.h>
 /******************* ma3x *******************************/  #include <errno.h>
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  extern int errno;
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  /* #include <sys/time.h> */
   double ***m;  #include <time.h>
   #include "timeval.h"
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  /* #include <libintl.h> */
   m += NR_END;  /* #define _(String) gettext (String) */
   m -= nrl;  
   #define MAXLINE 256
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define GNUPLOTPROGRAM "gnuplot"
   m[nrl] += NR_END;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   m[nrl] -= ncl;  #define FILENAMELENGTH 132
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   m[nrl][ncl] += NR_END;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)  #define NINTERVMAX 8
     m[nrl][j]=m[nrl][j-1]+nlay;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
    #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   for (i=nrl+1; i<=nrh; i++) {  #define NCOVMAX 8 /* Maximum number of covariates */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define MAXN 20000
     for (j=ncl+1; j<=nch; j++)  #define YEARM 12. /* Number of months per year */
       m[i][j]=m[i][j-1]+nlay;  #define AGESUP 130
   }  #define AGEBASE 40
   return m;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
 }  #ifdef UNIX
   #define DIRSEPARATOR '/'
 /*************************free ma3x ************************/  #define CHARSEPARATOR "/"
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define ODIRSEPARATOR '\\'
 {  #else
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #define DIRSEPARATOR '\\'
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define CHARSEPARATOR "\\"
   free((FREE_ARG)(m+nrl-NR_END));  #define ODIRSEPARATOR '/'
 }  #endif
   
 /***************** f1dim *************************/  /* $Id$ */
 extern int ncom;  /* $State$ */
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);  char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
    char fullversion[]="$Revision$ $Date$"; 
 double f1dim(double x)  char strstart[80];
 {  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   int j;  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   double f;  int nvar;
   double *xt;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
    int npar=NPARMAX;
   xt=vector(1,ncom);  int nlstate=2; /* Number of live states */
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  int ndeath=1; /* Number of dead states */
   f=(*nrfunc)(xt);  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   free_vector(xt,1,ncom);  int popbased=0;
   return f;  
 }  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav; /* Maxim number of waves */
 /*****************brent *************************/  int jmin, jmax; /* min, max spacing between 2 waves */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
 {  int gipmx, gsw; /* Global variables on the number of contributions 
   int iter;                     to the likelihood and the sum of weights (done by funcone)*/
   double a,b,d,etemp;  int mle, weightopt;
   double fu,fv,fw,fx;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   double ftemp;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   double e=0.0;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
    double jmean; /* Mean space between 2 waves */
   a=(ax < cx ? ax : cx);  double **oldm, **newm, **savm; /* Working pointers to matrices */
   b=(ax > cx ? ax : cx);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   x=w=v=bx;  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   fw=fv=fx=(*f)(x);  FILE *ficlog, *ficrespow;
   for (iter=1;iter<=ITMAX;iter++) {  int globpr; /* Global variable for printing or not */
     xm=0.5*(a+b);  double fretone; /* Only one call to likelihood */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  long ipmx; /* Number of contributions */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  double sw; /* Sum of weights */
     printf(".");fflush(stdout);  char filerespow[FILENAMELENGTH];
 #ifdef DEBUG  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
     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);  FILE *ficresilk;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 #endif  FILE *ficresprobmorprev;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  FILE *fichtm, *fichtmcov; /* Html File */
       *xmin=x;  FILE *ficreseij;
       return fx;  char filerese[FILENAMELENGTH];
     }  FILE *ficresstdeij;
     ftemp=fu;  char fileresstde[FILENAMELENGTH];
     if (fabs(e) > tol1) {  FILE *ficrescveij;
       r=(x-w)*(fx-fv);  char filerescve[FILENAMELENGTH];
       q=(x-v)*(fx-fw);  FILE  *ficresvij;
       p=(x-v)*q-(x-w)*r;  char fileresv[FILENAMELENGTH];
       q=2.0*(q-r);  FILE  *ficresvpl;
       if (q > 0.0) p = -p;  char fileresvpl[FILENAMELENGTH];
       q=fabs(q);  char title[MAXLINE];
       etemp=e;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       e=d;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  char command[FILENAMELENGTH];
       else {  int  outcmd=0;
         d=p/q;  
         u=x+d;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  char filelog[FILENAMELENGTH]; /* Log file */
       }  char filerest[FILENAMELENGTH];
     } else {  char fileregp[FILENAMELENGTH];
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  char popfile[FILENAMELENGTH];
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     fu=(*f)(u);  
     if (fu <= fx) {  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
       if (u >= x) a=x; else b=x;  struct timezone tzp;
       SHFT(v,w,x,u)  extern int gettimeofday();
         SHFT(fv,fw,fx,fu)  struct tm tmg, tm, tmf, *gmtime(), *localtime();
         } else {  long time_value;
           if (u < x) a=u; else b=u;  extern long time();
           if (fu <= fw || w == x) {  char strcurr[80], strfor[80];
             v=w;  
             w=u;  char *endptr;
             fv=fw;  long lval;
             fw=fu;  double dval;
           } else if (fu <= fv || v == x || v == w) {  
             v=u;  #define NR_END 1
             fv=fu;  #define FREE_ARG char*
           }  #define FTOL 1.0e-10
         }  
   }  #define NRANSI 
   nrerror("Too many iterations in brent");  #define ITMAX 200 
   *xmin=x;  
   return fx;  #define TOL 2.0e-4 
 }  
   #define CGOLD 0.3819660 
 /****************** mnbrak ***********************/  #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))  #define GOLD 1.618034 
 {  #define GLIMIT 100.0 
   double ulim,u,r,q, dum;  #define TINY 1.0e-20 
   double fu;  
    static double maxarg1,maxarg2;
   *fa=(*func)(*ax);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   *fb=(*func)(*bx);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   if (*fb > *fa) {    
     SHFT(dum,*ax,*bx,dum)  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       SHFT(dum,*fb,*fa,dum)  #define rint(a) floor(a+0.5)
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);  static double sqrarg;
   *fc=(*func)(*cx);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   while (*fb > *fc) {  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
     r=(*bx-*ax)*(*fb-*fc);  int agegomp= AGEGOMP;
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  int imx; 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  int stepm=1;
     ulim=(*bx)+GLIMIT*(*cx-*bx);  /* Stepm, step in month: minimum step interpolation*/
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);  int estepm;
     } else if ((*cx-u)*(u-ulim) > 0.0) {  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       fu=(*func)(u);  
       if (fu < *fc) {  int m,nb;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  long *num;
           SHFT(*fb,*fc,fu,(*func)(u))  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
           }  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  double **pmmij, ***probs;
       u=ulim;  double *ageexmed,*agecens;
       fu=(*func)(u);  double dateintmean=0;
     } else {  
       u=(*cx)+GOLD*(*cx-*bx);  double *weight;
       fu=(*func)(u);  int **s; /* Status */
     }  double *agedc, **covar, idx;
     SHFT(*ax,*bx,*cx,u)  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
       SHFT(*fa,*fb,*fc,fu)  double *lsurv, *lpop, *tpop;
       }  
 }  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   double ftolhess; /* Tolerance for computing hessian */
 /*************** linmin ************************/  
   /**************** split *************************/
 int ncom;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 double *pcom,*xicom;  {
 double (*nrfunc)(double []);    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
         the name of the file (name), its extension only (ext) and its first part of the name (finame)
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    */ 
 {    char  *ss;                            /* pointer */
   double brent(double ax, double bx, double cx,    int   l1, l2;                         /* length counters */
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);    l1 = strlen(path );                   /* length of path */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
               double *fc, double (*func)(double));    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   int j;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   double xx,xmin,bx,ax;      strcpy( name, path );               /* we got the fullname name because no directory */
   double fx,fb,fa;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
          printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   ncom=n;      /* get current working directory */
   pcom=vector(1,n);      /*    extern  char* getcwd ( char *buf , int len);*/
   xicom=vector(1,n);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   nrfunc=func;        return( GLOCK_ERROR_GETCWD );
   for (j=1;j<=n;j++) {      }
     pcom[j]=p[j];      /* got dirc from getcwd*/
     xicom[j]=xi[j];      printf(" DIRC = %s \n",dirc);
   }    } else {                              /* strip direcotry from path */
   ax=0.0;      ss++;                               /* after this, the filename */
   xx=1.0;      l2 = strlen( ss );                  /* length of filename */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      strcpy( name, ss );         /* save file name */
 #ifdef DEBUG      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      dirc[l1-l2] = 0;                    /* add zero */
 #endif      printf(" DIRC2 = %s \n",dirc);
   for (j=1;j<=n;j++) {    }
     xi[j] *= xmin;    /* We add a separator at the end of dirc if not exists */
     p[j] += xi[j];    l1 = strlen( dirc );                  /* length of directory */
   }    if( dirc[l1-1] != DIRSEPARATOR ){
   free_vector(xicom,1,n);      dirc[l1] =  DIRSEPARATOR;
   free_vector(pcom,1,n);      dirc[l1+1] = 0; 
 }      printf(" DIRC3 = %s \n",dirc);
     }
 /*************** powell ************************/    ss = strrchr( name, '.' );            /* find last / */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    if (ss >0){
             double (*func)(double []))      ss++;
 {      strcpy(ext,ss);                     /* save extension */
   void linmin(double p[], double xi[], int n, double *fret,      l1= strlen( name);
               double (*func)(double []));      l2= strlen(ss)+1;
   int i,ibig,j;      strncpy( finame, name, l1-l2);
   double del,t,*pt,*ptt,*xit;      finame[l1-l2]= 0;
   double fp,fptt;    }
   double *xits;  
   pt=vector(1,n);    return( 0 );                          /* we're done */
   ptt=vector(1,n);  }
   xit=vector(1,n);  
   xits=vector(1,n);  
   *fret=(*func)(p);  /******************************************/
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  void replace_back_to_slash(char *s, char*t)
     fp=(*fret);  {
     ibig=0;    int i;
     del=0.0;    int lg=0;
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    i=0;
     for (i=1;i<=n;i++)    lg=strlen(t);
       printf(" %d %.12f",i, p[i]);    for(i=0; i<= lg; i++) {
     printf("\n");      (s[i] = t[i]);
     for (i=1;i<=n;i++) {      if (t[i]== '\\') s[i]='/';
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    }
       fptt=(*fret);  }
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);  int nbocc(char *s, char occ)
 #endif  {
       printf("%d",i);fflush(stdout);    int i,j=0;
       linmin(p,xit,n,fret,func);    int lg=20;
       if (fabs(fptt-(*fret)) > del) {    i=0;
         del=fabs(fptt-(*fret));    lg=strlen(s);
         ibig=i;    for(i=0; i<= lg; i++) {
       }    if  (s[i] == occ ) j++;
 #ifdef DEBUG    }
       printf("%d %.12e",i,(*fret));    return j;
       for (j=1;j<=n;j++) {  }
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);  void cutv(char *u,char *v, char*t, char occ)
       }  {
       for(j=1;j<=n;j++)    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
         printf(" p=%.12e",p[j]);       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       printf("\n");       gives u="abcedf" and v="ghi2j" */
 #endif    int i,lg,j,p=0;
     }    i=0;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    for(j=0; j<=strlen(t)-1; j++) {
 #ifdef DEBUG      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
       int k[2],l;    }
       k[0]=1;  
       k[1]=-1;    lg=strlen(t);
       printf("Max: %.12e",(*func)(p));    for(j=0; j<p; j++) {
       for (j=1;j<=n;j++)      (u[j] = t[j]);
         printf(" %.12e",p[j]);    }
       printf("\n");       u[p]='\0';
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {     for(j=0; j<= lg; j++) {
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      if (j>=(p+1))(v[j-p-1] = t[j]);
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    }
         }  }
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  /********************** nrerror ********************/
 #endif  
   void nrerror(char error_text[])
   {
       free_vector(xit,1,n);    fprintf(stderr,"ERREUR ...\n");
       free_vector(xits,1,n);    fprintf(stderr,"%s\n",error_text);
       free_vector(ptt,1,n);    exit(EXIT_FAILURE);
       free_vector(pt,1,n);  }
       return;  /*********************** vector *******************/
     }  double *vector(int nl, int nh)
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  {
     for (j=1;j<=n;j++) {    double *v;
       ptt[j]=2.0*p[j]-pt[j];    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       xit[j]=p[j]-pt[j];    if (!v) nrerror("allocation failure in vector");
       pt[j]=p[j];    return v-nl+NR_END;
     }  }
     fptt=(*func)(ptt);  
     if (fptt < fp) {  /************************ free vector ******************/
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  void free_vector(double*v, int nl, int nh)
       if (t < 0.0) {  {
         linmin(p,xit,n,fret,func);    free((FREE_ARG)(v+nl-NR_END));
         for (j=1;j<=n;j++) {  }
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];  /************************ivector *******************************/
         }  int *ivector(long nl,long nh)
 #ifdef DEBUG  {
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    int *v;
         for(j=1;j<=n;j++)    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
           printf(" %.12e",xit[j]);    if (!v) nrerror("allocation failure in ivector");
         printf("\n");    return v-nl+NR_END;
 #endif  }
       }  
     }  /******************free ivector **************************/
   }  void free_ivector(int *v, long nl, long nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /**** Prevalence limit ****************/  }
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  /************************lvector *******************************/
 {  long *lvector(long nl,long nh)
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  {
      matrix by transitions matrix until convergence is reached */    long *v;
     v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   int i, ii,j,k;    if (!v) nrerror("allocation failure in ivector");
   double min, max, maxmin, maxmax,sumnew=0.;    return v-nl+NR_END;
   double **matprod2();  }
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;  /******************free lvector **************************/
   double agefin, delaymax=50 ; /* Max number of years to converge */  void free_lvector(long *v, long nl, long nh)
   {
   for (ii=1;ii<=nlstate+ndeath;ii++)    free((FREE_ARG)(v+nl-NR_END));
     for (j=1;j<=nlstate+ndeath;j++){  }
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
     }  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
    cov[1]=1.;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
    { 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    int **m; 
     newm=savm;    
     /* Covariates have to be included here again */    /* allocate pointers to rows */ 
      cov[2]=agefin;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
      if (!m) nrerror("allocation failure 1 in matrix()"); 
       for (k=1; k<=cptcovn;k++) {    m += NR_END; 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    m -= nrl; 
         /*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 (k=1; k<=cptcovage;k++)    /* allocate rows and set pointers to them */ 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       for (k=1; k<=cptcovprod;k++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    m[nrl] += NR_END; 
     m[nrl] -= ncl; 
       /*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]);*/    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    /* return pointer to array of pointers to rows */ 
     return m; 
     savm=oldm;  } 
     oldm=newm;  
     maxmax=0.;  /****************** free_imatrix *************************/
     for(j=1;j<=nlstate;j++){  void free_imatrix(m,nrl,nrh,ncl,nch)
       min=1.;        int **m;
       max=0.;        long nch,ncl,nrh,nrl; 
       for(i=1; i<=nlstate; i++) {       /* free an int matrix allocated by imatrix() */ 
         sumnew=0;  { 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         prlim[i][j]= newm[i][j]/(1-sumnew);    free((FREE_ARG) (m+nrl-NR_END)); 
         max=FMAX(max,prlim[i][j]);  } 
         min=FMIN(min,prlim[i][j]);  
       }  /******************* matrix *******************************/
       maxmin=max-min;  double **matrix(long nrl, long nrh, long ncl, long nch)
       maxmax=FMAX(maxmax,maxmin);  {
     }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     if(maxmax < ftolpl){    double **m;
       return prlim;  
     }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   }    if (!m) nrerror("allocation failure 1 in matrix()");
 }    m += NR_END;
     m -= nrl;
 /*************** transition probabilities ***************/  
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 {    m[nrl] += NR_END;
   double s1, s2;    m[nrl] -= ncl;
   /*double t34;*/  
   int i,j,j1, nc, ii, jj;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
     for(i=1; i<= nlstate; i++){    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     for(j=1; j<i;j++){     */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  }
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /*************************free matrix ************************/
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       }  {
       ps[i][j]=s2;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    free((FREE_ARG)(m+nrl-NR_END));
     }  }
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /******************* ma3x *******************************/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  {
       }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       ps[i][j]=(s2);    double ***m;
     }  
   }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     /*ps[3][2]=1;*/    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
   for(i=1; i<= nlstate; i++){    m -= nrl;
      s1=0;  
     for(j=1; j<i; j++)    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       s1+=exp(ps[i][j]);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     for(j=i+1; j<=nlstate+ndeath; j++)    m[nrl] += NR_END;
       s1+=exp(ps[i][j]);    m[nrl] -= ncl;
     ps[i][i]=1./(s1+1.);  
     for(j=1; j<i; j++)    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     for(j=i+1; j<=nlstate+ndeath; j++)    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       ps[i][j]= exp(ps[i][j])*ps[i][i];    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    m[nrl][ncl] += NR_END;
   } /* end i */    m[nrl][ncl] -= nll;
     for (j=ncl+1; j<=nch; j++) 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      m[nrl][j]=m[nrl][j-1]+nlay;
     for(jj=1; jj<= nlstate+ndeath; jj++){    
       ps[ii][jj]=0;    for (i=nrl+1; i<=nrh; i++) {
       ps[ii][ii]=1;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     }      for (j=ncl+1; j<=nch; j++) 
   }        m[i][j]=m[i][j-1]+nlay;
     }
     return m; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     for(jj=1; jj<= nlstate+ndeath; jj++){             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
      printf("%lf ",ps[ii][jj]);    */
    }  }
     printf("\n ");  
     }  /*************************free ma3x ************************/
     printf("\n ");printf("%lf ",cov[2]);*/  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 /*  {
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   goto end;*/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     return ps;    free((FREE_ARG)(m+nrl-NR_END));
 }  }
   
 /**************** Product of 2 matrices ******************/  /*************** function subdirf ***********/
   char *subdirf(char fileres[])
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  {
 {    /* Caution optionfilefiname is hidden */
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    strcpy(tmpout,optionfilefiname);
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    strcat(tmpout,"/"); /* Add to the right */
   /* in, b, out are matrice of pointers which should have been initialized    strcat(tmpout,fileres);
      before: only the contents of out is modified. The function returns    return tmpout;
      a pointer to pointers identical to out */  }
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)  /*************** function subdirf2 ***********/
     for(k=ncolol; k<=ncoloh; k++)  char *subdirf2(char fileres[], char *preop)
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  {
         out[i][k] +=in[i][j]*b[j][k];    
     /* Caution optionfilefiname is hidden */
   return out;    strcpy(tmpout,optionfilefiname);
 }    strcat(tmpout,"/");
     strcat(tmpout,preop);
     strcat(tmpout,fileres);
 /************* Higher Matrix Product ***************/    return tmpout;
   }
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  
 {  /*************** function subdirf3 ***********/
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  char *subdirf3(char fileres[], char *preop, char *preop2)
      duration (i.e. until  {
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    /* Caution optionfilefiname is hidden */
      (typically every 2 years instead of every month which is too big).    strcpy(tmpout,optionfilefiname);
      Model is determined by parameters x and covariates have to be    strcat(tmpout,"/");
      included manually here.    strcat(tmpout,preop);
     strcat(tmpout,preop2);
      */    strcat(tmpout,fileres);
     return tmpout;
   int i, j, d, h, k;  }
   double **out, cov[NCOVMAX];  
   double **newm;  /***************** f1dim *************************/
   extern int ncom; 
   /* Hstepm could be zero and should return the unit matrix */  extern double *pcom,*xicom;
   for (i=1;i<=nlstate+ndeath;i++)  extern double (*nrfunc)(double []); 
     for (j=1;j<=nlstate+ndeath;j++){   
       oldm[i][j]=(i==j ? 1.0 : 0.0);  double f1dim(double x) 
       po[i][j][0]=(i==j ? 1.0 : 0.0);  { 
     }    int j; 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    double f;
   for(h=1; h <=nhstepm; h++){    double *xt; 
     for(d=1; d <=hstepm; d++){   
       newm=savm;    xt=vector(1,ncom); 
       /* Covariates have to be included here again */    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       cov[1]=1.;    f=(*nrfunc)(xt); 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    free_vector(xt,1,ncom); 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    return f; 
       for (k=1; k<=cptcovage;k++)  } 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)  /*****************brent *************************/
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   { 
     int iter; 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    double a,b,d,etemp;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    double fu,fv,fw,fx;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    double ftemp;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       savm=oldm;    double e=0.0; 
       oldm=newm;   
     }    a=(ax < cx ? ax : cx); 
     for(i=1; i<=nlstate+ndeath; i++)    b=(ax > cx ? ax : cx); 
       for(j=1;j<=nlstate+ndeath;j++) {    x=w=v=bx; 
         po[i][j][h]=newm[i][j];    fw=fv=fx=(*f)(x); 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    for (iter=1;iter<=ITMAX;iter++) { 
          */      xm=0.5*(a+b); 
       }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   } /* end h */      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   return po;      printf(".");fflush(stdout);
 }      fprintf(ficlog,".");fflush(ficlog);
   #ifdef DEBUG
       printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 /*************** log-likelihood *************/      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);
 double func( double *x)      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 {  #endif
   int i, ii, j, k, mi, d, kk;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        *xmin=x; 
   double **out;        return fx; 
   double sw; /* Sum of weights */      } 
   double lli; /* Individual log likelihood */      ftemp=fu;
   long ipmx;      if (fabs(e) > tol1) { 
   /*extern weight */        r=(x-w)*(fx-fv); 
   /* We are differentiating ll according to initial status */        q=(x-v)*(fx-fw); 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        p=(x-v)*q-(x-w)*r; 
   /*for(i=1;i<imx;i++)        q=2.0*(q-r); 
     printf(" %d\n",s[4][i]);        if (q > 0.0) p = -p; 
   */        q=fabs(q); 
   cov[1]=1.;        etemp=e; 
         e=d; 
   for(k=1; k<=nlstate; k++) ll[k]=0.;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        else { 
     for(mi=1; mi<= wav[i]-1; mi++){          d=p/q; 
       for (ii=1;ii<=nlstate+ndeath;ii++)          u=x+d; 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          if (u-a < tol2 || b-u < tol2) 
       for(d=0; d<dh[mi][i]; d++){            d=SIGN(tol1,xm-x); 
         newm=savm;        } 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      } else { 
         for (kk=1; kk<=cptcovage;kk++) {        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      } 
         }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
              fu=(*f)(u); 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      if (fu <= fx) { 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        if (u >= x) a=x; else b=x; 
         savm=oldm;        SHFT(v,w,x,u) 
         oldm=newm;          SHFT(fv,fw,fx,fu) 
                  } else { 
                    if (u < x) a=u; else b=u; 
       } /* end mult */            if (fu <= fw || w == x) { 
                    v=w; 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);              w=u; 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/              fv=fw; 
       ipmx +=1;              fw=fu; 
       sw += weight[i];            } else if (fu <= fv || v == x || v == w) { 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;              v=u; 
     } /* end of wave */              fv=fu; 
   } /* end of individual */            } 
           } 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    } 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    nrerror("Too many iterations in brent"); 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    *xmin=x; 
   return -l;    return fx; 
 }  } 
   
   /****************** mnbrak ***********************/
 /*********** Maximum Likelihood Estimation ***************/  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))              double (*func)(double)) 
 {  { 
   int i,j, iter;    double ulim,u,r,q, dum;
   double **xi,*delti;    double fu; 
   double fret;   
   xi=matrix(1,npar,1,npar);    *fa=(*func)(*ax); 
   for (i=1;i<=npar;i++)    *fb=(*func)(*bx); 
     for (j=1;j<=npar;j++)    if (*fb > *fa) { 
       xi[i][j]=(i==j ? 1.0 : 0.0);      SHFT(dum,*ax,*bx,dum) 
   printf("Powell\n");        SHFT(dum,*fb,*fa,dum) 
   powell(p,xi,npar,ftol,&iter,&fret,func);        } 
     *cx=(*bx)+GOLD*(*bx-*ax); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    *fc=(*func)(*cx); 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
 }      q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 /**** Computes Hessian and covariance matrix ***/        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 {      if ((*bx-u)*(u-*cx) > 0.0) { 
   double  **a,**y,*x,pd;        fu=(*func)(u); 
   double **hess;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   int i, j,jk;        fu=(*func)(u); 
   int *indx;        if (fu < *fc) { 
           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double hessii(double p[], double delta, int theta, double delti[]);            SHFT(*fb,*fc,fu,(*func)(u)) 
   double hessij(double p[], double delti[], int i, int j);            } 
   void lubksb(double **a, int npar, int *indx, double b[]) ;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   void ludcmp(double **a, int npar, int *indx, double *d) ;        u=ulim; 
         fu=(*func)(u); 
   hess=matrix(1,npar,1,npar);      } else { 
         u=(*cx)+GOLD*(*cx-*bx); 
   printf("\nCalculation of the hessian matrix. Wait...\n");        fu=(*func)(u); 
   for (i=1;i<=npar;i++){      } 
     printf("%d",i);fflush(stdout);      SHFT(*ax,*bx,*cx,u) 
     hess[i][i]=hessii(p,ftolhess,i,delti);        SHFT(*fa,*fb,*fc,fu) 
     /*printf(" %f ",p[i]);*/        } 
     /*printf(" %lf ",hess[i][i]);*/  } 
   }  
    /*************** linmin ************************/
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++)  {  int ncom; 
       if (j>i) {  double *pcom,*xicom;
         printf(".%d%d",i,j);fflush(stdout);  double (*nrfunc)(double []); 
         hess[i][j]=hessij(p,delti,i,j);   
         hess[j][i]=hess[i][j];      void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         /*printf(" %lf ",hess[i][j]);*/  { 
       }    double brent(double ax, double bx, double cx, 
     }                 double (*f)(double), double tol, double *xmin); 
   }    double f1dim(double x); 
   printf("\n");    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    int j; 
      double xx,xmin,bx,ax; 
   a=matrix(1,npar,1,npar);    double fx,fb,fa;
   y=matrix(1,npar,1,npar);   
   x=vector(1,npar);    ncom=n; 
   indx=ivector(1,npar);    pcom=vector(1,n); 
   for (i=1;i<=npar;i++)    xicom=vector(1,n); 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    nrfunc=func; 
   ludcmp(a,npar,indx,&pd);    for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
   for (j=1;j<=npar;j++) {      xicom[j]=xi[j]; 
     for (i=1;i<=npar;i++) x[i]=0;    } 
     x[j]=1;    ax=0.0; 
     lubksb(a,npar,indx,x);    xx=1.0; 
     for (i=1;i<=npar;i++){    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       matcov[i][j]=x[i];    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     }  #ifdef DEBUG
   }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   printf("\n#Hessian matrix#\n");  #endif
   for (i=1;i<=npar;i++) {    for (j=1;j<=n;j++) { 
     for (j=1;j<=npar;j++) {      xi[j] *= xmin; 
       printf("%.3e ",hess[i][j]);      p[j] += xi[j]; 
     }    } 
     printf("\n");    free_vector(xicom,1,n); 
   }    free_vector(pcom,1,n); 
   } 
   /* Recompute Inverse */  
   for (i=1;i<=npar;i++)  char *asc_diff_time(long time_sec, char ascdiff[])
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  {
   ludcmp(a,npar,indx,&pd);    long sec_left, days, hours, minutes;
     days = (time_sec) / (60*60*24);
   /*  printf("\n#Hessian matrix recomputed#\n");    sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
   for (j=1;j<=npar;j++) {    sec_left = (sec_left) %(60*60);
     for (i=1;i<=npar;i++) x[i]=0;    minutes = (sec_left) /60;
     x[j]=1;    sec_left = (sec_left) % (60);
     lubksb(a,npar,indx,x);    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     for (i=1;i<=npar;i++){    return ascdiff;
       y[i][j]=x[i];  }
       printf("%.3e ",y[i][j]);  
     }  /*************** powell ************************/
     printf("\n");  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   }              double (*func)(double [])) 
   */  { 
     void linmin(double p[], double xi[], int n, double *fret, 
   free_matrix(a,1,npar,1,npar);                double (*func)(double [])); 
   free_matrix(y,1,npar,1,npar);    int i,ibig,j; 
   free_vector(x,1,npar);    double del,t,*pt,*ptt,*xit;
   free_ivector(indx,1,npar);    double fp,fptt;
   free_matrix(hess,1,npar,1,npar);    double *xits;
     int niterf, itmp;
   
 }    pt=vector(1,n); 
     ptt=vector(1,n); 
 /*************** hessian matrix ****************/    xit=vector(1,n); 
 double hessii( double x[], double delta, int theta, double delti[])    xits=vector(1,n); 
 {    *fret=(*func)(p); 
   int i;    for (j=1;j<=n;j++) pt[j]=p[j]; 
   int l=1, lmax=20;    for (*iter=1;;++(*iter)) { 
   double k1,k2;      fp=(*fret); 
   double p2[NPARMAX+1];      ibig=0; 
   double res;      del=0.0; 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      last_time=curr_time;
   double fx;      (void) gettimeofday(&curr_time,&tzp);
   int k=0,kmax=10;      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);
   double l1;      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); fflush(ficlog);
   /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
   fx=func(x);     for (i=1;i<=n;i++) {
   for (i=1;i<=npar;i++) p2[i]=x[i];        printf(" %d %.12f",i, p[i]);
   for(l=0 ; l <=lmax; l++){        fprintf(ficlog," %d %.12lf",i, p[i]);
     l1=pow(10,l);        fprintf(ficrespow," %.12lf", p[i]);
     delts=delt;      }
     for(k=1 ; k <kmax; k=k+1){      printf("\n");
       delt = delta*(l1*k);      fprintf(ficlog,"\n");
       p2[theta]=x[theta] +delt;      fprintf(ficrespow,"\n");fflush(ficrespow);
       k1=func(p2)-fx;      if(*iter <=3){
       p2[theta]=x[theta]-delt;        tm = *localtime(&curr_time.tv_sec);
       k2=func(p2)-fx;        strcpy(strcurr,asctime(&tm));
       /*res= (k1-2.0*fx+k2)/delt/delt; */  /*       asctime_r(&tm,strcurr); */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        forecast_time=curr_time; 
              itmp = strlen(strcurr);
 #ifdef DEBUG        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
       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);          strcurr[itmp-1]='\0';
 #endif        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        for(niterf=10;niterf<=30;niterf+=10){
         k=kmax;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
       }          tmf = *localtime(&forecast_time.tv_sec);
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  /*      asctime_r(&tmf,strfor); */
         k=kmax; l=lmax*10.;          strcpy(strfor,asctime(&tmf));
       }          itmp = strlen(strfor);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          if(strfor[itmp-1]=='\n')
         delts=delt;          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);
     }          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);
   }        }
   delti[theta]=delts;      }
   return res;      for (i=1;i<=n;i++) { 
          for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
 }        fptt=(*fret); 
   #ifdef DEBUG
 double hessij( double x[], double delti[], int thetai,int thetaj)        printf("fret=%lf \n",*fret);
 {        fprintf(ficlog,"fret=%lf \n",*fret);
   int i;  #endif
   int l=1, l1, lmax=20;        printf("%d",i);fflush(stdout);
   double k1,k2,k3,k4,res,fx;        fprintf(ficlog,"%d",i);fflush(ficlog);
   double p2[NPARMAX+1];        linmin(p,xit,n,fret,func); 
   int k;        if (fabs(fptt-(*fret)) > del) { 
           del=fabs(fptt-(*fret)); 
   fx=func(x);          ibig=i; 
   for (k=1; k<=2; k++) {        } 
     for (i=1;i<=npar;i++) p2[i]=x[i];  #ifdef DEBUG
     p2[thetai]=x[thetai]+delti[thetai]/k;        printf("%d %.12e",i,(*fret));
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        fprintf(ficlog,"%d %.12e",i,(*fret));
     k1=func(p2)-fx;        for (j=1;j<=n;j++) {
            xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     p2[thetai]=x[thetai]+delti[thetai]/k;          printf(" x(%d)=%.12e",j,xit[j]);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     k2=func(p2)-fx;        }
          for(j=1;j<=n;j++) {
     p2[thetai]=x[thetai]-delti[thetai]/k;          printf(" p=%.12e",p[j]);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          fprintf(ficlog," p=%.12e",p[j]);
     k3=func(p2)-fx;        }
          printf("\n");
     p2[thetai]=x[thetai]-delti[thetai]/k;        fprintf(ficlog,"\n");
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  #endif
     k4=func(p2)-fx;      } 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
 #ifdef DEBUG  #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);        int k[2],l;
 #endif        k[0]=1;
   }        k[1]=-1;
   return res;        printf("Max: %.12e",(*func)(p));
 }        fprintf(ficlog,"Max: %.12e",(*func)(p));
         for (j=1;j<=n;j++) {
 /************** Inverse of matrix **************/          printf(" %.12e",p[j]);
 void ludcmp(double **a, int n, int *indx, double *d)          fprintf(ficlog," %.12e",p[j]);
 {        }
   int i,imax,j,k;        printf("\n");
   double big,dum,sum,temp;        fprintf(ficlog,"\n");
   double *vv;        for(l=0;l<=1;l++) {
            for (j=1;j<=n;j++) {
   vv=vector(1,n);            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   *d=1.0;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   for (i=1;i<=n;i++) {            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     big=0.0;          }
     for (j=1;j<=n;j++)          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       if ((temp=fabs(a[i][j])) > big) big=temp;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        }
     vv[i]=1.0/big;  #endif
   }  
   for (j=1;j<=n;j++) {  
     for (i=1;i<j;i++) {        free_vector(xit,1,n); 
       sum=a[i][j];        free_vector(xits,1,n); 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        free_vector(ptt,1,n); 
       a[i][j]=sum;        free_vector(pt,1,n); 
     }        return; 
     big=0.0;      } 
     for (i=j;i<=n;i++) {      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       sum=a[i][j];      for (j=1;j<=n;j++) { 
       for (k=1;k<j;k++)        ptt[j]=2.0*p[j]-pt[j]; 
         sum -= a[i][k]*a[k][j];        xit[j]=p[j]-pt[j]; 
       a[i][j]=sum;        pt[j]=p[j]; 
       if ( (dum=vv[i]*fabs(sum)) >= big) {      } 
         big=dum;      fptt=(*func)(ptt); 
         imax=i;      if (fptt < fp) { 
       }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     }        if (t < 0.0) { 
     if (j != imax) {          linmin(p,xit,n,fret,func); 
       for (k=1;k<=n;k++) {          for (j=1;j<=n;j++) { 
         dum=a[imax][k];            xi[j][ibig]=xi[j][n]; 
         a[imax][k]=a[j][k];            xi[j][n]=xit[j]; 
         a[j][k]=dum;          }
       }  #ifdef DEBUG
       *d = -(*d);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       vv[imax]=vv[j];          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++){
     indx[j]=imax;            printf(" %.12e",xit[j]);
     if (a[j][j] == 0.0) a[j][j]=TINY;            fprintf(ficlog," %.12e",xit[j]);
     if (j != n) {          }
       dum=1.0/(a[j][j]);          printf("\n");
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          fprintf(ficlog,"\n");
     }  #endif
   }        }
   free_vector(vv,1,n);  /* Doesn't work */      } 
 ;    } 
 }  } 
   
 void lubksb(double **a, int n, int *indx, double b[])  /**** Prevalence limit (stable or period prevalence)  ****************/
 {  
   int i,ii=0,ip,j;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   double sum;  {
      /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   for (i=1;i<=n;i++) {       matrix by transitions matrix until convergence is reached */
     ip=indx[i];  
     sum=b[ip];    int i, ii,j,k;
     b[ip]=b[i];    double min, max, maxmin, maxmax,sumnew=0.;
     if (ii)    double **matprod2();
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    double **out, cov[NCOVMAX], **pmij();
     else if (sum) ii=i;    double **newm;
     b[i]=sum;    double agefin, delaymax=50 ; /* Max number of years to converge */
   }  
   for (i=n;i>=1;i--) {    for (ii=1;ii<=nlstate+ndeath;ii++)
     sum=b[i];      for (j=1;j<=nlstate+ndeath;j++){
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     b[i]=sum/a[i][i];      }
   }  
 }     cov[1]=1.;
    
 /************ Frequencies ********************/   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1)    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 {  /* Some frequencies */      newm=savm;
        /* Covariates have to be included here again */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;       cov[2]=agefin;
   double ***freq; /* Frequencies */    
   double *pp;        for (k=1; k<=cptcovn;k++) {
   double pos;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   FILE *ficresp;          /*      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]]);*/
   char fileresp[FILENAMELENGTH];        }
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   pp=vector(1,nlstate);        for (k=1; k<=cptcovprod;k++)
  probs= ma3x(1,130 ,1,8, 1,8);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   strcpy(fileresp,"p");  
   strcat(fileresp,fileres);        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   if((ficresp=fopen(fileresp,"w"))==NULL) {        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     printf("Problem with prevalence resultfile: %s\n", fileresp);        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     exit(0);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      savm=oldm;
   j1=0;      oldm=newm;
       maxmax=0.;
   j=cptcoveff;      for(j=1;j<=nlstate;j++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        min=1.;
         max=0.;
   for(k1=1; k1<=j;k1++){        for(i=1; i<=nlstate; i++) {
    for(i1=1; i1<=ncodemax[k1];i1++){          sumnew=0;
        j1++;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          prlim[i][j]= newm[i][j]/(1-sumnew);
          scanf("%d", i);*/          max=FMAX(max,prlim[i][j]);
         for (i=-1; i<=nlstate+ndeath; i++)            min=FMIN(min,prlim[i][j]);
          for (jk=-1; jk<=nlstate+ndeath; jk++)          }
            for(m=agemin; m <= agemax+3; m++)        maxmin=max-min;
              freq[i][jk][m]=0;        maxmax=FMAX(maxmax,maxmin);
              }
        for (i=1; i<=imx; i++) {      if(maxmax < ftolpl){
          bool=1;        return prlim;
          if  (cptcovn>0) {      }
            for (z1=1; z1<=cptcoveff; z1++)    }
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  }
                bool=0;  
          }  /*************** transition probabilities ***************/ 
           if (bool==1) {  
            for(m=fprev1; m<=lprev1; m++){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
              if(agev[m][i]==0) agev[m][i]=agemax+1;  {
              if(agev[m][i]==1) agev[m][i]=agemax+2;    double s1, s2;
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    /*double t34;*/
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    int i,j,j1, nc, ii, jj;
            }  
          }      for(i=1; i<= nlstate; i++){
        }        for(j=1; j<i;j++){
         if  (cptcovn>0) {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
          fprintf(ficresp, "\n#********** Variable ");            /*s2 += param[i][j][nc]*cov[nc];*/
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
        fprintf(ficresp, "**********\n#");  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
         }          }
        for(i=1; i<=nlstate;i++)          ps[i][j]=s2;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
        fprintf(ficresp, "\n");        }
                for(j=i+1; j<=nlstate+ndeath;j++){
   for(i=(int)agemin; i <= (int)agemax+3; i++){          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     if(i==(int)agemax+3)            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       printf("Total");  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     else          }
       printf("Age %d", i);          ps[i][j]=s2;
     for(jk=1; jk <=nlstate ; jk++){        }
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      }
         pp[jk] += freq[jk][m][i];      /*ps[3][2]=1;*/
     }      
     for(jk=1; jk <=nlstate ; jk++){      for(i=1; i<= nlstate; i++){
       for(m=-1, pos=0; m <=0 ; m++)        s1=0;
         pos += freq[jk][m][i];        for(j=1; j<i; j++)
       if(pp[jk]>=1.e-10)          s1+=exp(ps[i][j]);
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        for(j=i+1; j<=nlstate+ndeath; j++)
       else          s1+=exp(ps[i][j]);
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        ps[i][i]=1./(s1+1.);
     }        for(j=1; j<i; j++)
           ps[i][j]= exp(ps[i][j])*ps[i][i];
      for(jk=1; jk <=nlstate ; jk++){        for(j=i+1; j<=nlstate+ndeath; j++)
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          ps[i][j]= exp(ps[i][j])*ps[i][i];
         pp[jk] += freq[jk][m][i];        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
      }      } /* end i */
       
     for(jk=1,pos=0; jk <=nlstate ; jk++)      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       pos += pp[jk];        for(jj=1; jj<= nlstate+ndeath; jj++){
     for(jk=1; jk <=nlstate ; jk++){          ps[ii][jj]=0;
       if(pos>=1.e-5)          ps[ii][ii]=1;
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        }
       else      }
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      
       if( i <= (int) agemax){  
         if(pos>=1.e-5){  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
           probs[i][jk][j1]= pp[jk]/pos;  /*         printf("ddd %lf ",ps[ii][jj]); */
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  /*       } */
         }  /*       printf("\n "); */
       else  /*        } */
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  /*        printf("\n ");printf("%lf ",cov[2]); */
       }         /*
     }        for(i=1; i<= npar; i++) printf("%f ",x[i]);
     for(jk=-1; jk <=nlstate+ndeath; jk++)        goto end;*/
       for(m=-1; m <=nlstate+ndeath; m++)      return ps;
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  }
     if(i <= (int) agemax)  
       fprintf(ficresp,"\n");  /**************** Product of 2 matrices ******************/
     printf("\n");  
     }  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     }  {
  }    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   fclose(ficresp);    /* in, b, out are matrice of pointers which should have been initialized 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);       before: only the contents of out is modified. The function returns
   free_vector(pp,1,nlstate);       a pointer to pointers identical to out */
     long i, j, k;
 }  /* End of Freq */    for(i=nrl; i<= nrh; i++)
       for(k=ncolol; k<=ncoloh; k++)
 /************ Prevalence ********************/        for(j=ncl,out[i][k]=0.; j<=nch; j++)
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1)          out[i][k] +=in[i][j]*b[j][k];
 {  /* Some frequencies */  
      return out;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  }
   double ***freq; /* Frequencies */  
   double *pp;  
   double pos;  /************* Higher Matrix Product ***************/
   
   pp=vector(1,nlstate);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   probs= ma3x(1,130 ,1,8, 1,8);  {
      /* Computes the transition matrix starting at age 'age' over 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);       'nhstepm*hstepm*stepm' months (i.e. until
   j1=0;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         nhstepm*hstepm matrices. 
   j=cptcoveff;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}       (typically every 2 years instead of every month which is too big 
         for the memory).
  for(k1=1; k1<=j;k1++){       Model is determined by parameters x and covariates have to be 
     for(i1=1; i1<=ncodemax[k1];i1++){       included manually here. 
       j1++;  
         */
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)      int i, j, d, h, k;
           for(m=agemin; m <= agemax+3; m++)    double **out, cov[NCOVMAX];
           freq[i][jk][m]=0;    double **newm;
        
       for (i=1; i<=imx; i++) {    /* Hstepm could be zero and should return the unit matrix */
         bool=1;    for (i=1;i<=nlstate+ndeath;i++)
         if  (cptcovn>0) {      for (j=1;j<=nlstate+ndeath;j++){
           for (z1=1; z1<=cptcoveff; z1++)        oldm[i][j]=(i==j ? 1.0 : 0.0);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        po[i][j][0]=(i==j ? 1.0 : 0.0);
               bool=0;      }
               }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         if (bool==1) {    for(h=1; h <=nhstepm; h++){
           for(m=fprev1; m<=lprev1; m++){      for(d=1; d <=hstepm; d++){
             if(agev[m][i]==0) agev[m][i]=agemax+1;        newm=savm;
             if(agev[m][i]==1) agev[m][i]=agemax+2;        /* Covariates have to be included here again */
             freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        cov[1]=1.;
             freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
           }        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         }        for (k=1; k<=cptcovage;k++)
       }          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
        for(i=(int)agemin; i <= (int)agemax+3; i++){        for (k=1; k<=cptcovprod;k++)
         for(jk=1; jk <=nlstate ; jk++){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  
             pp[jk] += freq[jk][m][i];  
         }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         for(jk=1; jk <=nlstate ; jk++){        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
           for(m=-1, pos=0; m <=0 ; m++)        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
             pos += freq[jk][m][i];                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         }        savm=oldm;
                oldm=newm;
          for(jk=1; jk <=nlstate ; jk++){      }
            for(m=0, 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++) {
          }          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]);
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];           */
         }
          for(jk=1; jk <=nlstate ; jk++){              } /* end h */
            if( i <= (int) agemax){    return po;
              if(pos>=1.e-5){  }
                probs[i][jk][j1]= pp[jk]/pos;  
              }  
            }  /*************** log-likelihood *************/
          }  double func( double *x)
            {
          }    int i, ii, j, k, mi, d, kk;
     }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   }    double **out;
      double sw; /* Sum of weights */
      double lli; /* Individual log likelihood */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    int s1, s2;
   free_vector(pp,1,nlstate);    double bbh, survp;
      long ipmx;
 }  /* End of Freq */    /*extern weight */
 /************* Waves Concatenation ***************/    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    /*for(i=1;i<imx;i++) 
 {      printf(" %d\n",s[4][i]);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    */
      Death is a valid wave (if date is known).    cov[1]=1.;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    for(k=1; k<=nlstate; k++) ll[k]=0.;
      and mw[mi+1][i]. dh depends on stepm.  
      */    if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int i, mi, m;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        for(mi=1; mi<= wav[i]-1; mi++){
      double sum=0., jmean=0.;*/          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   int j, k=0,jk, ju, jl;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double sum=0.;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   jmin=1e+5;            }
   jmax=-1;          for(d=0; d<dh[mi][i]; d++){
   jmean=0.;            newm=savm;
   for(i=1; i<=imx; i++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     mi=0;            for (kk=1; kk<=cptcovage;kk++) {
     m=firstpass;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     while(s[m][i] <= nlstate){            }
       if(s[m][i]>=1)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         mw[++mi][i]=m;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       if(m >=lastpass)            savm=oldm;
         break;            oldm=newm;
       else          } /* end mult */
         m++;        
     }/* end while */          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     if (s[m][i] > nlstate){          /* But now since version 0.9 we anticipate for bias at large stepm.
       mi++;     /* Death is another wave */           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       /* if(mi==0)  never been interviewed correctly before death */           * (in months) between two waves is not a multiple of stepm, we rounded to 
          /* Only death is a correct wave */           * the nearest (and in case of equal distance, to the lowest) interval but now
       mw[mi][i]=m;           * 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
            * probability in order to take into account the bias as a fraction of the way
     wav[i]=mi;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
     if(mi==0)           * -stepm/2 to stepm/2 .
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);           * For stepm=1 the results are the same as for previous versions of Imach.
   }           * For stepm > 1 the results are less biased than in previous versions. 
            */
   for(i=1; i<=imx; i++){          s1=s[mw[mi][i]][i];
     for(mi=1; mi<wav[i];mi++){          s2=s[mw[mi+1][i]][i];
       if (stepm <=0)          bbh=(double)bh[mi][i]/(double)stepm; 
         dh[mi][i]=1;          /* bias bh is positive if real duration
       else{           * is higher than the multiple of stepm and negative otherwise.
         if (s[mw[mi+1][i]][i] > nlstate) {           */
           if (agedc[i] < 2*AGESUP) {          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          if( s2 > nlstate){ 
           if(j==0) j=1;  /* Survives at least one month after exam */            /* i.e. if s2 is a death state and if the date of death is known 
           k=k+1;               then the contribution to the likelihood is the probability to 
           if (j >= jmax) jmax=j;               die between last step unit time and current  step unit time, 
           if (j <= jmin) jmin=j;               which is also equal to probability to die before dh 
           sum=sum+j;               minus probability to die before dh-stepm . 
           /* if (j<10) printf("j=%d num=%d ",j,i); */               In version up to 0.92 likelihood was computed
           }          as if date of death was unknown. Death was treated as any other
         }          health state: the date of the interview describes the actual state
         else{          and not the date of a change in health state. The former idea was
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          to consider that at each interview the state was recorded
           k=k+1;          (healthy, disable or death) and IMaCh was corrected; but when we
           if (j >= jmax) jmax=j;          introduced the exact date of death then we should have modified
           else if (j <= jmin)jmin=j;          the contribution of an exact death to the likelihood. This new
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          contribution is smaller and very dependent of the step unit
           sum=sum+j;          stepm. It is no more the probability to die between last interview
         }          and month of death but the probability to survive from last
         jk= j/stepm;          interview up to one month before death multiplied by the
         jl= j -jk*stepm;          probability to die within a month. Thanks to Chris
         ju= j -(jk+1)*stepm;          Jackson for correcting this bug.  Former versions increased
         if(jl <= -ju)          mortality artificially. The bad side is that we add another loop
           dh[mi][i]=jk;          which slows down the processing. The difference can be up to 10%
         else          lower mortality.
           dh[mi][i]=jk+1;            */
         if(dh[mi][i]==0)            lli=log(out[s1][s2] - savm[s1][s2]);
           dh[mi][i]=1; /* At least one step */  
       }  
     }          } else if  (s2==-2) {
   }            for (j=1,survp=0. ; j<=nlstate; j++) 
   jmean=sum/k;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            /*survp += out[s1][j]; */
  }            lli= log(survp);
 /*********** Tricode ****************************/          }
 void tricode(int *Tvar, int **nbcode, int imx)          
 {          else if  (s2==-4) { 
   int Ndum[20],ij=1, k, j, i;            for (j=3,survp=0. ; j<=nlstate; j++)  
   int cptcode=0;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   cptcoveff=0;            lli= log(survp); 
            } 
   for (k=0; k<19; k++) Ndum[k]=0;  
   for (k=1; k<=7; k++) ncodemax[k]=0;          else if  (s2==-5) { 
             for (j=1,survp=0. ; j<=2; j++)  
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     for (i=1; i<=imx; i++) {            lli= log(survp); 
       ij=(int)(covar[Tvar[j]][i]);          } 
       Ndum[ij]++;          
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          else{
       if (ij > cptcode) cptcode=ij;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
           } 
     for (i=0; i<=cptcode; i++) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       if(Ndum[i]!=0) ncodemax[j]++;          /*if(lli ==000.0)*/
     }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     ij=1;          ipmx +=1;
           sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (i=1; i<=ncodemax[j]; i++) {        } /* end of wave */
       for (k=0; k<=19; k++) {      } /* end of individual */
         if (Ndum[k] != 0) {    }  else if(mle==2){
           nbcode[Tvar[j]][ij]=k;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           ij++;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
         if (ij > ncodemax[j]) break;          for (ii=1;ii<=nlstate+ndeath;ii++)
       }              for (j=1;j<=nlstate+ndeath;j++){
     }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }                savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
  for (k=0; k<19; k++) Ndum[k]=0;          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
  for (i=1; i<=ncovmodel-2; i++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       ij=Tvar[i];            for (kk=1; kk<=cptcovage;kk++) {
       Ndum[ij]++;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     }            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
  ij=1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
  for (i=1; i<=10; i++) {            savm=oldm;
    if((Ndum[i]!=0) && (i<=ncov)){            oldm=newm;
      Tvaraff[ij]=i;          } /* end mult */
      ij++;        
    }          s1=s[mw[mi][i]][i];
  }          s2=s[mw[mi+1][i]][i];
            bbh=(double)bh[mi][i]/(double)stepm; 
     cptcoveff=ij-1;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
 }          ipmx +=1;
           sw += weight[i];
 /*********** Health Expectancies ****************/          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)      } /* end of individual */
 {    }  else if(mle==3){  /* exponential inter-extrapolation */
   /* Health expectancies */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int i, j, nhstepm, hstepm, h;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double age, agelim,hf;        for(mi=1; mi<= wav[i]-1; mi++){
   double ***p3mat;          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   fprintf(ficreseij,"# Health expectancies\n");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficreseij,"# Age");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for(i=1; i<=nlstate;i++)            }
     for(j=1; j<=nlstate;j++)          for(d=0; d<dh[mi][i]; d++){
       fprintf(ficreseij," %1d-%1d",i,j);            newm=savm;
   fprintf(ficreseij,"\n");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   hstepm=1*YEARM; /*  Every j years of age (in month) */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   agelim=AGESUP;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            savm=oldm;
     /* nhstepm age range expressed in number of stepm */            oldm=newm;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);          } /* end mult */
     /* Typically if 20 years = 20*12/6=40 stepm */        
     if (stepm >= YEARM) hstepm=1;          s1=s[mw[mi][i]][i];
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */          s2=s[mw[mi+1][i]][i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          bbh=(double)bh[mi][i]/(double)stepm; 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          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 */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          ipmx +=1;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
     for(i=1; i<=nlstate;i++)      } /* end of individual */
       for(j=1; j<=nlstate;j++)    }else if (mle==4){  /* ml=4 no inter-extrapolation */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           eij[i][j][(int)age] +=p3mat[i][j][h];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
              for (ii=1;ii<=nlstate+ndeath;ii++)
     hf=1;            for (j=1;j<=nlstate+ndeath;j++){
     if (stepm >= YEARM) hf=stepm/YEARM;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     fprintf(ficreseij,"%.0f",age );              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i=1; i<=nlstate;i++)            }
       for(j=1; j<=nlstate;j++){          for(d=0; d<dh[mi][i]; d++){
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);            newm=savm;
       }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     fprintf(ficreseij,"\n");            for (kk=1; kk<=cptcovage;kk++) {
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
 }          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 /************ Variance ******************/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 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)            savm=oldm;
 {            oldm=newm;
   /* Variance of health expectancies */          } /* end mult */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        
   double **newm;          s1=s[mw[mi][i]][i];
   double **dnewm,**doldm;          s2=s[mw[mi+1][i]][i];
   int i, j, nhstepm, hstepm, h;          if( s2 > nlstate){ 
   int k, cptcode;            lli=log(out[s1][s2] - savm[s1][s2]);
   double *xp;          }else{
   double **gp, **gm;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   double ***gradg, ***trgradg;          }
   double ***p3mat;          ipmx +=1;
   double age,agelim;          sw += weight[i];
   int theta;          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]); */
    fprintf(ficresvij,"# Covariances of life expectancies\n");        } /* end of wave */
   fprintf(ficresvij,"# Age");      } /* end of individual */
   for(i=1; i<=nlstate;i++)    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     for(j=1; j<=nlstate;j++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   fprintf(ficresvij,"\n");        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   xp=vector(1,npar);            for (j=1;j<=nlstate+ndeath;j++){
   dnewm=matrix(1,nlstate,1,npar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   doldm=matrix(1,nlstate,1,nlstate);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
   hstepm=1*YEARM; /* Every year of age */          for(d=0; d<dh[mi][i]; d++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            newm=savm;
   agelim = AGESUP;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            for (kk=1; kk<=cptcovage;kk++) {
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     if (stepm >= YEARM) hstepm=1;            }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     gp=matrix(0,nhstepm,1,nlstate);            savm=oldm;
     gm=matrix(0,nhstepm,1,nlstate);            oldm=newm;
           } /* end mult */
     for(theta=1; theta <=npar; theta++){        
       for(i=1; i<=npar; i++){ /* Computes gradient */          s1=s[mw[mi][i]][i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          s2=s[mw[mi+1][i]][i];
       }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            ipmx +=1;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       if (popbased==1) {          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         for(i=1; i<=nlstate;i++)        } /* end of wave */
           prlim[i][i]=probs[(int)age][i][ij];      } /* end of individual */
       }    } /* End of if */
          for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       for(j=1; j<= nlstate; j++){    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         for(h=0; h<=nhstepm; h++){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    return -l;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  }
         }  
       }  /*************** log-likelihood *************/
      double funcone( double *x)
       for(i=1; i<=npar; i++) /* Computes gradient */  {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    /* Same as likeli but slower because of a lot of printf and if */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      int i, ii, j, k, mi, d, kk;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
       if (popbased==1) {    double lli; /* Individual log likelihood */
         for(i=1; i<=nlstate;i++)    double llt;
           prlim[i][i]=probs[(int)age][i][ij];    int s1, s2;
       }    double bbh, survp;
     /*extern weight */
       for(j=1; j<= nlstate; j++){    /* We are differentiating ll according to initial status */
         for(h=0; h<=nhstepm; h++){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    /*for(i=1;i<imx;i++) 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      printf(" %d\n",s[4][i]);
         }    */
       }    cov[1]=1.;
   
       for(j=1; j<= nlstate; j++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
         for(h=0; h<=nhstepm; h++){  
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     } /* End theta */      for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(h=0; h<=nhstepm; h++)            savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<=nlstate;j++)          }
         for(theta=1; theta <=npar; theta++)        for(d=0; d<dh[mi][i]; d++){
           trgradg[h][j][theta]=gradg[h][theta][j];          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(i=1;i<=nlstate;i++)          for (kk=1; kk<=cptcovage;kk++) {
       for(j=1;j<=nlstate;j++)            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         vareij[i][j][(int)age] =0.;          }
     for(h=0;h<=nhstepm;h++){          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(k=0;k<=nhstepm;k++){                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          savm=oldm;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          oldm=newm;
         for(i=1;i<=nlstate;i++)        } /* end mult */
           for(j=1;j<=nlstate;j++)        
             vareij[i][j][(int)age] += doldm[i][j];        s1=s[mw[mi][i]][i];
       }        s2=s[mw[mi+1][i]][i];
     }        bbh=(double)bh[mi][i]/(double)stepm; 
     h=1;        /* bias is positive if real duration
     if (stepm >= YEARM) h=stepm/YEARM;         * is higher than the multiple of stepm and negative otherwise.
     fprintf(ficresvij,"%.0f ",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," %.4f", h*vareij[i][j][(int)age]);        } else if  (s2==-2) {
       }          for (j=1,survp=0. ; j<=nlstate; j++) 
     fprintf(ficresvij,"\n");            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     free_matrix(gp,0,nhstepm,1,nlstate);          lli= log(survp);
     free_matrix(gm,0,nhstepm,1,nlstate);        }else if (mle==1){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        } else if(mle==2){
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          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 */
   } /* End age */        } else if(mle==3){  /* exponential inter-extrapolation */
            lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   free_vector(xp,1,npar);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   free_matrix(doldm,1,nlstate,1,npar);          lli=log(out[s1][s2]); /* Original formula */
   free_matrix(dnewm,1,nlstate,1,nlstate);        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
           lli=log(out[s1][s2]); /* Original formula */
 }        } /* End of if */
         ipmx +=1;
 /************ Variance of prevlim ******************/        sw += weight[i];
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)        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]); */
   /* Variance of prevalence limit */        if(globpr){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   double **newm;   %11.6f %11.6f %11.6f ", \
   double **dnewm,**doldm;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   int i, j, nhstepm, hstepm;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   int k, cptcode;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   double *xp;            llt +=ll[k]*gipmx/gsw;
   double *gp, *gm;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   double **gradg, **trgradg;          }
   double age,agelim;          fprintf(ficresilk," %10.6f\n", -llt);
   int theta;        }
          } /* end of wave */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    } /* end of individual */
   fprintf(ficresvpl,"# Age");    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   for(i=1; i<=nlstate;i++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       fprintf(ficresvpl," %1d-%1d",i,i);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   fprintf(ficresvpl,"\n");    if(globpr==0){ /* First time we count the contributions and weights */
       gipmx=ipmx;
   xp=vector(1,npar);      gsw=sw;
   dnewm=matrix(1,nlstate,1,npar);    }
   doldm=matrix(1,nlstate,1,nlstate);    return -l;
    }
   hstepm=1*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   agelim = AGESUP;  /*************** function likelione ***********/
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  {
     if (stepm >= YEARM) hstepm=1;    /* This routine should help understanding what is done with 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */       the selection of individuals/waves and
     gradg=matrix(1,npar,1,nlstate);       to check the exact contribution to the likelihood.
     gp=vector(1,nlstate);       Plotting could be done.
     gm=vector(1,nlstate);     */
     int k;
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */    if(*globpri !=0){ /* Just counts and sums, no printings */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      strcpy(fileresilk,"ilk"); 
       }      strcat(fileresilk,fileres);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       for(i=1;i<=nlstate;i++)        printf("Problem with resultfile: %s\n", fileresilk);
         gp[i] = prlim[i][i];        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
          }
       for(i=1; i<=npar; i++) /* Computes gradient */      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");
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(i=1;i<=nlstate;i++)      for(k=1; k<=nlstate; k++) 
         gm[i] = prlim[i][i];        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       for(i=1;i<=nlstate;i++)    }
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  
     } /* End theta */    *fretone=(*funcone)(p);
     if(*globpri !=0){
     trgradg =matrix(1,nlstate,1,npar);      fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     for(j=1; j<=nlstate;j++)      fflush(fichtm); 
       for(theta=1; theta <=npar; theta++)    } 
         trgradg[j][theta]=gradg[theta][j];    return;
   }
     for(i=1;i<=nlstate;i++)  
       varpl[i][(int)age] =0.;  
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  /*********** Maximum Likelihood Estimation ***************/
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  
     for(i=1;i<=nlstate;i++)  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  {
     int i,j, iter;
     fprintf(ficresvpl,"%.0f ",age );    double **xi;
     for(i=1; i<=nlstate;i++)    double fret;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    double fretone; /* Only one call to likelihood */
     fprintf(ficresvpl,"\n");    /*  char filerespow[FILENAMELENGTH];*/
     free_vector(gp,1,nlstate);    xi=matrix(1,npar,1,npar);
     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);        xi[i][j]=(i==j ? 1.0 : 0.0);
   } /* End age */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
   free_vector(xp,1,npar);    strcat(filerespow,fileres);
   free_matrix(doldm,1,nlstate,1,npar);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   free_matrix(dnewm,1,nlstate,1,nlstate);      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
 }    }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
 /************ Variance of one-step probabilities  ******************/    for (i=1;i<=nlstate;i++)
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)      for(j=1;j<=nlstate+ndeath;j++)
 {        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   int i, j;    fprintf(ficrespow,"\n");
   int k=0, cptcode;  
   double **dnewm,**doldm;    powell(p,xi,npar,ftol,&iter,&fret,func);
   double *xp;  
   double *gp, *gm;    free_matrix(xi,1,npar,1,npar);
   double **gradg, **trgradg;    fclose(ficrespow);
   double age,agelim, cov[NCOVMAX];    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   int theta;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   char fileresprob[FILENAMELENGTH];    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   
   strcpy(fileresprob,"prob");  }
   strcat(fileresprob,fileres);  
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  /**** Computes Hessian and covariance matrix ***/
     printf("Problem with resultfile: %s\n", fileresprob);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   }  {
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    double  **a,**y,*x,pd;
      double **hess;
     int i, j,jk;
   xp=vector(1,npar);    int *indx;
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
      double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   cov[1]=1;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   for (age=bage; age<=fage; age ++){    void ludcmp(double **a, int npar, int *indx, double *d) ;
     cov[2]=age;    double gompertz(double p[]);
     gradg=matrix(1,npar,1,9);    hess=matrix(1,npar,1,npar);
     trgradg=matrix(1,9,1,npar);  
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    printf("\nCalculation of the hessian matrix. Wait...\n");
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
        for (i=1;i<=npar;i++){
     for(theta=1; theta <=npar; theta++){      printf("%d",i);fflush(stdout);
       for(i=1; i<=npar; i++)      fprintf(ficlog,"%d",i);fflush(ficlog);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);     
             hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      
          /*  printf(" %f ",p[i]);
       k=0;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       for(i=1; i<= (nlstate+ndeath); i++){    }
         for(j=1; j<=(nlstate+ndeath);j++){    
            k=k+1;    for (i=1;i<=npar;i++) {
           gp[k]=pmmij[i][j];      for (j=1;j<=npar;j++)  {
         }        if (j>i) { 
       }          printf(".%d%d",i,j);fflush(stdout);
           fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       for(i=1; i<=npar; i++)          hess[i][j]=hessij(p,delti,i,j,func,npar);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          
              hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        }
       k=0;      }
       for(i=1; i<=(nlstate+ndeath); i++){    }
         for(j=1; j<=(nlstate+ndeath);j++){    printf("\n");
           k=k+1;    fprintf(ficlog,"\n");
           gm[k]=pmmij[i][j];  
         }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
          
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    a=matrix(1,npar,1,npar);
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      y=matrix(1,npar,1,npar);
     }    x=vector(1,npar);
     indx=ivector(1,npar);
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    for (i=1;i<=npar;i++)
       for(theta=1; theta <=npar; theta++)      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       trgradg[j][theta]=gradg[theta][j];    ludcmp(a,npar,indx,&pd);
    
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    for (j=1;j<=npar;j++) {
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
      pmij(pmmij,cov,ncovmodel,x,nlstate);      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
      k=0;        matcov[i][j]=x[i];
      for(i=1; i<=(nlstate+ndeath); i++){      }
        for(j=1; j<=(nlstate+ndeath);j++){    }
          k=k+1;  
          gm[k]=pmmij[i][j];    printf("\n#Hessian matrix#\n");
         }    fprintf(ficlog,"\n#Hessian matrix#\n");
      }    for (i=1;i<=npar;i++) { 
            for (j=1;j<=npar;j++) { 
      /*printf("\n%d ",(int)age);        printf("%.3e ",hess[i][j]);
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        fprintf(ficlog,"%.3e ",hess[i][j]);
              }
       printf("\n");
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      fprintf(ficlog,"\n");
      }*/    }
   
   fprintf(ficresprob,"\n%d ",(int)age);    /* Recompute Inverse */
     for (i=1;i<=npar;i++)
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    ludcmp(a,npar,indx,&pd);
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  
   }    /*  printf("\n#Hessian matrix recomputed#\n");
   
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    for (j=1;j<=npar;j++) {
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      for (i=1;i<=npar;i++) x[i]=0;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      x[j]=1;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      lubksb(a,npar,indx,x);
 }      for (i=1;i<=npar;i++){ 
  free_vector(xp,1,npar);        y[i][j]=x[i];
 fclose(ficresprob);        printf("%.3e ",y[i][j]);
  exit(0);        fprintf(ficlog,"%.3e ",y[i][j]);
 }      }
       printf("\n");
 /***********************************************/      fprintf(ficlog,"\n");
 /**************** Main Program *****************/    }
 /***********************************************/    */
   
 /*int main(int argc, char *argv[])*/    free_matrix(a,1,npar,1,npar);
 int main()    free_matrix(y,1,npar,1,npar);
 {    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    free_matrix(hess,1,npar,1,npar);
   double agedeb, agefin,hf;  
   double agemin=1.e20, agemax=-1.e20;  
   }
   double fret;  
   double **xi,tmp,delta;  /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   double dum; /* Dummy variable */  {
   double ***p3mat;    int i;
   int *indx;    int l=1, lmax=20;
   char line[MAXLINE], linepar[MAXLINE];    double k1,k2;
   char title[MAXLINE];    double p2[NPARMAX+1];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    double res;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   char filerest[FILENAMELENGTH];    double fx;
   char fileregp[FILENAMELENGTH];    int k=0,kmax=10;
   char popfile[FILENAMELENGTH];    double l1;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  
   int firstobs=1, lastobs=10;    fx=func(x);
   int sdeb, sfin; /* Status at beginning and end */    for (i=1;i<=npar;i++) p2[i]=x[i];
   int c,  h , cpt,l;    for(l=0 ; l <=lmax; l++){
   int ju,jl, mi;      l1=pow(10,l);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      delts=delt;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      for(k=1 ; k <kmax; k=k+1){
   int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast,popforecast=0;        delt = delta*(l1*k);
   int hstepm, nhstepm;        p2[theta]=x[theta] +delt;
   int *popage;        k1=func(p2)-fx;
         p2[theta]=x[theta]-delt;
   double bage, fage, age, agelim, agebase;        k2=func(p2)-fx;
   double ftolpl=FTOL;        /*res= (k1-2.0*fx+k2)/delt/delt; */
   double **prlim;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   double *severity;        
   double ***param; /* Matrix of parameters */  #ifdef DEBUG
   double  *p;        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);
   double **matcov; /* Matrix of covariance */        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);
   double ***delti3; /* Scale */  #endif
   double *delti; /* Scale */        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   double ***eij, ***vareij;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   double **varpl; /* Variances of prevalence limits by age */          k=kmax;
   double *epj, vepp;        }
   double kk1, kk2;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   double *popeffectif,*popcount;          k=kmax; l=lmax*10.;
         }
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   char *alph[]={"a","a","b","c","d","e"}, str[4];          delts=delt;
         }
       }
   char z[1]="c", occ;    }
 #include <sys/time.h>    delti[theta]=delts;
 #include <time.h>    return res; 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    
   /* long total_usecs;  }
   struct timeval start_time, end_time;  
    double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  {
     int i;
     int l=1, l1, lmax=20;
   printf("\nIMACH, Version 0.7");    double k1,k2,k3,k4,res,fx;
   printf("\nEnter the parameter file name: ");    double p2[NPARMAX+1];
     int k;
 #ifdef windows  
   scanf("%s",pathtot);    fx=func(x);
   getcwd(pathcd, size);    for (k=1; k<=2; k++) {
   /*cygwin_split_path(pathtot,path,optionfile);      for (i=1;i<=npar;i++) p2[i]=x[i];
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      p2[thetai]=x[thetai]+delti[thetai]/k;
   /* cutv(path,optionfile,pathtot,'\\');*/      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k1=func(p2)-fx;
 split(pathtot, path,optionfile);    
   chdir(path);      p2[thetai]=x[thetai]+delti[thetai]/k;
   replace(pathc,path);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 #endif      k2=func(p2)-fx;
 #ifdef unix    
   scanf("%s",optionfile);      p2[thetai]=x[thetai]-delti[thetai]/k;
 #endif      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
 /*-------- arguments in the command line --------*/    
       p2[thetai]=x[thetai]-delti[thetai]/k;
   strcpy(fileres,"r");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   strcat(fileres, optionfile);      k4=func(p2)-fx;
       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   /*---------arguments file --------*/  #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);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     printf("Problem with optionfile %s\n",optionfile);  #endif
     goto end;    }
   }    return res;
   }
   strcpy(filereso,"o");  
   strcat(filereso,fileres);  /************** Inverse of matrix **************/
   if((ficparo=fopen(filereso,"w"))==NULL) {  void ludcmp(double **a, int n, int *indx, double *d) 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  { 
   }    int i,imax,j,k; 
     double big,dum,sum,temp; 
   /* Reads comments: lines beginning with '#' */    double *vv; 
   while((c=getc(ficpar))=='#' && c!= EOF){   
     ungetc(c,ficpar);    vv=vector(1,n); 
     fgets(line, MAXLINE, ficpar);    *d=1.0; 
     puts(line);    for (i=1;i<=n;i++) { 
     fputs(line,ficparo);      big=0.0; 
   }      for (j=1;j<=n;j++) 
   ungetc(c,ficpar);        if ((temp=fabs(a[i][j])) > big) big=temp; 
       if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   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);      vv[i]=1.0/big; 
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    } 
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    for (j=1;j<=n;j++) { 
 while((c=getc(ficpar))=='#' && c!= EOF){      for (i=1;i<j;i++) { 
     ungetc(c,ficpar);        sum=a[i][j]; 
     fgets(line, MAXLINE, ficpar);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     puts(line);        a[i][j]=sum; 
     fputs(line,ficparo);      } 
   }      big=0.0; 
   ungetc(c,ficpar);      for (i=j;i<=n;i++) { 
          sum=a[i][j]; 
   fscanf(ficpar,"fprevalence=%d lprevalence=%d pop_based=%d\n",&fprev,&lprev,&popbased);        for (k=1;k<j;k++) 
   fprintf(ficparo,"fprevalence=%d lprevalence=%d pop_based=%d\n",fprev,lprev,popbased);          sum -= a[i][k]*a[k][j]; 
          a[i][j]=sum; 
  while((c=getc(ficpar))=='#' && c!= EOF){        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     ungetc(c,ficpar);          big=dum; 
     fgets(line, MAXLINE, ficpar);          imax=i; 
     puts(line);        } 
     fputs(line,ficparo);      } 
   }      if (j != imax) { 
   ungetc(c,ficpar);        for (k=1;k<=n;k++) { 
            dum=a[imax][k]; 
   fscanf(ficpar,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",&fprevfore,&lprevfore,&nforecast,&mobilav);          a[imax][k]=a[j][k]; 
   fprintf(ficparo,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",fprevfore,lprevfore,nforecast,mobilav);          a[j][k]=dum; 
              } 
          *d = -(*d); 
 while((c=getc(ficpar))=='#' && c!= EOF){        vv[imax]=vv[j]; 
     ungetc(c,ficpar);      } 
     fgets(line, MAXLINE, ficpar);      indx[j]=imax; 
     puts(line);      if (a[j][j] == 0.0) a[j][j]=TINY; 
     fputs(line,ficparo);      if (j != n) { 
   }        dum=1.0/(a[j][j]); 
   ungetc(c,ficpar);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
        } 
   fscanf(ficpar,"popforecast=%d popfile=%s\n",&popforecast,popfile);    } 
      free_vector(vv,1,n);  /* Doesn't work */
   covar=matrix(0,NCOVMAX,1,n);  ;
   cptcovn=0;  } 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  
   void lubksb(double **a, int n, int *indx, double b[]) 
   ncovmodel=2+cptcovn;  { 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    int i,ii=0,ip,j; 
      double sum; 
   /* Read guess parameters */   
   /* Reads comments: lines beginning with '#' */    for (i=1;i<=n;i++) { 
   while((c=getc(ficpar))=='#' && c!= EOF){      ip=indx[i]; 
     ungetc(c,ficpar);      sum=b[ip]; 
     fgets(line, MAXLINE, ficpar);      b[ip]=b[i]; 
     puts(line);      if (ii) 
     fputs(line,ficparo);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   }      else if (sum) ii=i; 
   ungetc(c,ficpar);      b[i]=sum; 
      } 
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    for (i=n;i>=1;i--) { 
     for(i=1; i <=nlstate; i++)      sum=b[i]; 
     for(j=1; j <=nlstate+ndeath-1; j++){      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       fscanf(ficpar,"%1d%1d",&i1,&j1);      b[i]=sum/a[i][i]; 
       fprintf(ficparo,"%1d%1d",i1,j1);    } 
       printf("%1d%1d",i,j);  } 
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);  void pstamp(FILE *fichier)
         printf(" %lf",param[i][j][k]);  {
         fprintf(ficparo," %lf",param[i][j][k]);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
       }  }
       fscanf(ficpar,"\n");  
       printf("\n");  /************ Frequencies ********************/
       fprintf(ficparo,"\n");  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[])
     }  {  /* Some frequencies */
      
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     int first;
   p=param[1][1];    double ***freq; /* Frequencies */
      double *pp, **prop;
   /* Reads comments: lines beginning with '#' */    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   while((c=getc(ficpar))=='#' && c!= EOF){    char fileresp[FILENAMELENGTH];
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    pp=vector(1,nlstate);
     puts(line);    prop=matrix(1,nlstate,iagemin,iagemax+3);
     fputs(line,ficparo);    strcpy(fileresp,"p");
   }    strcat(fileresp,fileres);
   ungetc(c,ficpar);    if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      exit(0);
   for(i=1; i <=nlstate; i++){    }
     for(j=1; j <=nlstate+ndeath-1; j++){    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    j1=0;
       printf("%1d%1d",i,j);    
       fprintf(ficparo,"%1d%1d",i1,j1);    j=cptcoveff;
       for(k=1; k<=ncovmodel;k++){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         fscanf(ficpar,"%le",&delti3[i][j][k]);  
         printf(" %le",delti3[i][j][k]);    first=1;
         fprintf(ficparo," %le",delti3[i][j][k]);  
       }    for(k1=1; k1<=j;k1++){
       fscanf(ficpar,"\n");      for(i1=1; i1<=ncodemax[k1];i1++){
       printf("\n");        j1++;
       fprintf(ficparo,"\n");        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     }          scanf("%d", i);*/
   }        for (i=-5; i<=nlstate+ndeath; i++)  
   delti=delti3[1][1];          for (jk=-5; jk<=nlstate+ndeath; jk++)  
              for(m=iagemin; m <= iagemax+3; m++)
   /* Reads comments: lines beginning with '#' */              freq[i][jk][m]=0;
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      for (i=1; i<=nlstate; i++)  
     fgets(line, MAXLINE, ficpar);        for(m=iagemin; m <= iagemax+3; m++)
     puts(line);          prop[i][m]=0;
     fputs(line,ficparo);        
   }        dateintsum=0;
   ungetc(c,ficpar);        k2cpt=0;
          for (i=1; i<=imx; i++) {
   matcov=matrix(1,npar,1,npar);          bool=1;
   for(i=1; i <=npar; i++){          if  (cptcovn>0) {
     fscanf(ficpar,"%s",&str);            for (z1=1; z1<=cptcoveff; z1++) 
     printf("%s",str);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     fprintf(ficparo,"%s",str);                bool=0;
     for(j=1; j <=i; j++){          }
       fscanf(ficpar," %le",&matcov[i][j]);          if (bool==1){
       printf(" %.5le",matcov[i][j]);            for(m=firstpass; m<=lastpass; m++){
       fprintf(ficparo," %.5le",matcov[i][j]);              k2=anint[m][i]+(mint[m][i]/12.);
     }              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     fscanf(ficpar,"\n");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     printf("\n");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     fprintf(ficparo,"\n");                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   }                if (m<lastpass) {
   for(i=1; i <=npar; i++)                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     for(j=i+1;j<=npar;j++)                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       matcov[i][j]=matcov[j][i];                }
                    
   printf("\n");                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
                   k2cpt++;
     /*-------- data file ----------*/                }
     if((ficres =fopen(fileres,"w"))==NULL) {                /*}*/
       printf("Problem with resultfile: %s\n", fileres);goto end;            }
     }          }
     fprintf(ficres,"#%s\n",version);        }
             
     if((fic=fopen(datafile,"r"))==NULL)    {        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       printf("Problem with datafile: %s\n", datafile);goto end;        pstamp(ficresp);
     }        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
     n= lastobs;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     severity = vector(1,maxwav);          fprintf(ficresp, "**********\n#");
     outcome=imatrix(1,maxwav+1,1,n);        }
     num=ivector(1,n);        for(i=1; i<=nlstate;i++) 
     moisnais=vector(1,n);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     annais=vector(1,n);        fprintf(ficresp, "\n");
     moisdc=vector(1,n);        
     andc=vector(1,n);        for(i=iagemin; i <= iagemax+3; i++){
     agedc=vector(1,n);          if(i==iagemax+3){
     cod=ivector(1,n);            fprintf(ficlog,"Total");
     weight=vector(1,n);            fprintf(fichtm,"<br>Total<br>");
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          }else{
     mint=matrix(1,maxwav,1,n);            if(first==1){
     anint=matrix(1,maxwav,1,n);              first=0;
     s=imatrix(1,maxwav+1,1,n);              printf("See log file for details...\n");
     adl=imatrix(1,maxwav+1,1,n);                }
     tab=ivector(1,NCOVMAX);            fprintf(ficlog,"Age %d", i);
     ncodemax=ivector(1,8);          }
           for(jk=1; jk <=nlstate ; jk++){
     i=1;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     while (fgets(line, MAXLINE, fic) != NULL)    {              pp[jk] += freq[jk][m][i]; 
       if ((i >= firstobs) && (i <=lastobs)) {          }
                  for(jk=1; jk <=nlstate ; jk++){
         for (j=maxwav;j>=1;j--){            for(m=-1, pos=0; m <=0 ; m++)
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);              pos += freq[jk][m][i];
           strcpy(line,stra);            if(pp[jk]>=1.e-10){
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              if(first==1){
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         }              }
                      fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);            }else{
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);              if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);            }
           }
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  
         for (j=ncov;j>=1;j--){          for(jk=1; jk <=nlstate ; jk++){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         }              pp[jk] += freq[jk][m][i];
         num[i]=atol(stra);          }       
                  for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){            pos += pp[jk];
           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;}*/            posprop += prop[jk][i];
           }
         i=i+1;          for(jk=1; jk <=nlstate ; jk++){
       }            if(pos>=1.e-5){
     }              if(first==1)
     /* printf("ii=%d", ij);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
        scanf("%d",i);*/              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   imx=i-1; /* Number of individuals */            }else{
               if(first==1)
   /* for (i=1; i<=imx; i++){                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     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( i <= iagemax){
     }              if(pos>=1.e-5){
     for (i=1; i<=imx; i++) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
   /* Calculation of the number of parameter from char model*/                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   Tvar=ivector(1,15);              }
   Tprod=ivector(1,15);              else
   Tvaraff=ivector(1,15);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   Tvard=imatrix(1,15,1,2);            }
   Tage=ivector(1,15);                }
              
   if (strlen(model) >1){          for(jk=-1; jk <=nlstate+ndeath; jk++)
     j=0, j1=0, k1=1, k2=1;            for(m=-1; m <=nlstate+ndeath; m++)
     j=nbocc(model,'+');              if(freq[jk][m][i] !=0 ) {
     j1=nbocc(model,'*');              if(first==1)
     cptcovn=j+1;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     cptcovprod=j1;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                  }
              if(i <= iagemax)
     strcpy(modelsav,model);            fprintf(ficresp,"\n");
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          if(first==1)
       printf("Error. Non available option model=%s ",model);            printf("Others in log...\n");
       goto end;          fprintf(ficlog,"\n");
     }        }
          }
     for(i=(j+1); i>=1;i--){    }
       cutv(stra,strb,modelsav,'+');    dateintmean=dateintsum/k2cpt; 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);   
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    fclose(ficresp);
       /*scanf("%d",i);*/    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
       if (strchr(strb,'*')) {    free_vector(pp,1,nlstate);
         cutv(strd,strc,strb,'*');    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
         if (strcmp(strc,"age")==0) {    /* End of Freq */
           cptcovprod--;  }
           cutv(strb,stre,strd,'V');  
           Tvar[i]=atoi(stre);  /************ Prevalence ********************/
           cptcovage++;  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)
             Tage[cptcovage]=i;  {  
             /*printf("stre=%s ", stre);*/    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         }       in each health status at the date of interview (if between dateprev1 and dateprev2).
         else if (strcmp(strd,"age")==0) {       We still use firstpass and lastpass as another selection.
           cptcovprod--;    */
           cutv(strb,stre,strc,'V');   
           Tvar[i]=atoi(stre);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
           cptcovage++;    double ***freq; /* Frequencies */
           Tage[cptcovage]=i;    double *pp, **prop;
         }    double pos,posprop; 
         else {    double  y2; /* in fractional years */
           cutv(strb,stre,strc,'V');    int iagemin, iagemax;
           Tvar[i]=ncov+k1;  
           cutv(strb,strc,strd,'V');    iagemin= (int) agemin;
           Tprod[k1]=i;    iagemax= (int) agemax;
           Tvard[k1][1]=atoi(strc);    /*pp=vector(1,nlstate);*/
           Tvard[k1][2]=atoi(stre);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
           Tvar[cptcovn+k2]=Tvard[k1][1];    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    j1=0;
           for (k=1; k<=lastobs;k++)    
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    j=cptcoveff;
           k1++;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           k2=k2+2;    
         }    for(k1=1; k1<=j;k1++){
       }      for(i1=1; i1<=ncodemax[k1];i1++){
       else {        j1++;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        
        /*  scanf("%d",i);*/        for (i=1; i<=nlstate; i++)  
       cutv(strd,strc,strb,'V');          for(m=iagemin; m <= iagemax+3; m++)
       Tvar[i]=atoi(strc);            prop[i][m]=0.0;
       }       
       strcpy(modelsav,stra);          for (i=1; i<=imx; i++) { /* Each individual */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          bool=1;
         scanf("%d",i);*/          if  (cptcovn>0) {
     }            for (z1=1; z1<=cptcoveff; z1++) 
 }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                  bool=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);          if (bool==1) { 
   scanf("%d ",i);*/            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     fclose(fic);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     /*  if(mle==1){*/                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     if (weightopt != 1) { /* Maximisation without weights*/                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       for(i=1;i<=n;i++) weight[i]=1.0;                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
     }                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     /*-calculation of age at interview from date of interview and age at death -*/                  /*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]]);*/
     agev=matrix(1,maxwav,1,imx);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
    for (i=1; i<=imx; i++)                } 
      for(m=2; (m<= maxwav); m++)              }
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){            } /* end selection of waves */
          anint[m][i]=9999;          }
          s[m][i]=-1;        }
        }        for(i=iagemin; i <= iagemax+3; i++){  
              
     for (i=1; i<=imx; i++)  {          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);            posprop += prop[jk][i]; 
       for(m=1; (m<= maxwav); m++){          } 
         if(s[m][i] >0){  
           if (s[m][i] == nlstate+1) {          for(jk=1; jk <=nlstate ; jk++){     
             if(agedc[i]>0)            if( i <=  iagemax){ 
               if(moisdc[i]!=99 && andc[i]!=9999)              if(posprop>=1.e-5){ 
               agev[m][i]=agedc[i];                probs[i][jk][j1]= prop[jk][i]/posprop;
             else {              } 
               if (andc[i]!=9999){            } 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);          }/* end jk */ 
               agev[m][i]=-1;        }/* end i */ 
               }      } /* end i1 */
             }    } /* end k1 */
           }    
           else if(s[m][i] !=9){ /* Should no more exist */    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    /*free_vector(pp,1,nlstate);*/
             if(mint[m][i]==99 || anint[m][i]==9999)    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
               agev[m][i]=1;  }  /* End of prevalence */
             else if(agev[m][i] <agemin){  
               agemin=agev[m][i];  /************* Waves Concatenation ***************/
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/  
             }  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(agev[m][i] >agemax){  {
               agemax=agev[m][i];    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/       Death is a valid wave (if date is known).
             }       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
             /*agev[m][i]=anint[m][i]-annais[i];*/       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
             /*   agev[m][i] = age[i]+2*m;*/       and mw[mi+1][i]. dh depends on stepm.
           }       */
           else { /* =9 */  
             agev[m][i]=1;    int i, mi, m;
             s[m][i]=-1;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           }       double sum=0., jmean=0.;*/
         }    int first;
         else /*= 0 Unknown */    int j, k=0,jk, ju, jl;
           agev[m][i]=1;    double sum=0.;
       }    first=0;
        jmin=1e+5;
     }    jmax=-1;
     for (i=1; i<=imx; i++)  {    jmean=0.;
       for(m=1; (m<= maxwav); m++){    for(i=1; i<=imx; i++){
         if (s[m][i] > (nlstate+ndeath)) {      mi=0;
           printf("Error: Wrong value in nlstate or ndeath\n");        m=firstpass;
           goto end;      while(s[m][i] <= nlstate){
         }        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
       }          mw[++mi][i]=m;
     }        if(m >=lastpass)
           break;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        else
           m++;
     free_vector(severity,1,maxwav);      }/* end while */
     free_imatrix(outcome,1,maxwav+1,1,n);      if (s[m][i] > nlstate){
     free_vector(moisnais,1,n);        mi++;     /* Death is another wave */
     free_vector(annais,1,n);        /* if(mi==0)  never been interviewed correctly before death */
     free_matrix(mint,1,maxwav,1,n);           /* Only death is a correct wave */
     free_matrix(anint,1,maxwav,1,n);        mw[mi][i]=m;
     free_vector(moisdc,1,n);      }
     free_vector(andc,1,n);  
       wav[i]=mi;
          if(mi==0){
     wav=ivector(1,imx);        nbwarn++;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        if(first==0){
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
              first=1;
     /* Concatenates waves */        }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        if(first==1){
           fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         }
       Tcode=ivector(1,100);      } /* end mi==0 */
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    } /* End individuals */
       ncodemax[1]=1;  
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    for(i=1; i<=imx; i++){
            for(mi=1; mi<wav[i];mi++){
    codtab=imatrix(1,100,1,10);        if (stepm <=0)
    h=0;          dh[mi][i]=1;
    m=pow(2,cptcoveff);        else{
            if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
    for(k=1;k<=cptcoveff; k++){            if (agedc[i] < 2*AGESUP) {
      for(i=1; i <=(m/pow(2,k));i++){              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
        for(j=1; j <= ncodemax[k]; j++){              if(j==0) j=1;  /* Survives at least one month after exam */
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){              else if(j<0){
            h++;                nberr++;
            if (h>m) h=1;codtab[h][k]=j;                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
          }                j=1; /* Temporary Dangerous patch */
        }                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
      }                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
    }                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               }
               k=k+1;
    /*for(i=1; i <=m ;i++){              if (j >= jmax){
      for(k=1; k <=cptcovn; k++){                jmax=j;
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);                ijmax=i;
      }              }
      printf("\n");              if (j <= jmin){
    }                jmin=j;
    scanf("%d",i);*/                ijmin=i;
                  }
    /* Calculates basic frequencies. Computes observed prevalence at single age              sum=sum+j;
        and prints on file fileres'p'. */              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          }
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          else{
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /*        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]); */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
                  k=k+1;
     /* For Powell, parameters are in a vector p[] starting at p[1]            if (j >= jmax) {
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */              jmax=j;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */              ijmax=i;
             }
     if(mle==1){            else if (j <= jmin){
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);              jmin=j;
     }              ijmin=i;
                }
     /*--------- results files --------------*/            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     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);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
    fprintf(ficres,"fprevalence=%d lprevalence=%d pop_based=%d\n",fprev,lprev,popbased);            if(j<0){
    fprintf(ficres,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",fprevfore,lprevfore,nforecast,mobilav);              nberr++;
               printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
    jk=1;              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]);
    fprintf(ficres,"# Parameters\n");            }
    printf("# Parameters\n");            sum=sum+j;
    for(i=1,jk=1; i <=nlstate; i++){          }
      for(k=1; k <=(nlstate+ndeath); k++){          jk= j/stepm;
        if (k != i)          jl= j -jk*stepm;
          {          ju= j -(jk+1)*stepm;
            printf("%d%d ",i,k);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
            fprintf(ficres,"%1d%1d ",i,k);            if(jl==0){
            for(j=1; j <=ncovmodel; j++){              dh[mi][i]=jk;
              printf("%f ",p[jk]);              bh[mi][i]=0;
              fprintf(ficres,"%f ",p[jk]);            }else{ /* We want a negative bias in order to only have interpolation ie
              jk++;                    * at the price of an extra matrix product in likelihood */
            }              dh[mi][i]=jk+1;
            printf("\n");              bh[mi][i]=ju;
            fprintf(ficres,"\n");            }
          }          }else{
      }            if(jl <= -ju){
    }              dh[mi][i]=jk;
  if(mle==1){              bh[mi][i]=jl;       /* bias is positive if real duration
     /* Computing hessian and covariance matrix */                                   * is higher than the multiple of stepm and negative otherwise.
     ftolhess=ftol; /* Usually correct */                                   */
     hesscov(matcov, p, npar, delti, ftolhess, func);            }
  }            else{
     fprintf(ficres,"# Scales\n");              dh[mi][i]=jk+1;
     printf("# Scales\n");              bh[mi][i]=ju;
      for(i=1,jk=1; i <=nlstate; i++){            }
       for(j=1; j <=nlstate+ndeath; j++){            if(dh[mi][i]==0){
         if (j!=i) {              dh[mi][i]=1; /* At least one step */
           fprintf(ficres,"%1d%1d",i,j);              bh[mi][i]=ju; /* At least one step */
           printf("%1d%1d",i,j);              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
           for(k=1; k<=ncovmodel;k++){            }
             printf(" %.5e",delti[jk]);          } /* end if mle */
             fprintf(ficres," %.5e",delti[jk]);        }
             jk++;      } /* end wave */
           }    }
           printf("\n");    jmean=sum/k;
           fprintf(ficres,"\n");    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);
         }    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);
       }   }
       }  
      /*********** Tricode ****************************/
     k=1;  void tricode(int *Tvar, int **nbcode, int imx)
     fprintf(ficres,"# Covariance\n");  {
     printf("# Covariance\n");    
     for(i=1;i<=npar;i++){    int Ndum[20],ij=1, k, j, i, maxncov=19;
       /*  if (k>nlstate) k=1;    int cptcode=0;
       i1=(i-1)/(ncovmodel*nlstate)+1;    cptcoveff=0; 
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);   
       printf("%s%d%d",alph[k],i1,tab[i]);*/    for (k=0; k<maxncov; k++) Ndum[k]=0;
       fprintf(ficres,"%3d",i);    for (k=1; k<=7; k++) ncodemax[k]=0;
       printf("%3d",i);  
       for(j=1; j<=i;j++){    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
         fprintf(ficres," %.5e",matcov[i][j]);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
         printf(" %.5e",matcov[i][j]);                                 modality*/ 
       }        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
       fprintf(ficres,"\n");        Ndum[ij]++; /*store the modality */
       printf("\n");        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       k++;        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     }                                         Tvar[j]. If V=sex and male is 0 and 
                                             female is 1, then  cptcode=1.*/
     while((c=getc(ficpar))=='#' && c!= EOF){      }
       ungetc(c,ficpar);  
       fgets(line, MAXLINE, ficpar);      for (i=0; i<=cptcode; i++) {
       puts(line);        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 */
       fputs(line,ficparo);      }
     }  
     ungetc(c,ficpar);      ij=1; 
        for (i=1; i<=ncodemax[j]; i++) {
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);        for (k=0; k<= maxncov; k++) {
              if (Ndum[k] != 0) {
     if (fage <= 2) {            nbcode[Tvar[j]][ij]=k; 
       bage = agemin;            /* 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; */
       fage = agemax;            
     }            ij++;
           }
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          if (ij > ncodemax[j]) break; 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        }  
       } 
        }  
 /*------------ gnuplot -------------*/  
 chdir(pathcd);   for (k=0; k< maxncov; k++) Ndum[k]=0;
   if((ficgp=fopen("graph.plt","w"))==NULL) {  
     printf("Problem with file graph.gp");goto end;   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.*/
 #ifdef windows     ij=Tvar[i];
   fprintf(ficgp,"cd \"%s\" \n",pathc);     Ndum[ij]++;
 #endif   }
 m=pow(2,cptcoveff);  
     ij=1;
  /* 1eme*/   for (i=1; i<= maxncov; i++) {
   for (cpt=1; cpt<= nlstate ; cpt ++) {     if((Ndum[i]!=0) && (i<=ncovcol)){
    for (k1=1; k1<= m ; k1 ++) {       Tvaraff[ij]=i; /*For printing */
        ij++;
 #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);   }
 #endif   
 #ifdef unix   cptcoveff=ij-1; /*Number of simple covariates*/
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);  }
 #endif  
   /*********** Health Expectancies ****************/
 for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   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);    /* Health expectancies, no variances */
     for (i=1; i<= nlstate ; i ++) {    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    double age, agelim, hf;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double ***p3mat;
 }    double eip;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  
      for (i=1; i<= nlstate ; i ++) {    pstamp(ficreseij);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficreseij,"# Age");
 }      for(i=1; i<=nlstate;i++){
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      for(j=1; j<=nlstate;j++){
 #ifdef unix        fprintf(ficreseij," e%1d%1d ",i,j);
 fprintf(ficgp,"\nset ter gif small size 400,300");      }
 #endif      fprintf(ficreseij," e%1d. ",i);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    }
    }    fprintf(ficreseij,"\n");
   }  
   /*2 eme*/    
     if(estepm < stepm){
   for (k1=1; k1<= m ; k1 ++) {      printf ("Problem %d lower than %d\n",estepm, stepm);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    }
        else  hstepm=estepm;   
     for (i=1; i<= nlstate+1 ; i ++) {    /* We compute the life expectancy from trapezoids spaced every estepm months
       k=2*i;     * This is mainly to measure the difference between two models: for example
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);     * if stepm=24 months pijx are given only every 2 years and by summing them
       for (j=1; j<= nlstate+1 ; j ++) {     * we are calculating an estimate of the Life Expectancy assuming a linear 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");     * progression in between and thus overestimating or underestimating according
   else fprintf(ficgp," \%%*lf (\%%*lf)");     * 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 (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");     * to compare the new estimate of Life expectancy with the same linear 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);     * hypothesis. A more precise result, taking into account a more precise
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);     * curvature will be obtained if estepm is as small as stepm. */
       for (j=1; j<= nlstate+1 ; j ++) {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /* For example we decided to compute the life expectancy with the smallest unit */
         else fprintf(ficgp," \%%*lf (\%%*lf)");    /* 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(ficgp,"\" t\"\" w l 0,");       nstepm is the number of stepm from age to agelin. 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);       Look at hpijx to understand the reason of that which relies in memory size
       for (j=1; j<= nlstate+1 ; j ++) {       and note for a fixed period like estepm months */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   else fprintf(ficgp," \%%*lf (\%%*lf)");       survival function given by stepm (the optimization length). Unfortunately it
 }         means that if the survival funtion is printed only each two years of age and if
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       else fprintf(ficgp,"\" t\"\" w l 0,");       results. So we changed our mind and took the option of the best precision.
     }    */
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   }  
      agelim=AGESUP;
   /*3eme*/    /* nhstepm age range expressed in number of stepm */
     nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   for (k1=1; k1<= m ; k1 ++) {    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     for (cpt=1; cpt<= nlstate ; cpt ++) {    /* if (stepm >= YEARM) hstepm=1;*/
       k=2+nlstate*(cpt-1);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       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);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for (i=1; i< nlstate ; i ++) {  
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     }      
   }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
        
   /* CV preval stat */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   for (k1=1; k1<= m ; k1 ++) {      
     for (cpt=1; cpt<nlstate ; cpt ++) {      printf("%d|",(int)age);fflush(stdout);
       k=3;      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);      
       for (i=1; i< nlstate ; i ++)      /* Computing expectancies */
         fprintf(ficgp,"+$%d",k+i+1);      for(i=1; i<=nlstate;i++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        for(j=1; j<=nlstate;j++)
                for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       l=3+(nlstate+ndeath)*cpt;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            
       for (i=1; i< nlstate ; i ++) {            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
         l=3+(nlstate+ndeath)*cpt;  
         fprintf(ficgp,"+$%d",l+i+1);          }
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        fprintf(ficreseij,"%3.0f",age );
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      for(i=1; i<=nlstate;i++){
     }        eip=0;
   }          for(j=1; j<=nlstate;j++){
           eip +=eij[i][j][(int)age];
   /* proba elementaires */          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
    for(i=1,jk=1; i <=nlstate; i++){        }
     for(k=1; k <=(nlstate+ndeath); k++){        fprintf(ficreseij,"%9.4f", eip );
       if (k != i) {      }
         for(j=1; j <=ncovmodel; j++){      fprintf(ficreseij,"\n");
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/      
           /*fprintf(ficgp,"%s",alph[1]);*/    }
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           jk++;    printf("\n");
           fprintf(ficgp,"\n");    fprintf(ficlog,"\n");
         }    
       }  }
     }  
     }  void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
   
   for(jk=1; jk <=m; jk++) {  {
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    /* Covariances of health expectancies eij and of total life expectancies according
    i=1;     to initial status i, ei. .
    for(k2=1; k2<=nlstate; k2++) {    */
      k3=i;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
      for(k=1; k<=(nlstate+ndeath); k++) {    double age, agelim, hf;
        if (k != k2){    double ***p3matp, ***p3matm, ***varhe;
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    double **dnewm,**doldm;
 ij=1;    double *xp, *xm;
         for(j=3; j <=ncovmodel; j++) {    double **gp, **gm;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double ***gradg, ***trgradg;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    int theta;
             ij++;  
           }    double eip, vip;
           else  
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
         }    xp=vector(1,npar);
           fprintf(ficgp,")/(1");    xm=vector(1,npar);
            dnewm=matrix(1,nlstate*nlstate,1,npar);
         for(k1=1; k1 <=nlstate; k1++){      doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    
 ij=1;    pstamp(ficresstdeij);
           for(j=3; j <=ncovmodel; j++){    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    fprintf(ficresstdeij,"# Age");
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    for(i=1; i<=nlstate;i++){
             ij++;      for(j=1; j<=nlstate;j++)
           }        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
           else      fprintf(ficresstdeij," e%1d. ",i);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    }
           }    fprintf(ficresstdeij,"\n");
           fprintf(ficgp,")");  
         }    pstamp(ficrescveij);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    fprintf(ficrescveij,"# Age");
         i=i+ncovmodel;    for(i=1; i<=nlstate;i++)
        }      for(j=1; j<=nlstate;j++){
      }        cptj= (j-1)*nlstate+i;
    }        for(i2=1; i2<=nlstate;i2++)
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);          for(j2=1; j2<=nlstate;j2++){
   }            cptj2= (j2-1)*nlstate+i2;
                if(cptj2 <= cptj)
   fclose(ficgp);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
              }
 chdir(path);      }
        fprintf(ficrescveij,"\n");
     free_ivector(wav,1,imx);    
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    if(estepm < stepm){
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        printf ("Problem %d lower than %d\n",estepm, stepm);
     free_ivector(num,1,n);    }
     free_vector(agedc,1,n);    else  hstepm=estepm;   
     /*free_matrix(covar,1,NCOVMAX,1,n);*/    /* We compute the life expectancy from trapezoids spaced every estepm months
     fclose(ficparo);     * This is mainly to measure the difference between two models: for example
     fclose(ficres);     * if stepm=24 months pijx are given only every 2 years and by summing them
     /*  }*/     * we are calculating an estimate of the Life Expectancy assuming a linear 
         * progression in between and thus overestimating or underestimating according
    /*________fin mle=1_________*/     * to the curvature of the survival function. If, for the same date, we 
         * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
       * hypothesis. A more precise result, taking into account a more precise
     /* No more information from the sample is required now */     * curvature will be obtained if estepm is as small as stepm. */
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    /* For example we decided to compute the life expectancy with the smallest unit */
     ungetc(c,ficpar);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     fgets(line, MAXLINE, ficpar);       nhstepm is the number of hstepm from age to agelim 
     puts(line);       nstepm is the number of stepm from age to agelin. 
     fputs(line,ficparo);       Look at hpijx to understand the reason of that which relies in memory size
   }       and note for a fixed period like estepm months */
   ungetc(c,ficpar);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         survival function given by stepm (the optimization length). Unfortunately it
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);       means that if the survival funtion is printed only each two years of age and if
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);       results. So we changed our mind and took the option of the best precision.
 /*--------- index.htm --------*/    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   strcpy(optionfilehtm,optionfile);  
   strcat(optionfilehtm,".htm");    /* If stepm=6 months */
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    /* nhstepm age range expressed in number of stepm */
     printf("Problem with %s \n",optionfilehtm);goto end;    agelim=AGESUP;
   }    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">    /* if (stepm >= YEARM) hstepm=1;*/
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 Total number of observations=%d <br>    
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 <hr  size=\"2\" color=\"#EC5E5E\">    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 <li>Outputs files<br><br>\n    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    gp=matrix(0,nhstepm,1,nlstate*nlstate);
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    gm=matrix(0,nhstepm,1,nlstate*nlstate);
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>  
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    for (age=bage; age<=fage; age ++){ 
         - 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>      /* Computed by stepm unit matrices, product of hstepm matrices, stored
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>   
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 <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);  
       /* Computing  Variances of health expectancies */
  fprintf(fichtm," <li>Graphs</li><p>");      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
  m=cptcoveff;      for(theta=1; theta <=npar; theta++){
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
  j1=0;          xm[i] = x[i] - (i==theta ?delti[theta]:0);
  for(k1=1; k1<=m;k1++){        }
    for(i1=1; i1<=ncodemax[k1];i1++){        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
        j1++;        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
        if (cptcovn > 0) {    
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        for(j=1; j<= nlstate; j++){
          for (cpt=1; cpt<=cptcoveff;cpt++)          for(i=1; i<=nlstate; i++){
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);            for(h=0; h<=nhstepm-1; h++){
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
        }              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>            }
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);              }
        for(cpt=1; cpt<nlstate;cpt++){        }
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>       
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        for(ij=1; ij<= nlstate*nlstate; ij++)
        }          for(h=0; h<=nhstepm-1; h++){
     for(cpt=1; cpt<=nlstate;cpt++) {            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          }
 interval) in state (%d): v%s%d%d.gif <br>      }/* End theta */
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        
      }      
      for(cpt=1; cpt<=nlstate;cpt++) {      for(h=0; h<=nhstepm-1; h++)
         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*nlstate;j++)
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          for(theta=1; theta <=npar; theta++)
      }            trgradg[h][j][theta]=gradg[h][theta][j];
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      
 health expectancies in states (1) and (2): e%s%d.gif<br>  
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);       for(ij=1;ij<=nlstate*nlstate;ij++)
 fprintf(fichtm,"\n</body>");        for(ji=1;ji<=nlstate*nlstate;ji++)
    }          varhe[ij][ji][(int)age] =0.;
  }  
 fclose(fichtm);       printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   /*--------------- Prevalence limit --------------*/       for(h=0;h<=nhstepm-1;h++){
          for(k=0;k<=nhstepm-1;k++){
   strcpy(filerespl,"pl");          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   strcat(filerespl,fileres);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          for(ij=1;ij<=nlstate*nlstate;ij++)
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;            for(ji=1;ji<=nlstate*nlstate;ji++)
   }              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);        }
   fprintf(ficrespl,"#Prevalence limit\n");      }
   fprintf(ficrespl,"#Age ");      /* Computing expectancies */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   fprintf(ficrespl,"\n");      for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++)
   prlim=matrix(1,nlstate,1,nlstate);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            /* 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]);*/
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          }
   k=0;  
   agebase=agemin;      fprintf(ficresstdeij,"%3.0f",age );
   agelim=agemax;      for(i=1; i<=nlstate;i++){
   ftolpl=1.e-10;        eip=0.;
   i1=cptcoveff;        vip=0.;
   if (cptcovn < 1){i1=1;}        for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
   for(cptcov=1;cptcov<=i1;cptcov++){          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
         k=k+1;          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        }
         fprintf(ficrespl,"\n#******");        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
         for(j=1;j<=cptcoveff;j++)      }
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficresstdeij,"\n");
         fprintf(ficrespl,"******\n");  
              fprintf(ficrescveij,"%3.0f",age );
         for (age=agebase; age<=agelim; age++){      for(i=1; i<=nlstate;i++)
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        for(j=1; j<=nlstate;j++){
           fprintf(ficrespl,"%.0f",age );          cptj= (j-1)*nlstate+i;
           for(i=1; i<=nlstate;i++)          for(i2=1; i2<=nlstate;i2++)
           fprintf(ficrespl," %.5f", prlim[i][i]);            for(j2=1; j2<=nlstate;j2++){
           fprintf(ficrespl,"\n");              cptj2= (j2-1)*nlstate+i2;
         }              if(cptj2 <= cptj)
       }                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
     }            }
   fclose(ficrespl);        }
       fprintf(ficrescveij,"\n");
   /*------------- h Pij x at various ages ------------*/     
      }
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   }    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   printf("Computing pij: result on file '%s' \n", filerespij);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    printf("\n");
   /*if (stepm<=24) stepsize=2;*/    fprintf(ficlog,"\n");
   
   agelim=AGESUP;    free_vector(xm,1,npar);
   hstepm=stepsize*YEARM; /* Every year of age */    free_vector(xp,1,npar);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
      free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   k=0;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   for(cptcov=1;cptcov<=i1;cptcov++){  }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;  /************ Variance ******************/
         fprintf(ficrespij,"\n#****** ");  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
         for(j=1;j<=cptcoveff;j++)  {
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* Variance of health expectancies */
         fprintf(ficrespij,"******\n");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
            /* double **newm;*/
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    double **dnewm,**doldm;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double **dnewmp,**doldmp;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    int i, j, nhstepm, hstepm, h, nstepm ;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int k, cptcode;
           oldm=oldms;savm=savms;    double *xp;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double **gp, **gm;  /* for var eij */
           fprintf(ficrespij,"# Age");    double ***gradg, ***trgradg; /*for var eij */
           for(i=1; i<=nlstate;i++)    double **gradgp, **trgradgp; /* for var p point j */
             for(j=1; j<=nlstate+ndeath;j++)    double *gpp, *gmp; /* for var p point j */
               fprintf(ficrespij," %1d-%1d",i,j);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
           fprintf(ficrespij,"\n");    double ***p3mat;
           for (h=0; h<=nhstepm; h++){    double age,agelim, hf;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    double ***mobaverage;
             for(i=1; i<=nlstate;i++)    int theta;
               for(j=1; j<=nlstate+ndeath;j++)    char digit[4];
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    char digitp[25];
             fprintf(ficrespij,"\n");  
           }    char fileresprobmorprev[FILENAMELENGTH];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           fprintf(ficrespij,"\n");    if(popbased==1){
         }      if(mobilav!=0)
     }        strcpy(digitp,"-populbased-mobilav-");
   }      else strcpy(digitp,"-populbased-nomobil-");
     }
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    else 
       strcpy(digitp,"-stablbased-");
   fclose(ficrespij);  
     if (mobilav!=0) {
   /*---------- Forecasting ------------------*/      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   strcpy(fileresf,"f");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   strcat(fileresf,fileres);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   if((ficresf=fopen(fileresf,"w"))==NULL) {      }
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;    }
   }  
   printf("Computing forecasting: result on file '%s' \n", fileresf);    strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprevfore, lprevfore);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
  free_matrix(agev,1,maxwav,1,imx);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   /* Mobile average */    strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   if (mobilav==1) {    }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)   
       for (i=1; i<=nlstate;i++)    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    pstamp(ficresprobmorprev);
           mobaverage[(int)agedeb][i][cptcod]=0.;    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
        fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for (agedeb=bage+4; agedeb<=fage; agedeb++){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       for (i=1; i<=nlstate;i++){      fprintf(ficresprobmorprev," p.%-d SE",j);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      for(i=1; i<=nlstate;i++)
           for (cpt=0;cpt<=4;cpt++){        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    }  
           }    fprintf(ficresprobmorprev,"\n");
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    fprintf(ficgp,"\n# Routine varevsij");
         }    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
       }    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);
   }  /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    pstamp(ficresvij);
   if (stepm<=12) stepsize=1;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
   agelim=AGESUP;      fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
   hstepm=stepsize*YEARM; /* Every year of age */    else
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
      fprintf(ficresvij,"# Age");
   if (popforecast==1) {    for(i=1; i<=nlstate;i++)
     if((ficpop=fopen(popfile,"r"))==NULL)    {      for(j=1; j<=nlstate;j++)
       printf("Problem with population file : %s\n",popfile);goto end;        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     }    fprintf(ficresvij,"\n");
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);    xp=vector(1,npar);
     popcount=vector(0,AGESUP);    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     i=1;      dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       {  
         i=i+1;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       }    gpp=vector(nlstate+1,nlstate+ndeath);
     imx=i;    gmp=vector(nlstate+1,nlstate+ndeath);
      trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    
   }    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   for(cptcov=1;cptcov<=i1;cptcov++){    }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    else  hstepm=estepm;   
       k=k+1;    /* For example we decided to compute the life expectancy with the smallest unit */
       fprintf(ficresf,"\n#****** ");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       for(j=1;j<=cptcoveff;j++) {       nhstepm is the number of hstepm from age to agelim 
         fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       nstepm is the number of stepm from age to agelin. 
       }       Look at hpijx to understand the reason of that which relies in memory size
       fprintf(ficresf,"******\n");       and note for a fixed period like k years */
       fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);       survival function given by stepm (the optimization length). Unfortunately it
       if (popforecast==1)  fprintf(ficresf," [Population]");       means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       for (agedeb=fage; agedeb>=bage; agedeb--){       results. So we changed our mind and took the option of the best precision.
         fprintf(ficresf,"\n%.f %.f 0",agedeb, agedeb);    */
        if (mobilav==1) {    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         for(j=1; j<=nlstate;j++)    agelim = AGESUP;
           fprintf(ficresf," %.3f",mobaverage[(int)agedeb][j][cptcod]);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         }      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         else {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           for(j=1; j<=nlstate;j++)      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficresf," %.3f",probs[(int)agedeb][j][cptcod]);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
         }        gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
        for(j=1; j<=ndeath;j++) fprintf(ficresf," 0.00000");  
        if (popforecast==1) fprintf(ficresf," [%.f] ",popeffectif[(int)agedeb]);  
       }      for(theta=1; theta <=npar; theta++){
              for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       for (cpt=1; cpt<=nforecast;cpt++) {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         fprintf(ficresf,"\n");        }
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         nhstepm = nhstepm/hstepm;  
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/        if (popbased==1) {
           if(mobilav ==0){
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(i=1; i<=nlstate;i++)
         oldm=oldms;savm=savms;              prlim[i][i]=probs[(int)age][i][ij];
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            }else{ /* mobilav */ 
                            for(i=1; i<=nlstate;i++)
         for (h=0; h<=nhstepm; h++){              prlim[i][i]=mobaverage[(int)age][i][ij];
                  }
          if (h*hstepm/YEARM*stepm==cpt)        }
             fprintf(ficresf,"\n%.f %.f %.f",agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);    
                  for(j=1; j<= nlstate; j++){
                    for(h=0; h<=nhstepm; h++){
          for(j=1; j<=nlstate+ndeath;j++) {            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
            kk1=0.;kk2=0;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
            for(i=1; i<=nlstate;i++) {                  }
              if (mobilav==1)        }
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];        /* This for computing probability of death (h=1 means
              else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];           computed over hstepm matrices product = hstepm*stepm months) 
              if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];           as a weighted average of prlim.
             }        */
            if (h*hstepm/YEARM*stepm==cpt) {        for(j=nlstate+1;j<=nlstate+ndeath;j++){
              fprintf(ficresf," %.3f", kk1);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
                if (popforecast==1) fprintf(ficresf," [%.f]", kk2);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
            }        }    
           }        /* end probability of death */
         }  
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
                  xp[i] = x[i] - (i==theta ?delti[theta]:0);
       }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     }   
   }        if (popbased==1) {
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          if(mobilav ==0){
   if (popforecast==1) {            for(i=1; i<=nlstate;i++)
     free_ivector(popage,0,AGESUP);              prlim[i][i]=probs[(int)age][i][ij];
     free_vector(popeffectif,0,AGESUP);          }else{ /* mobilav */ 
     free_vector(popcount,0,AGESUP);            for(i=1; i<=nlstate;i++)
   }              prlim[i][i]=mobaverage[(int)age][i][ij];
   free_imatrix(s,1,maxwav+1,1,n);          }
   free_vector(weight,1,n);        }
   fclose(ficresf);  
   /*---------- Health expectancies and variances ------------*/        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
   strcpy(filerest,"t");            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   strcat(filerest,fileres);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   if((ficrest=fopen(filerest,"w"))==NULL) {          }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;        }
   }        /* This for computing probability of death (h=1 means
   printf("Computing Total LEs with variances: file '%s' \n", filerest);           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
   strcpy(filerese,"e");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   strcat(filerese,fileres);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   if((ficreseij=fopen(filerese,"w"))==NULL) {           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        }    
   }        /* end probability of death */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
         for(j=1; j<= nlstate; j++) /* vareij */
  strcpy(fileresv,"v");          for(h=0; h<=nhstepm; h++){
   strcat(fileresv,fileres);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   if((ficresvij=fopen(fileresv,"w"))==NULL) {          }
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){      } /* End theta */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       fprintf(ficrest,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)      for(h=0; h<=nhstepm; h++) /* veij */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(j=1; j<=nlstate;j++)
       fprintf(ficrest,"******\n");          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
       fprintf(ficreseij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);        for(theta=1; theta <=npar; theta++)
       fprintf(ficreseij,"******\n");          trgradgp[j][theta]=gradgp[theta][j];
     
       fprintf(ficresvij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      for(i=1;i<=nlstate;i++)
       fprintf(ficresvij,"******\n");        for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;      for(h=0;h<=nhstepm;h++){
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);          for(k=0;k<=nhstepm;k++){
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       oldm=oldms;savm=savms;          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          for(i=1;i<=nlstate;i++)
                  for(j=1;j<=nlstate;j++)
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        }
       fprintf(ficrest,"\n");      }
            
       hf=1;      /* pptj */
       if (stepm >= YEARM) hf=stepm/YEARM;      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       epj=vector(1,nlstate+1);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(age=bage; age <=fage ;age++){      for(j=nlstate+1;j<=nlstate+ndeath;j++)
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
         if (popbased==1) {          varppt[j][i]=doldmp[j][i];
           for(i=1; i<=nlstate;i++)      /* end ppptj */
             prlim[i][i]=probs[(int)age][i][k];      /*  x centered again */
         }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
              prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
         fprintf(ficrest," %.0f",age);   
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      if (popbased==1) {
           for(i=1, epj[j]=0.;i <=nlstate;i++) {        if(mobilav ==0){
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];          for(i=1; i<=nlstate;i++)
           }            prlim[i][i]=probs[(int)age][i][ij];
           epj[nlstate+1] +=epj[j];        }else{ /* mobilav */ 
         }          for(i=1; i<=nlstate;i++)
         for(i=1, vepp=0.;i <=nlstate;i++)            prlim[i][i]=mobaverage[(int)age][i][ij];
           for(j=1;j <=nlstate;j++)        }
             vepp += vareij[i][j][(int)age];      }
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));               
         for(j=1;j <=nlstate;j++){      /* This for computing probability of death (h=1 means
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         }         as a weighted average of prlim.
         fprintf(ficrest,"\n");      */
       }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
     }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   }          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
              }    
              /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
  fclose(ficreseij);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
  fclose(ficresvij);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   fclose(ficrest);        for(i=1; i<=nlstate;i++){
   fclose(ficpar);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   free_vector(epj,1,nlstate+1);        }
   /*  scanf("%d ",i); */      } 
       fprintf(ficresprobmorprev,"\n");
   /*------- Variance limit prevalence------*/    
       fprintf(ficresvij,"%.0f ",age );
 strcpy(fileresvpl,"vpl");      for(i=1; i<=nlstate;i++)
   strcat(fileresvpl,fileres);        for(j=1; j<=nlstate;j++){
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        }
     exit(0);      fprintf(ficresvij,"\n");
   }      free_matrix(gp,0,nhstepm,1,nlstate);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
  k=0;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
  for(cptcov=1;cptcov<=i1;cptcov++){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    } /* End age */
      k=k+1;    free_vector(gpp,nlstate+1,nlstate+ndeath);
      fprintf(ficresvpl,"\n#****** ");    free_vector(gmp,nlstate+1,nlstate+ndeath);
      for(j=1;j<=cptcoveff;j++)    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      fprintf(ficresvpl,"******\n");    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
          /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
      oldm=oldms;savm=savms;  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
    }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
  }    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));
   fclose(ficresvpl);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   /*---------- End : free ----------------*/    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);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    /*  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);
    */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
    
      free_vector(xp,1,npar);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(doldm,1,nlstate,1,nlstate);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(dnewm,1,nlstate,1,npar);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
      free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   free_matrix(matcov,1,npar,1,npar);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_vector(delti,1,npar);    fclose(ficresprobmorprev);
      fflush(ficgp);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    fflush(fichtm); 
   }  /* end varevsij */
   printf("End of Imach\n");  
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  /************ Variance of prevlim ******************/
    void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   /* 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);*/  {
   /*printf("Total time was %d uSec.\n", total_usecs);*/    /* Variance of prevalence limit */
   /*------ End -----------*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     double **dnewm,**doldm;
  end:    int i, j, nhstepm, hstepm;
 #ifdef windows    int k, cptcode;
  chdir(pathcd);    double *xp;
 #endif    double *gp, *gm;
      double **gradg, **trgradg;
  system("..\\gp37mgw\\wgnuplot graph.plt");    double age,agelim;
     int theta;
 #ifdef windows    
   while (z[0] != 'q') {    pstamp(ficresvpl);
     chdir(pathcd);    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    fprintf(ficresvpl,"# Age");
     scanf("%s",z);    for(i=1; i<=nlstate;i++)
     if (z[0] == 'c') system("./imach");        fprintf(ficresvpl," %1d-%1d",i,i);
     else if (z[0] == 'e') {    fprintf(ficresvpl,"\n");
       chdir(path);  
       system(optionfilehtm);    xp=vector(1,npar);
     }    dnewm=matrix(1,nlstate,1,npar);
     else if (z[0] == 'q') exit(0);    doldm=matrix(1,nlstate,1,nlstate);
   }    
 #endif    hstepm=1*YEARM; /* Every year of age */
 }    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         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++)
           gp[i] = prlim[i][i];
       
         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++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       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");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     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 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);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
    xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    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>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           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 ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           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_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             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,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (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: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,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: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,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 health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (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\"Period (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); */
         k=2+(nlstate+1)*(cpt-1);
         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+i,cpt,i+1);
           /*      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);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* 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  *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; /* Dirty */
       }
     }
     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); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     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);
       goto end;
       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 \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\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 while opening datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem while opening 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;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         exit(1);
       }
       weight[i]=dval; 
       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 for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    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,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><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",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><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\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\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",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             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,pathcd); /* 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("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",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,pathcd); /* 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  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (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*/
       pstamp(ficrespij);
       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 Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: 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(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       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#****** ");
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\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, strstart);  
           cvevsij(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);
           }
   
           pstamp(ficrest);
           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( 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(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (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>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*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.1.16  
changed lines
  Added in v.1.124


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