Diff for /imach/src/imach.c between versions 1.4 and 1.119

version 1.4, 2001/05/02 17:34:41 version 1.119, 2006/03/15 17:42:26
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      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.119  2006/03/15 17:42:26  brouard
   individuals from different ages are interviewed on their health status    (Module): Bug if status = -2, the loglikelihood was
   or degree of  disability. At least a second wave of interviews    computed as likelihood omitting the logarithm. Version O.98e
   ("longitudinal") should  measure each new individual health status.  
   Health expectancies are computed from the transistions observed between    Revision 1.118  2006/03/14 18:20:07  brouard
   waves and are computed for each degree of severity of disability (number    (Module): varevsij Comments added explaining the second
   of life states). More degrees you consider, more time is necessary to    table of variances if popbased=1 .
   reach the Maximum Likelihood of the parameters involved in the model.    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   The simplest model is the multinomial logistic model where pij is    (Module): Function pstamp added
   the probabibility to be observed in state j at the second wave conditional    (Module): Version 0.98d
   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'    Revision 1.117  2006/03/14 17:16:22  brouard
   is a covariate. If you want to have a more complex model than "constant and    (Module): varevsij Comments added explaining the second
   age", you should modify the program where the markup    table of variances if popbased=1 .
     *Covariates have to be included here again* invites you to do it.    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   More covariates you add, less is the speed of the convergence.    (Module): Function pstamp added
     (Module): Version 0.98d
   The advantage that this computer programme claims, comes from that if the  
   delay between waves is not identical for each individual, or if some    Revision 1.116  2006/03/06 10:29:27  brouard
   individual missed an interview, the information is not rounded or lost, but    (Module): Variance-covariance wrong links and
   taken into account using an interpolation or extrapolation.    varian-covariance of ej. is needed (Saito).
   hPijx is the probability to be  
   observed in state i at age x+h conditional to the observed state i at age    Revision 1.115  2006/02/27 12:17:45  brouard
   x. The delay 'h' can be split into an exact number (nh*stepm) of    (Module): One freematrix added in mlikeli! 0.98c
   unobserved intermediate  states. This elementary transition (by month or  
   quarter trimester, semester or year) is model as a multinomial logistic.    Revision 1.114  2006/02/26 12:57:58  brouard
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    (Module): Some improvements in processing parameter
   and the contribution of each individual to the likelihood is simply hPijx.    filename with strsep.
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.113  2006/02/24 14:20:24  brouard
   of the life expectancies. It also computes the prevalence limits.    (Module): Memory leaks checks with valgrind and:
      datafile was not closed, some imatrix were not freed and on matrix
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    allocation too.
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.112  2006/01/30 09:55:26  brouard
   from the European Union.    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.111  2006/01/25 20:38:18  brouard
   can be accessed at http://euroreves.ined.fr/imach .    (Module): Lots of cleaning and bugs added (Gompertz)
   **********************************************************************/    (Module): Comments can be added in data file. Missing date values
      can be a simple dot '.'.
 #include <math.h>  
 #include <stdio.h>    Revision 1.110  2006/01/25 00:51:50  brouard
 #include <stdlib.h>    (Module): Lots of cleaning and bugs added (Gompertz)
 #include <unistd.h>  
     Revision 1.109  2006/01/24 19:37:15  brouard
 #define MAXLINE 256    (Module): Comments (lines starting with a #) are allowed in data.
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.108  2006/01/19 18:05:42  lievre
 #define windows    Gnuplot problem appeared...
     To be fixed
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.107  2006/01/19 16:20:37  brouard
     Test existence of gnuplot in imach path
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.106  2006/01/19 13:24:36  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Some cleaning and links added in html output
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.105  2006/01/05 20:23:19  lievre
 #define YEARM 12. /* Number of months per year */    *** empty log message ***
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.104  2005/09/30 16:11:43  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
 int nvar;    that the person is alive, then we can code his/her status as -2
 static int cptcov;    (instead of missing=-1 in earlier versions) and his/her
 int cptcovn;    contributions to the likelihood is 1 - Prob of dying from last
 int npar=NPARMAX;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 int nlstate=2; /* Number of live states */    the healthy state at last known wave). Version is 0.98
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.103  2005/09/30 15:54:49  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.102  2004/09/15 17:31:30  brouard
 int mle, weightopt;    Add the possibility to read data file including tab characters.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.101  2004/09/15 10:38:38  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Fix on curr_time
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;    Revision 1.100  2004/07/12 18:29:06  brouard
 FILE *ficgp, *fichtm;    Add version for Mac OS X. Just define UNIX in Makefile
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.99  2004/06/05 08:57:40  brouard
  FILE  *ficresvij;    *** empty log message ***
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.98  2004/05/16 15:05:56  brouard
   char fileresvpl[FILENAMELENGTH];    New version 0.97 . First attempt to estimate force of mortality
     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 .
     This is the basic analysis of mortality and should be done before any
     other analysis, in order to test if the mortality estimated from the
 #define NR_END 1    cross-longitudinal survey is different from the mortality estimated
 #define FREE_ARG char*    from other sources like vital statistic data.
 #define FTOL 1.0e-10  
     The same imach parameter file can be used but the option for mle should be -3.
 #define NRANSI  
 #define ITMAX 200    Agnès, who wrote this part of the code, tried to keep most of the
     former routines in order to include the new code within the former code.
 #define TOL 2.0e-4  
     The output is very simple: only an estimate of the intercept and of
 #define CGOLD 0.3819660    the slope with 95% confident intervals.
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Current limitations:
     A) Even if you enter covariates, i.e. with the
 #define GOLD 1.618034    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #define GLIMIT 100.0    B) There is no computation of Life Expectancy nor Life Table.
 #define TINY 1.0e-20  
     Revision 1.97  2004/02/20 13:25:42  lievre
 static double maxarg1,maxarg2;    Version 0.96d. Population forecasting command line is (temporarily)
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    suppressed.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.96  2003/07/15 15:38:55  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #define rint(a) floor(a+0.5)    rewritten within the same printf. Workaround: many printfs.
   
 static double sqrarg;    Revision 1.95  2003/07/08 07:54:34  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    * imach.c (Repository):
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    (Repository): Using imachwizard code to output a more meaningful covariance
     matrix (cov(a12,c31) instead of numbers.
 int imx;  
 int stepm;    Revision 1.94  2003/06/27 13:00:02  brouard
 /* Stepm, step in month: minimum step interpolation*/    Just cleaning
   
 int m,nb;    Revision 1.93  2003/06/25 16:33:55  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax;    (Module): On windows (cygwin) function asctime_r doesn't
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    exist so I changed back to asctime which exists.
 double **pmmij;    (Module): Version 0.96b
   
 double *weight;    Revision 1.92  2003/06/25 16:30:45  brouard
 int **s; /* Status */    (Module): On windows (cygwin) function asctime_r doesn't
 double *agedc, **covar, idx;    exist so I changed back to asctime which exists.
 int **nbcode, *Tcode, *Tvar, **codtab;  
     Revision 1.91  2003/06/25 15:30:29  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    * imach.c (Repository): Duplicated warning errors corrected.
 double ftolhess; /* Tolerance for computing hessian */    (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.
   
 void replace(char *s, char*t)    Revision 1.90  2003/06/24 12:34:15  brouard
 {    (Module): Some bugs corrected for windows. Also, when
   int i;    mle=-1 a template is output in file "or"mypar.txt with the design
   int lg=20;    of the covariance matrix to be input.
   i=0;  
   lg=strlen(t);    Revision 1.89  2003/06/24 12:30:52  brouard
   for(i=0; i<= lg; i++) {    (Module): Some bugs corrected for windows. Also, when
     (s[i] = t[i]);    mle=-1 a template is output in file "or"mypar.txt with the design
     if (t[i]== '\\') s[i]='/';    of the covariance matrix to be input.
   }  
 }    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
   int i,j=0;    Version 0.96
   int lg=20;  
   i=0;    Revision 1.86  2003/06/17 20:04:08  brouard
   lg=strlen(s);    (Module): Change position of html and gnuplot routines and added
   for(i=0; i<= lg; i++) {    routine fileappend.
   if  (s[i] == occ ) j++;  
   }    Revision 1.85  2003/06/17 13:12:43  brouard
   return j;    * imach.c (Repository): Check when date of death was earlier that
 }    current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
 void cutv(char *u,char *v, char*t, char occ)    was wrong (infinity). We still send an "Error" but patch by
 {    assuming that the date of death was just one stepm after the
   int i,lg,j,p;    interview.
   i=0;    (Repository): Because some people have very long ID (first column)
   for(j=0; j<=strlen(t)-1; j++) {    we changed int to long in num[] and we added a new lvector for
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    memory allocation. But we also truncated to 8 characters (left
   }    truncation)
     (Repository): No more line truncation errors.
   lg=strlen(t);  
   for(j=0; j<p; j++) {    Revision 1.84  2003/06/13 21:44:43  brouard
     (u[j] = t[j]);    * imach.c (Repository): Replace "freqsummary" at a correct
     u[p]='\0';    place. It differs from routine "prevalence" which may be called
   }    many times. Probs is memory consuming and must be used with
     parcimony.
    for(j=0; j<= lg; j++) {    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }    Revision 1.83  2003/06/10 13:39:11  lievre
 }    *** empty log message ***
   
 /********************** nrerror ********************/    Revision 1.82  2003/06/05 15:57:20  brouard
     Add log in  imach.c and  fullversion number is now printed.
 void nrerror(char error_text[])  
 {  */
   fprintf(stderr,"ERREUR ...\n");  /*
   fprintf(stderr,"%s\n",error_text);     Interpolated Markov Chain
   exit(1);  
 }    Short summary of the programme:
 /*********************** vector *******************/    
 double *vector(int nl, int nh)    This program computes Healthy Life Expectancies from
 {    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   double *v;    first survey ("cross") where individuals from different ages are
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    interviewed on their health status or degree of disability (in the
   if (!v) nrerror("allocation failure in vector");    case of a health survey which is our main interest) -2- at least a
   return v-nl+NR_END;    second wave of interviews ("longitudinal") which measure each change
 }    (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
 /************************ free vector ******************/    model. More health states you consider, more time is necessary to reach the
 void free_vector(double*v, int nl, int nh)    Maximum Likelihood of the parameters involved in the model.  The
 {    simplest model is the multinomial logistic model where pij is the
   free((FREE_ARG)(v+nl-NR_END));    probability to be observed in state j at the second wave
 }    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
 /************************ivector *******************************/    'age' is age and 'sex' is a covariate. If you want to have a more
 int *ivector(long nl,long nh)    complex model than "constant and age", you should modify the program
 {    where the markup *Covariates have to be included here again* invites
   int *v;    you to do it.  More covariates you add, slower the
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    convergence.
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;    The advantage of this computer programme, compared to a simple
 }    multinomial logistic model, is clear when the delay between waves is not
     identical for each individual. Also, if a individual missed an
 /******************free ivector **************************/    intermediate interview, the information is lost, but taken into
 void free_ivector(int *v, long nl, long nh)    account using an interpolation or extrapolation.  
 {  
   free((FREE_ARG)(v+nl-NR_END));    hPijx is the probability to be observed in state i at age x+h
 }    conditional to the observed state i at age x. The delay 'h' can be
     split into an exact number (nh*stepm) of unobserved intermediate
 /******************* imatrix *******************************/    states. This elementary transition (by month, quarter,
 int **imatrix(long nrl, long nrh, long ncl, long nch)    semester or year) is modelled as a multinomial logistic.  The hPx
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    matrix is simply the matrix product of nh*stepm elementary matrices
 {    and the contribution of each individual to the likelihood is simply
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    hPijx.
   int **m;  
      Also this programme outputs the covariance matrix of the parameters but also
   /* allocate pointers to rows */    of the life expectancies. It also computes the period (stable) prevalence. 
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    
   if (!m) nrerror("allocation failure 1 in matrix()");    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   m += NR_END;             Institut national d'études démographiques, Paris.
   m -= nrl;    This software have been partly granted by Euro-REVES, a concerted action
      from the European Union.
      It is copyrighted identically to a GNU software product, ie programme and
   /* allocate rows and set pointers to them */    software can be distributed freely for non commercial use. Latest version
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    can be accessed at http://euroreves.ined.fr/imach .
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   m[nrl] -= ncl;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
      
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    **********************************************************************/
    /*
   /* return pointer to array of pointers to rows */    main
   return m;    read parameterfile
 }    read datafile
     concatwav
 /****************** free_imatrix *************************/    freqsummary
 void free_imatrix(m,nrl,nrh,ncl,nch)    if (mle >= 1)
       int **m;      mlikeli
       long nch,ncl,nrh,nrl;    print results files
      /* free an int matrix allocated by imatrix() */    if mle==1 
 {       computes hessian
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    read end of parameter file: agemin, agemax, bage, fage, estepm
   free((FREE_ARG) (m+nrl-NR_END));        begin-prev-date,...
 }    open gnuplot file
     open html file
 /******************* matrix *******************************/    period (stable) prevalence
 double **matrix(long nrl, long nrh, long ncl, long nch)     for age prevalim()
 {    h Pij x
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    variance of p varprob
   double **m;    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Variance-covariance of DFLE
   if (!m) nrerror("allocation failure 1 in matrix()");    prevalence()
   m += NR_END;     movingaverage()
   m -= nrl;    varevsij() 
     if popbased==1 varevsij(,popbased)
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    total life expectancies
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Variance of period (stable) prevalence
   m[nrl] += NR_END;   end
   m[nrl] -= ncl;  */
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;  
 }   
   #include <math.h>
 /*************************free matrix ************************/  #include <stdio.h>
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  #include <stdlib.h>
 {  #include <string.h>
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #include <unistd.h>
   free((FREE_ARG)(m+nrl-NR_END));  
 }  #include <limits.h>
   #include <sys/types.h>
 /******************* ma3x *******************************/  #include <sys/stat.h>
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  #include <errno.h>
 {  extern int errno;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  /* #include <sys/time.h> */
   #include <time.h>
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #include "timeval.h"
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  /* #include <libintl.h> */
   m -= nrl;  /* #define _(String) gettext (String) */
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define MAXLINE 256
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  #define GNUPLOTPROGRAM "gnuplot"
   m[nrl] -= ncl;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   m[nrl][ncl] -= nll;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;  #define NINTERVMAX 8
    #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   for (i=nrl+1; i<=nrh; i++) {  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define NCOVMAX 8 /* Maximum number of covariates */
     for (j=ncl+1; j<=nch; j++)  #define MAXN 20000
       m[i][j]=m[i][j-1]+nlay;  #define YEARM 12. /* Number of months per year */
   }  #define AGESUP 130
   return m;  #define AGEBASE 40
 }  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   #ifdef UNIX
 /*************************free ma3x ************************/  #define DIRSEPARATOR '/'
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define CHARSEPARATOR "/"
 {  #define ODIRSEPARATOR '\\'
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #else
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define DIRSEPARATOR '\\'
   free((FREE_ARG)(m+nrl-NR_END));  #define CHARSEPARATOR "\\"
 }  #define ODIRSEPARATOR '/'
   #endif
 /***************** f1dim *************************/  
 extern int ncom;  /* $Id$ */
 extern double *pcom,*xicom;  /* $State$ */
 extern double (*nrfunc)(double []);  
    char version[]="Imach version 0.98e, March 2006, INED-EUROREVES-Institut de longevite ";
 double f1dim(double x)  char fullversion[]="$Revision$ $Date$"; 
 {  char strstart[80];
   int j;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   double f;  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   double *xt;  int nvar;
    int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   xt=vector(1,ncom);  int npar=NPARMAX;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  int nlstate=2; /* Number of live states */
   f=(*nrfunc)(xt);  int ndeath=1; /* Number of dead states */
   free_vector(xt,1,ncom);  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   return f;  int popbased=0;
 }  
   int *wav; /* Number of waves for this individuual 0 is possible */
 /*****************brent *************************/  int maxwav; /* Maxim number of waves */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  int jmin, jmax; /* min, max spacing between 2 waves */
 {  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   int iter;  int gipmx, gsw; /* Global variables on the number of contributions 
   double a,b,d,etemp;                     to the likelihood and the sum of weights (done by funcone)*/
   double fu,fv,fw,fx;  int mle, weightopt;
   double ftemp;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   double e=0.0;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
               * wave mi and wave mi+1 is not an exact multiple of stepm. */
   a=(ax < cx ? ax : cx);  double jmean; /* Mean space between 2 waves */
   b=(ax > cx ? ax : cx);  double **oldm, **newm, **savm; /* Working pointers to matrices */
   x=w=v=bx;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   fw=fv=fx=(*f)(x);  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   for (iter=1;iter<=ITMAX;iter++) {  FILE *ficlog, *ficrespow;
     xm=0.5*(a+b);  int globpr; /* Global variable for printing or not */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  double fretone; /* Only one call to likelihood */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  long ipmx; /* Number of contributions */
     printf(".");fflush(stdout);  double sw; /* Sum of weights */
 #ifdef DEBUG  char filerespow[FILENAMELENGTH];
     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);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  FILE *ficresilk;
 #endif  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  FILE *ficresprobmorprev;
       *xmin=x;  FILE *fichtm, *fichtmcov; /* Html File */
       return fx;  FILE *ficreseij;
     }  char filerese[FILENAMELENGTH];
     ftemp=fu;  FILE *ficresstdeij;
     if (fabs(e) > tol1) {  char fileresstde[FILENAMELENGTH];
       r=(x-w)*(fx-fv);  FILE *ficrescveij;
       q=(x-v)*(fx-fw);  char filerescve[FILENAMELENGTH];
       p=(x-v)*q-(x-w)*r;  FILE  *ficresvij;
       q=2.0*(q-r);  char fileresv[FILENAMELENGTH];
       if (q > 0.0) p = -p;  FILE  *ficresvpl;
       q=fabs(q);  char fileresvpl[FILENAMELENGTH];
       etemp=e;  char title[MAXLINE];
       e=d;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       else {  char command[FILENAMELENGTH];
         d=p/q;  int  outcmd=0;
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
           d=SIGN(tol1,xm-x);  
       }  char filelog[FILENAMELENGTH]; /* Log file */
     } else {  char filerest[FILENAMELENGTH];
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  char fileregp[FILENAMELENGTH];
     }  char popfile[FILENAMELENGTH];
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     if (fu <= fx) {  
       if (u >= x) a=x; else b=x;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
       SHFT(v,w,x,u)  struct timezone tzp;
         SHFT(fv,fw,fx,fu)  extern int gettimeofday();
         } else {  struct tm tmg, tm, tmf, *gmtime(), *localtime();
           if (u < x) a=u; else b=u;  long time_value;
           if (fu <= fw || w == x) {  extern long time();
             v=w;  char strcurr[80], strfor[80];
             w=u;  
             fv=fw;  char *endptr;
             fw=fu;  long lval;
           } 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 *******************************/
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     newm=savm;  { 
     /* Covariates have to be included here again */    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     cov[1]=1.;    int **m; 
     cov[2]=agefin;    
     if (cptcovn>0){    /* allocate pointers to rows */ 
       for (k=1; k<=cptcovn;k++) {cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];/*printf("Tcode[ij]=%d nbcode=%d\n",Tcode[ij],nbcode[k][Tcode[ij]]);*/}    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     }    if (!m) nrerror("allocation failure 1 in matrix()"); 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    m += NR_END; 
     m -= nrl; 
     savm=oldm;    
     oldm=newm;    
     maxmax=0.;    /* allocate rows and set pointers to them */ 
     for(j=1;j<=nlstate;j++){    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       min=1.;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       max=0.;    m[nrl] += NR_END; 
       for(i=1; i<=nlstate; i++) {    m[nrl] -= ncl; 
         sumnew=0;    
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
         prlim[i][j]= newm[i][j]/(1-sumnew);    
         max=FMAX(max,prlim[i][j]);    /* return pointer to array of pointers to rows */ 
         min=FMIN(min,prlim[i][j]);    return m; 
       }  } 
       maxmin=max-min;  
       maxmax=FMAX(maxmax,maxmin);  /****************** free_imatrix *************************/
     }  void free_imatrix(m,nrl,nrh,ncl,nch)
     if(maxmax < ftolpl){        int **m;
       return prlim;        long nch,ncl,nrh,nrl; 
     }       /* free an int matrix allocated by imatrix() */ 
   }  { 
 }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     free((FREE_ARG) (m+nrl-NR_END)); 
 /*************** transition probabilities **********/  } 
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  /******************* matrix *******************************/
 {  double **matrix(long nrl, long nrh, long ncl, long nch)
   double s1, s2;  {
   /*double t34;*/    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   int i,j,j1, nc, ii, jj;    double **m;
   
     for(i=1; i<= nlstate; i++){    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     for(j=1; j<i;j++){    if (!m) nrerror("allocation failure 1 in matrix()");
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    m += NR_END;
         /*s2 += param[i][j][nc]*cov[nc];*/    m -= nrl;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       ps[i][j]=s2;    m[nrl] += NR_END;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    m[nrl] -= ncl;
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    return m;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/     */
       }  }
       ps[i][j]=s2;  
     }  /*************************free matrix ************************/
   }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   for(i=1; i<= nlstate; i++){  {
      s1=0;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     for(j=1; j<i; j++)    free((FREE_ARG)(m+nrl-NR_END));
       s1+=exp(ps[i][j]);  }
     for(j=i+1; j<=nlstate+ndeath; j++)  
       s1+=exp(ps[i][j]);  /******************* ma3x *******************************/
     ps[i][i]=1./(s1+1.);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     for(j=1; j<i; j++)  {
       ps[i][j]= exp(ps[i][j])*ps[i][i];    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     for(j=i+1; j<=nlstate+ndeath; j++)    double ***m;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   } /* end i */    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    m -= nrl;
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       ps[ii][ii]=1;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     }    m[nrl] += NR_END;
   }    m[nrl] -= ncl;
   
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
    }    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     printf("\n ");    m[nrl][ncl] += NR_END;
     }    m[nrl][ncl] -= nll;
     printf("\n ");printf("%lf ",cov[2]);*/    for (j=ncl+1; j<=nch; j++) 
 /*      m[nrl][j]=m[nrl][j-1]+nlay;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    
   goto end;*/    for (i=nrl+1; i<=nrh; i++) {
     return ps;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 }      for (j=ncl+1; j<=nch; j++) 
         m[i][j]=m[i][j-1]+nlay;
 /**************** Product of 2 matrices ******************/    }
     return m; 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 {             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    */
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  }
   /* in, b, out are matrice of pointers which should have been initialized  
      before: only the contents of out is modified. The function returns  /*************************free ma3x ************************/
      a pointer to pointers identical to out */  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   long i, j, k;  {
   for(i=nrl; i<= nrh; i++)    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     for(k=ncolol; k<=ncoloh; k++)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    free((FREE_ARG)(m+nrl-NR_END));
         out[i][k] +=in[i][j]*b[j][k];  }
   
   return out;  /*************** function subdirf ***********/
 }  char *subdirf(char fileres[])
   {
     /* Caution optionfilefiname is hidden */
 /************* Higher Matrix Product ***************/    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    strcat(tmpout,fileres);
 {    return tmpout;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  }
      duration (i.e. until  
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  /*************** function subdirf2 ***********/
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  char *subdirf2(char fileres[], char *preop)
      (typically every 2 years instead of every month which is too big).  {
      Model is determined by parameters x and covariates have to be    
      included manually here.    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
      */    strcat(tmpout,"/");
     strcat(tmpout,preop);
   int i, j, d, h, k;    strcat(tmpout,fileres);
   double **out, cov[NCOVMAX];    return tmpout;
   double **newm;  }
   
   /* Hstepm could be zero and should return the unit matrix */  /*************** function subdirf3 ***********/
   for (i=1;i<=nlstate+ndeath;i++)  char *subdirf3(char fileres[], char *preop, char *preop2)
     for (j=1;j<=nlstate+ndeath;j++){  {
       oldm[i][j]=(i==j ? 1.0 : 0.0);    
       po[i][j][0]=(i==j ? 1.0 : 0.0);    /* Caution optionfilefiname is hidden */
     }    strcpy(tmpout,optionfilefiname);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    strcat(tmpout,"/");
   for(h=1; h <=nhstepm; h++){    strcat(tmpout,preop);
     for(d=1; d <=hstepm; d++){    strcat(tmpout,preop2);
       newm=savm;    strcat(tmpout,fileres);
       /* Covariates have to be included here again */    return tmpout;
       cov[1]=1.;  }
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  
       if (cptcovn>0){  /***************** f1dim *************************/
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];  extern int ncom; 
     }  extern double *pcom,*xicom;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  extern double (*nrfunc)(double []); 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/   
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  double f1dim(double x) 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  { 
       savm=oldm;    int j; 
       oldm=newm;    double f;
     }    double *xt; 
     for(i=1; i<=nlstate+ndeath; i++)   
       for(j=1;j<=nlstate+ndeath;j++) {    xt=vector(1,ncom); 
         po[i][j][h]=newm[i][j];    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    f=(*nrfunc)(xt); 
          */    free_vector(xt,1,ncom); 
       }    return f; 
   } /* end h */  } 
   return po;  
 }  /*****************brent *************************/
   double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   { 
 /*************** log-likelihood *************/    int iter; 
 double func( double *x)    double a,b,d,etemp;
 {    double fu,fv,fw,fx;
   int i, ii, j, k, mi, d;    double ftemp;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   double **out;    double e=0.0; 
   double sw; /* Sum of weights */   
   double lli; /* Individual log likelihood */    a=(ax < cx ? ax : cx); 
   long ipmx;    b=(ax > cx ? ax : cx); 
   /*extern weight */    x=w=v=bx; 
   /* We are differentiating ll according to initial status */    fw=fv=fx=(*f)(x); 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    for (iter=1;iter<=ITMAX;iter++) { 
   /*for(i=1;i<imx;i++)      xm=0.5*(a+b); 
 printf(" %d\n",s[4][i]);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   */      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       printf(".");fflush(stdout);
   for(k=1; k<=nlstate; k++) ll[k]=0.;      fprintf(ficlog,".");fflush(ficlog);
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  #ifdef DEBUG
        for(mi=1; mi<= wav[i]-1; mi++){      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);
       for (ii=1;ii<=nlstate+ndeath;ii++)      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);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
             for(d=0; d<dh[mi][i]; d++){  #endif
         newm=savm;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
           cov[1]=1.;        *xmin=x; 
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        return fx; 
           if (cptcovn>0){      } 
             for (k=1; k<=cptcovn;k++) cov[2+k]=covar[1+k-1][i];      ftemp=fu;
             }      if (fabs(e) > tol1) { 
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        r=(x-w)*(fx-fv); 
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        q=(x-v)*(fx-fw); 
           savm=oldm;        p=(x-v)*q-(x-w)*r; 
           oldm=newm;        q=2.0*(q-r); 
         if (q > 0.0) p = -p; 
         q=fabs(q); 
       } /* end mult */        etemp=e; 
            e=d; 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       ipmx +=1;        else { 
       sw += weight[i];          d=p/q; 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          u=x+d; 
     } /* end of wave */          if (u-a < tol2 || b-u < tol2) 
   } /* end of individual */            d=SIGN(tol1,xm-x); 
         } 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      } else { 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      } 
   return -l;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 }      fu=(*f)(u); 
       if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
 /*********** Maximum Likelihood Estimation ***************/        SHFT(v,w,x,u) 
           SHFT(fv,fw,fx,fu) 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))          } else { 
 {            if (u < x) a=u; else b=u; 
   int i,j, iter;            if (fu <= fw || w == x) { 
   double **xi,*delti;              v=w; 
   double fret;              w=u; 
   xi=matrix(1,npar,1,npar);              fv=fw; 
   for (i=1;i<=npar;i++)              fw=fu; 
     for (j=1;j<=npar;j++)            } else if (fu <= fv || v == x || v == w) { 
       xi[i][j]=(i==j ? 1.0 : 0.0);              v=u; 
   printf("Powell\n");              fv=fu; 
   powell(p,xi,npar,ftol,&iter,&fret,func);            } 
           } 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    } 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));    nrerror("Too many iterations in brent"); 
     *xmin=x; 
 }    return fx; 
   } 
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /****************** mnbrak ***********************/
 {  
   double  **a,**y,*x,pd;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   double **hess;              double (*func)(double)) 
   int i, j,jk;  { 
   int *indx;    double ulim,u,r,q, dum;
     double fu; 
   double hessii(double p[], double delta, int theta, double delti[]);   
   double hessij(double p[], double delti[], int i, int j);    *fa=(*func)(*ax); 
   void lubksb(double **a, int npar, int *indx, double b[]) ;    *fb=(*func)(*bx); 
   void ludcmp(double **a, int npar, int *indx, double *d) ;    if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
         SHFT(dum,*fb,*fa,dum) 
   hess=matrix(1,npar,1,npar);        } 
     *cx=(*bx)+GOLD*(*bx-*ax); 
   printf("\nCalculation of the hessian matrix. Wait...\n");    *fc=(*func)(*cx); 
   for (i=1;i<=npar;i++){    while (*fb > *fc) { 
     printf("%d",i);fflush(stdout);      r=(*bx-*ax)*(*fb-*fc); 
     hess[i][i]=hessii(p,ftolhess,i,delti);      q=(*bx-*cx)*(*fb-*fa); 
     /*printf(" %f ",p[i]);*/      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
   for (i=1;i<=npar;i++) {      if ((*bx-u)*(u-*cx) > 0.0) { 
     for (j=1;j<=npar;j++)  {        fu=(*func)(u); 
       if (j>i) {      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         printf(".%d%d",i,j);fflush(stdout);        fu=(*func)(u); 
         hess[i][j]=hessij(p,delti,i,j);        if (fu < *fc) { 
         hess[j][i]=hess[i][j];          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       }            SHFT(*fb,*fc,fu,(*func)(u)) 
     }            } 
   }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   printf("\n");        u=ulim; 
         fu=(*func)(u); 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      } else { 
          u=(*cx)+GOLD*(*cx-*bx); 
   a=matrix(1,npar,1,npar);        fu=(*func)(u); 
   y=matrix(1,npar,1,npar);      } 
   x=vector(1,npar);      SHFT(*ax,*bx,*cx,u) 
   indx=ivector(1,npar);        SHFT(*fa,*fb,*fc,fu) 
   for (i=1;i<=npar;i++)        } 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  } 
   ludcmp(a,npar,indx,&pd);  
   /*************** linmin ************************/
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  int ncom; 
     x[j]=1;  double *pcom,*xicom;
     lubksb(a,npar,indx,x);  double (*nrfunc)(double []); 
     for (i=1;i<=npar;i++){   
       matcov[i][j]=x[i];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     }  { 
   }    double brent(double ax, double bx, double cx, 
                  double (*f)(double), double tol, double *xmin); 
   printf("\n#Hessian matrix#\n");    double f1dim(double x); 
   for (i=1;i<=npar;i++) {    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     for (j=1;j<=npar;j++) {                double *fc, double (*func)(double)); 
       printf("%.3e ",hess[i][j]);    int j; 
     }    double xx,xmin,bx,ax; 
     printf("\n");    double fx,fb,fa;
   }   
     ncom=n; 
   /* Recompute Inverse */    pcom=vector(1,n); 
   for (i=1;i<=npar;i++)    xicom=vector(1,n); 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    nrfunc=func; 
   ludcmp(a,npar,indx,&pd);    for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
   /*  printf("\n#Hessian matrix recomputed#\n");      xicom[j]=xi[j]; 
     } 
   for (j=1;j<=npar;j++) {    ax=0.0; 
     for (i=1;i<=npar;i++) x[i]=0;    xx=1.0; 
     x[j]=1;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     lubksb(a,npar,indx,x);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     for (i=1;i<=npar;i++){  #ifdef DEBUG
       y[i][j]=x[i];    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       printf("%.3e ",y[i][j]);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     }  #endif
     printf("\n");    for (j=1;j<=n;j++) { 
   }      xi[j] *= xmin; 
   */      p[j] += xi[j]; 
     } 
   free_matrix(a,1,npar,1,npar);    free_vector(xicom,1,n); 
   free_matrix(y,1,npar,1,npar);    free_vector(pcom,1,n); 
   free_vector(x,1,npar);  } 
   free_ivector(indx,1,npar);  
   free_matrix(hess,1,npar,1,npar);  char *asc_diff_time(long time_sec, char ascdiff[])
   {
     long sec_left, days, hours, minutes;
 }    days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
 /*************** hessian matrix ****************/    hours = (sec_left) / (60*60) ;
 double hessii( double x[], double delta, int theta, double delti[])    sec_left = (sec_left) %(60*60);
 {    minutes = (sec_left) /60;
   int i;    sec_left = (sec_left) % (60);
   int l=1, lmax=20;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   double k1,k2;    return ascdiff;
   double p2[NPARMAX+1];  }
   double res;  
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  /*************** powell ************************/
   double fx;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   int k=0,kmax=10;              double (*func)(double [])) 
   double l1;  { 
     void linmin(double p[], double xi[], int n, double *fret, 
   fx=func(x);                double (*func)(double [])); 
   for (i=1;i<=npar;i++) p2[i]=x[i];    int i,ibig,j; 
   for(l=0 ; l <=lmax; l++){    double del,t,*pt,*ptt,*xit;
     l1=pow(10,l);    double fp,fptt;
     delts=delt;    double *xits;
     for(k=1 ; k <kmax; k=k+1){    int niterf, itmp;
       delt = delta*(l1*k);  
       p2[theta]=x[theta] +delt;    pt=vector(1,n); 
       k1=func(p2)-fx;    ptt=vector(1,n); 
       p2[theta]=x[theta]-delt;    xit=vector(1,n); 
       k2=func(p2)-fx;    xits=vector(1,n); 
       /*res= (k1-2.0*fx+k2)/delt/delt; */    *fret=(*func)(p); 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    for (j=1;j<=n;j++) pt[j]=p[j]; 
          for (*iter=1;;++(*iter)) { 
 #ifdef DEBUG      fp=(*fret); 
       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);      ibig=0; 
 #endif      del=0.0; 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      last_time=curr_time;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      (void) gettimeofday(&curr_time,&tzp);
         k=kmax;      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
       }      /*    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
         k=kmax; l=lmax*10.;      */
       }     for (i=1;i<=n;i++) {
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        printf(" %d %.12f",i, p[i]);
         delts=delt;        fprintf(ficlog," %d %.12lf",i, p[i]);
       }        fprintf(ficrespow," %.12lf", p[i]);
     }      }
   }      printf("\n");
   delti[theta]=delts;      fprintf(ficlog,"\n");
   return res;      fprintf(ficrespow,"\n");fflush(ficrespow);
        if(*iter <=3){
 }        tm = *localtime(&curr_time.tv_sec);
         strcpy(strcurr,asctime(&tm));
 double hessij( double x[], double delti[], int thetai,int thetaj)  /*       asctime_r(&tm,strcurr); */
 {        forecast_time=curr_time; 
   int i;        itmp = strlen(strcurr);
   int l=1, l1, lmax=20;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   double k1,k2,k3,k4,res,fx;          strcurr[itmp-1]='\0';
   double p2[NPARMAX+1];        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   int k;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         for(niterf=10;niterf<=30;niterf+=10){
   fx=func(x);          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   for (k=1; k<=2; k++) {          tmf = *localtime(&forecast_time.tv_sec);
     for (i=1;i<=npar;i++) p2[i]=x[i];  /*      asctime_r(&tmf,strfor); */
     p2[thetai]=x[thetai]+delti[thetai]/k;          strcpy(strfor,asctime(&tmf));
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          itmp = strlen(strfor);
     k1=func(p2)-fx;          if(strfor[itmp-1]=='\n')
            strfor[itmp-1]='\0';
     p2[thetai]=x[thetai]+delti[thetai]/k;          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);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          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);
     k2=func(p2)-fx;        }
        }
     p2[thetai]=x[thetai]-delti[thetai]/k;      for (i=1;i<=n;i++) { 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     k3=func(p2)-fx;        fptt=(*fret); 
    #ifdef DEBUG
     p2[thetai]=x[thetai]-delti[thetai]/k;        printf("fret=%lf \n",*fret);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        fprintf(ficlog,"fret=%lf \n",*fret);
     k4=func(p2)-fx;  #endif
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        printf("%d",i);fflush(stdout);
 #ifdef DEBUG        fprintf(ficlog,"%d",i);fflush(ficlog);
     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);        linmin(p,xit,n,fret,func); 
 #endif        if (fabs(fptt-(*fret)) > del) { 
   }          del=fabs(fptt-(*fret)); 
   return res;          ibig=i; 
 }        } 
   #ifdef DEBUG
 /************** Inverse of matrix **************/        printf("%d %.12e",i,(*fret));
 void ludcmp(double **a, int n, int *indx, double *d)        fprintf(ficlog,"%d %.12e",i,(*fret));
 {        for (j=1;j<=n;j++) {
   int i,imax,j,k;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   double big,dum,sum,temp;          printf(" x(%d)=%.12e",j,xit[j]);
   double *vv;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
          }
   vv=vector(1,n);        for(j=1;j<=n;j++) {
   *d=1.0;          printf(" p=%.12e",p[j]);
   for (i=1;i<=n;i++) {          fprintf(ficlog," p=%.12e",p[j]);
     big=0.0;        }
     for (j=1;j<=n;j++)        printf("\n");
       if ((temp=fabs(a[i][j])) > big) big=temp;        fprintf(ficlog,"\n");
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  #endif
     vv[i]=1.0/big;      } 
   }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   for (j=1;j<=n;j++) {  #ifdef DEBUG
     for (i=1;i<j;i++) {        int k[2],l;
       sum=a[i][j];        k[0]=1;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        k[1]=-1;
       a[i][j]=sum;        printf("Max: %.12e",(*func)(p));
     }        fprintf(ficlog,"Max: %.12e",(*func)(p));
     big=0.0;        for (j=1;j<=n;j++) {
     for (i=j;i<=n;i++) {          printf(" %.12e",p[j]);
       sum=a[i][j];          fprintf(ficlog," %.12e",p[j]);
       for (k=1;k<j;k++)        }
         sum -= a[i][k]*a[k][j];        printf("\n");
       a[i][j]=sum;        fprintf(ficlog,"\n");
       if ( (dum=vv[i]*fabs(sum)) >= big) {        for(l=0;l<=1;l++) {
         big=dum;          for (j=1;j<=n;j++) {
         imax=i;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       }            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     if (j != imax) {          }
       for (k=1;k<=n;k++) {          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         dum=a[imax][k];          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         a[imax][k]=a[j][k];        }
         a[j][k]=dum;  #endif
       }  
       *d = -(*d);  
       vv[imax]=vv[j];        free_vector(xit,1,n); 
     }        free_vector(xits,1,n); 
     indx[j]=imax;        free_vector(ptt,1,n); 
     if (a[j][j] == 0.0) a[j][j]=TINY;        free_vector(pt,1,n); 
     if (j != n) {        return; 
       dum=1.0/(a[j][j]);      } 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     }      for (j=1;j<=n;j++) { 
   }        ptt[j]=2.0*p[j]-pt[j]; 
   free_vector(vv,1,n);  /* Doesn't work */        xit[j]=p[j]-pt[j]; 
 ;        pt[j]=p[j]; 
 }      } 
       fptt=(*func)(ptt); 
 void lubksb(double **a, int n, int *indx, double b[])      if (fptt < fp) { 
 {        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   int i,ii=0,ip,j;        if (t < 0.0) { 
   double sum;          linmin(p,xit,n,fret,func); 
            for (j=1;j<=n;j++) { 
   for (i=1;i<=n;i++) {            xi[j][ibig]=xi[j][n]; 
     ip=indx[i];            xi[j][n]=xit[j]; 
     sum=b[ip];          }
     b[ip]=b[i];  #ifdef DEBUG
     if (ii)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     else if (sum) ii=i;          for(j=1;j<=n;j++){
     b[i]=sum;            printf(" %.12e",xit[j]);
   }            fprintf(ficlog," %.12e",xit[j]);
   for (i=n;i>=1;i--) {          }
     sum=b[i];          printf("\n");
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          fprintf(ficlog,"\n");
     b[i]=sum/a[i][i];  #endif
   }        }
 }      } 
     } 
 /************ Frequencies ********************/  } 
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)  
 {  /* Some frequencies */  /**** Prevalence limit (stable or period prevalence)  ****************/
    
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   double ***freq; /* Frequencies */  {
   double *pp;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   double pos;       matrix by transitions matrix until convergence is reached */
   FILE *ficresp;  
   char fileresp[FILENAMELENGTH];    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
   pp=vector(1,nlstate);    double **matprod2();
     double **out, cov[NCOVMAX], **pmij();
   strcpy(fileresp,"p");    double **newm;
   strcat(fileresp,fileres);    double agefin, delaymax=50 ; /* Max number of years to converge */
   if((ficresp=fopen(fileresp,"w"))==NULL) {  
     printf("Problem with prevalence resultfile: %s\n", fileresp);    for (ii=1;ii<=nlstate+ndeath;ii++)
     exit(0);      for (j=1;j<=nlstate+ndeath;j++){
   }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      }
   j1=0;  
      cov[1]=1.;
   j=cptcovn;   
   if (cptcovn<1) {j=1;ncodemax[1]=1;}   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   for(k1=1; k1<=j;k1++){      newm=savm;
    for(i1=1; i1<=ncodemax[k1];i1++){      /* Covariates have to be included here again */
        j1++;       cov[2]=agefin;
     
         for (i=-1; i<=nlstate+ndeath; i++)          for (k=1; k<=cptcovn;k++) {
          for (jk=-1; jk<=nlstate+ndeath; jk++)            cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
            for(m=agemin; m <= agemax+3; m++)          /*      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]]);*/
              freq[i][jk][m]=0;        }
                for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
        for (i=1; i<=imx; i++) {        for (k=1; k<=cptcovprod;k++)
          bool=1;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
          if  (cptcovn>0) {  
            for (z1=1; z1<=cptcovn; z1++)        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
              if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
          }        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
           if (bool==1) {      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
            for(m=firstpass; m<=lastpass-1; m++){  
              if(agev[m][i]==0) agev[m][i]=agemax+1;      savm=oldm;
              if(agev[m][i]==1) agev[m][i]=agemax+2;      oldm=newm;
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      maxmax=0.;
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      for(j=1;j<=nlstate;j++){
            }        min=1.;
          }        max=0.;
        }        for(i=1; i<=nlstate; i++) {
         if  (cptcovn>0) {          sumnew=0;
          fprintf(ficresp, "\n#Variable");          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
          for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);          prlim[i][j]= newm[i][j]/(1-sumnew);
        }          max=FMAX(max,prlim[i][j]);
        fprintf(ficresp, "\n#");          min=FMIN(min,prlim[i][j]);
        for(i=1; i<=nlstate;i++)        }
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        maxmin=max-min;
        fprintf(ficresp, "\n");        maxmax=FMAX(maxmax,maxmin);
              }
   for(i=(int)agemin; i <= (int)agemax+3; i++){      if(maxmax < ftolpl){
     if(i==(int)agemax+3)        return prlim;
       printf("Total");      }
     else    }
       printf("Age %d", i);  }
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  /*************** transition probabilities ***************/ 
         pp[jk] += freq[jk][m][i];  
     }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     for(jk=1; jk <=nlstate ; jk++){  {
       for(m=-1, pos=0; m <=0 ; m++)    double s1, s2;
         pos += freq[jk][m][i];    /*double t34;*/
       if(pp[jk]>=1.e-10)    int i,j,j1, nc, ii, jj;
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  
       else      for(i=1; i<= nlstate; i++){
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        for(j=1; j<i;j++){
     }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     for(jk=1; jk <=nlstate ; jk++){            /*s2 += param[i][j][nc]*cov[nc];*/
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         pp[jk] += freq[jk][m][i];  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
     }          }
     for(jk=1,pos=0; jk <=nlstate ; jk++)          ps[i][j]=s2;
       pos += pp[jk];  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
     for(jk=1; jk <=nlstate ; jk++){        }
       if(pos>=1.e-5)        for(j=i+1; j<=nlstate+ndeath;j++){
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       else            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
       if( i <= (int) agemax){          }
         if(pos>=1.e-5)          ps[i][j]=s2;
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        }
       else      }
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      /*ps[3][2]=1;*/
       }      
     }      for(i=1; i<= nlstate; i++){
     for(jk=-1; jk <=nlstate+ndeath; jk++)        s1=0;
       for(m=-1; m <=nlstate+ndeath; m++)        for(j=1; j<i; j++)
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          s1+=exp(ps[i][j]);
     if(i <= (int) agemax)        for(j=i+1; j<=nlstate+ndeath; j++)
       fprintf(ficresp,"\n");          s1+=exp(ps[i][j]);
     printf("\n");        ps[i][i]=1./(s1+1.);
     }        for(j=1; j<i; j++)
     }          ps[i][j]= exp(ps[i][j])*ps[i][i];
  }        for(j=i+1; j<=nlstate+ndeath; j++)
            ps[i][j]= exp(ps[i][j])*ps[i][i];
   fclose(ficresp);        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      } /* end i */
   free_vector(pp,1,nlstate);      
       for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
 }  /* End of Freq */        for(jj=1; jj<= nlstate+ndeath; jj++){
           ps[ii][jj]=0;
 /************* Waves Concatenation ***************/          ps[ii][ii]=1;
         }
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      }
 {      
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  
      Death is a valid wave (if date is known).  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  /*         printf("ddd %lf ",ps[ii][jj]); */
      and mw[mi+1][i]. dh depends on stepm.  /*       } */
      */  /*       printf("\n "); */
   /*        } */
   int i, mi, m;  /*        printf("\n ");printf("%lf ",cov[2]); */
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;         /*
 float sum=0.;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
         goto end;*/
   for(i=1; i<=imx; i++){      return ps;
     mi=0;  }
     m=firstpass;  
     while(s[m][i] <= nlstate){  /**************** Product of 2 matrices ******************/
       if(s[m][i]>=1)  
         mw[++mi][i]=m;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       if(m >=lastpass)  {
         break;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       else       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         m++;    /* in, b, out are matrice of pointers which should have been initialized 
     }/* end while */       before: only the contents of out is modified. The function returns
     if (s[m][i] > nlstate){       a pointer to pointers identical to out */
       mi++;     /* Death is another wave */    long i, j, k;
       /* if(mi==0)  never been interviewed correctly before death */    for(i=nrl; i<= nrh; i++)
          /* Only death is a correct wave */      for(k=ncolol; k<=ncoloh; k++)
       mw[mi][i]=m;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     }          out[i][k] +=in[i][j]*b[j][k];
   
     wav[i]=mi;    return out;
     if(mi==0)  }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  
   }  
   /************* Higher Matrix Product ***************/
   for(i=1; i<=imx; i++){  
     for(mi=1; mi<wav[i];mi++){  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       if (stepm <=0)  {
         dh[mi][i]=1;    /* Computes the transition matrix starting at age 'age' over 
       else{       'nhstepm*hstepm*stepm' months (i.e. until
         if (s[mw[mi+1][i]][i] > nlstate) {       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);       nhstepm*hstepm matrices. 
           if(j=0) j=1;  /* Survives at least one month after exam */       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         }       (typically every 2 years instead of every month which is too big 
         else{       for the memory).
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));       Model is determined by parameters x and covariates have to be 
           k=k+1;       included manually here. 
           if (j >= jmax) jmax=j;  
           else if (j <= jmin)jmin=j;       */
           sum=sum+j;  
         }    int i, j, d, h, k;
         jk= j/stepm;    double **out, cov[NCOVMAX];
         jl= j -jk*stepm;    double **newm;
         ju= j -(jk+1)*stepm;  
         if(jl <= -ju)    /* Hstepm could be zero and should return the unit matrix */
           dh[mi][i]=jk;    for (i=1;i<=nlstate+ndeath;i++)
         else      for (j=1;j<=nlstate+ndeath;j++){
           dh[mi][i]=jk+1;        oldm[i][j]=(i==j ? 1.0 : 0.0);
         if(dh[mi][i]==0)        po[i][j][0]=(i==j ? 1.0 : 0.0);
           dh[mi][i]=1; /* At least one step */      }
       }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     }    for(h=1; h <=nhstepm; h++){
   }      for(d=1; d <=hstepm; d++){
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);        newm=savm;
 }        /* Covariates have to be included here again */
 /*********** Tricode ****************************/        cov[1]=1.;
 void tricode(int *Tvar, int **nbcode, int imx)        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]]];
   int Ndum[80],ij, k, j, i;        for (k=1; k<=cptcovage;k++)
   int cptcode=0;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   for (k=0; k<79; k++) Ndum[k]=0;        for (k=1; k<=cptcovprod;k++)
   for (k=1; k<=7; k++) ncodemax[k]=0;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
    
   for (j=1; j<=cptcovn; j++) {  
     for (i=1; i<=imx; i++) {        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       ij=(int)(covar[Tvar[j]][i]);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       Ndum[ij]++;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       if (ij > cptcode) cptcode=ij;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     }        savm=oldm;
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/        oldm=newm;
     for (i=0; i<=cptcode; i++) {      }
       if(Ndum[i]!=0) ncodemax[j]++;      for(i=1; i<=nlstate+ndeath; i++)
     }        for(j=1;j<=nlstate+ndeath;j++) {
            po[i][j][h]=newm[i][j];
     ij=1;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     for (i=1; i<=ncodemax[j]; i++) {           */
       for (k=0; k<=79; k++) {        }
         if (Ndum[k] != 0) {    } /* end h */
           nbcode[Tvar[j]][ij]=k;    return po;
           ij++;  }
         }  
         if (ij > ncodemax[j]) break;  
       }    /*************** log-likelihood *************/
     }  double func( double *x)
   }    {
     int i, ii, j, k, mi, d, kk;
   }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
 /*********** Health Expectancies ****************/    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    int s1, s2;
 {    double bbh, survp;
   /* Health expectancies */    long ipmx;
   int i, j, nhstepm, hstepm, h;    /*extern weight */
   double age, agelim,hf;    /* We are differentiating ll according to initial status */
   double ***p3mat;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      /*for(i=1;i<imx;i++) 
   fprintf(ficreseij,"# Health expectancies\n");      printf(" %d\n",s[4][i]);
   fprintf(ficreseij,"# Age");    */
   for(i=1; i<=nlstate;i++)    cov[1]=1.;
     for(j=1; j<=nlstate;j++)  
       fprintf(ficreseij," %1d-%1d",i,j);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   fprintf(ficreseij,"\n");  
     if(mle==1){
   hstepm=1*YEARM; /*  Every j years of age (in month) */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   agelim=AGESUP;          for (ii=1;ii<=nlstate+ndeath;ii++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            for (j=1;j<=nlstate+ndeath;j++){
     /* nhstepm age range expressed in number of stepm */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     /* Typically if 20 years = 20*12/6=40 stepm */            }
     if (stepm >= YEARM) hstepm=1;          for(d=0; d<dh[mi][i]; d++){
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */            newm=savm;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            for (kk=1; kk<=cptcovage;kk++) {
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(i=1; i<=nlstate;i++)            savm=oldm;
       for(j=1; j<=nlstate;j++)            oldm=newm;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          } /* end mult */
           eij[i][j][(int)age] +=p3mat[i][j][h];        
         }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
              /* But now since version 0.9 we anticipate for bias at large stepm.
     hf=1;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     if (stepm >= YEARM) hf=stepm/YEARM;           * (in months) between two waves is not a multiple of stepm, we rounded to 
     fprintf(ficreseij,"%.0f",age );           * the nearest (and in case of equal distance, to the lowest) interval but now
     for(i=1; i<=nlstate;i++)           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       for(j=1; j<=nlstate;j++){           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);           * probability in order to take into account the bias as a fraction of the way
       }           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
     fprintf(ficreseij,"\n");           * -stepm/2 to stepm/2 .
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           * 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. 
 }           */
           s1=s[mw[mi][i]][i];
 /************ Variance ******************/          s2=s[mw[mi+1][i]][i];
 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)          bbh=(double)bh[mi][i]/(double)stepm; 
 {          /* bias bh is positive if real duration
   /* Variance of health expectancies */           * is higher than the multiple of stepm and negative otherwise.
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/           */
   double **newm;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   double **dnewm,**doldm;          if( s2 > nlstate){ 
   int i, j, nhstepm, hstepm, h;            /* i.e. if s2 is a death state and if the date of death is known 
   int k, cptcode;               then the contribution to the likelihood is the probability to 
    double *xp;               die between last step unit time and current  step unit time, 
   double **gp, **gm;               which is also equal to probability to die before dh 
   double ***gradg, ***trgradg;               minus probability to die before dh-stepm . 
   double ***p3mat;               In version up to 0.92 likelihood was computed
   double age,agelim;          as if date of death was unknown. Death was treated as any other
   int theta;          health state: the date of the interview describes the actual state
           and not the date of a change in health state. The former idea was
    fprintf(ficresvij,"# Covariances of life expectancies\n");          to consider that at each interview the state was recorded
   fprintf(ficresvij,"# Age");          (healthy, disable or death) and IMaCh was corrected; but when we
   for(i=1; i<=nlstate;i++)          introduced the exact date of death then we should have modified
     for(j=1; j<=nlstate;j++)          the contribution of an exact death to the likelihood. This new
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          contribution is smaller and very dependent of the step unit
   fprintf(ficresvij,"\n");          stepm. It is no more the probability to die between last interview
           and month of death but the probability to survive from last
   xp=vector(1,npar);          interview up to one month before death multiplied by the
   dnewm=matrix(1,nlstate,1,npar);          probability to die within a month. Thanks to Chris
   doldm=matrix(1,nlstate,1,nlstate);          Jackson for correcting this bug.  Former versions increased
            mortality artificially. The bad side is that we add another loop
   hstepm=1*YEARM; /* Every year of age */          which slows down the processing. The difference can be up to 10%
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          lower mortality.
   agelim = AGESUP;            */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            lli=log(out[s1][s2] - savm[s1][s2]);
     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 */          } else if  (s2==-2) {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for (j=1,survp=0. ; j<=nlstate; j++) 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);              survp += out[s1][j];
     gp=matrix(0,nhstepm,1,nlstate);            lli= log(survp);
     gm=matrix(0,nhstepm,1,nlstate);          }
           
     for(theta=1; theta <=npar; theta++){  /*      else if  (s2==-4) { */
       for(i=1; i<=npar; i++){ /* Computes gradient */  /*        for (j=3,survp=0. ; j<=nlstate; j++)  */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  /*          survp += out[s1][j]; */
       }  /*        lli= survp; */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    /*      } */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          
       for(j=1; j<= nlstate; j++){  /*      else if  (s2==-5) { */
         for(h=0; h<=nhstepm; h++){  /*        for (j=1,survp=0. ; j<=2; j++)  */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  /*          survp += out[s1][j]; */
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  /*        lli= survp; */
         }  /*      } */
       }  
      
       for(i=1; i<=npar; i++) /* Computes gradient */          else{
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              /*  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 */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          } 
       for(j=1; j<= nlstate; j++){          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         for(h=0; h<=nhstepm; h++){          /*if(lli ==000.0)*/
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          ipmx +=1;
         }          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(j=1; j<= nlstate; j++)        } /* end of wave */
         for(h=0; h<=nhstepm; h++){      } /* end of individual */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    }  else if(mle==2){
         }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     } /* End theta */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
     for(h=0; h<=nhstepm; h++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<=nlstate;j++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(theta=1; theta <=npar; theta++)            }
           trgradg[h][j][theta]=gradg[h][theta][j];          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
     for(i=1;i<=nlstate;i++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(j=1;j<=nlstate;j++)            for (kk=1; kk<=cptcovage;kk++) {
         vareij[i][j][(int)age] =0.;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(h=0;h<=nhstepm;h++){            }
       for(k=0;k<=nhstepm;k++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            savm=oldm;
         for(i=1;i<=nlstate;i++)            oldm=newm;
           for(j=1;j<=nlstate;j++)          } /* end mult */
             vareij[i][j][(int)age] += doldm[i][j];        
       }          s1=s[mw[mi][i]][i];
     }          s2=s[mw[mi+1][i]][i];
     h=1;          bbh=(double)bh[mi][i]/(double)stepm; 
     if (stepm >= YEARM) h=stepm/YEARM;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     fprintf(ficresvij,"%.0f ",age );          ipmx +=1;
     for(i=1; i<=nlstate;i++)          sw += weight[i];
       for(j=1; j<=nlstate;j++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);        } /* end of wave */
       }      } /* end of individual */
     fprintf(ficresvij,"\n");    }  else if(mle==3){  /* exponential inter-extrapolation */
     free_matrix(gp,0,nhstepm,1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     free_matrix(gm,0,nhstepm,1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for (j=1;j<=nlstate+ndeath;j++){
   } /* End age */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(xp,1,npar);            }
   free_matrix(doldm,1,nlstate,1,npar);          for(d=0; d<dh[mi][i]; d++){
   free_matrix(dnewm,1,nlstate,1,nlstate);            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 /************ 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)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /* Variance of prevalence limit */            savm=oldm;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            oldm=newm;
   double **newm;          } /* end mult */
   double **dnewm,**doldm;        
   int i, j, nhstepm, hstepm;          s1=s[mw[mi][i]][i];
   int k, cptcode;          s2=s[mw[mi+1][i]][i];
   double *xp;          bbh=(double)bh[mi][i]/(double)stepm; 
   double *gp, *gm;          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 */
   double **gradg, **trgradg;          ipmx +=1;
   double age,agelim;          sw += weight[i];
   int theta;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
            } /* end of wave */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      } /* end of individual */
   fprintf(ficresvpl,"# Age");    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   for(i=1; i<=nlstate;i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       fprintf(ficresvpl," %1d-%1d",i,i);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   fprintf(ficresvpl,"\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 */          
     gradg=matrix(1,npar,1,nlstate);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     gp=vector(1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     gm=vector(1,nlstate);            savm=oldm;
             oldm=newm;
     for(theta=1; theta <=npar; theta++){          } /* end mult */
       for(i=1; i<=npar; i++){ /* Computes gradient */        
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          s1=s[mw[mi][i]][i];
       }          s2=s[mw[mi+1][i]][i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          if( s2 > nlstate){ 
       for(i=1;i<=nlstate;i++)            lli=log(out[s1][s2] - savm[s1][s2]);
         gp[i] = prlim[i][i];          }else{
                lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       for(i=1; i<=npar; i++) /* Computes gradient */          }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          ipmx +=1;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          sw += weight[i];
       for(i=1;i<=nlstate;i++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         gm[i] = prlim[i][i];  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         } /* end of wave */
       for(i=1;i<=nlstate;i++)      } /* end of individual */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     } /* End theta */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     trgradg =matrix(1,nlstate,1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
     for(j=1; j<=nlstate;j++)            for (j=1;j<=nlstate+ndeath;j++){
       for(theta=1; theta <=npar; theta++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         trgradg[j][theta]=gradg[theta][j];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
     for(i=1;i<=nlstate;i++)          for(d=0; d<dh[mi][i]; d++){
       varpl[i][(int)age] =0.;            newm=savm;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);            for (kk=1; kk<=cptcovage;kk++) {
     for(i=1;i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            }
           
     fprintf(ficresvpl,"%.0f ",age );            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for(i=1; i<=nlstate;i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            savm=oldm;
     fprintf(ficresvpl,"\n");            oldm=newm;
     free_vector(gp,1,nlstate);          } /* end mult */
     free_vector(gm,1,nlstate);        
     free_matrix(gradg,1,npar,1,nlstate);          s1=s[mw[mi][i]][i];
     free_matrix(trgradg,1,nlstate,1,npar);          s2=s[mw[mi+1][i]][i];
   } /* End age */          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ipmx +=1;
   free_vector(xp,1,npar);          sw += weight[i];
   free_matrix(doldm,1,nlstate,1,npar);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   free_matrix(dnewm,1,nlstate,1,nlstate);          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         } /* end of wave */
 }      } /* end of individual */
     } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
 /***********************************************/    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
 /**************** Main Program *****************/    return -l;
 /***********************************************/  }
   
 /*int main(int argc, char *argv[])*/  /*************** log-likelihood *************/
 int main()  double funcone( double *x)
 {  {
     /* Same as likeli but slower because of a lot of printf and if */
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;    int i, ii, j, k, mi, d, kk;
   double agedeb, agefin,hf;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   double agemin=1.e20, agemax=-1.e20;    double **out;
     double lli; /* Individual log likelihood */
   double fret;    double llt;
   double **xi,tmp,delta;    int s1, s2;
     double bbh, survp;
   double dum; /* Dummy variable */    /*extern weight */
   double ***p3mat;    /* We are differentiating ll according to initial status */
   int *indx;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   char line[MAXLINE], linepar[MAXLINE];    /*for(i=1;i<imx;i++) 
   char title[MAXLINE];      printf(" %d\n",s[4][i]);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    */
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];    cov[1]=1.;
   char filerest[FILENAMELENGTH];  
   char fileregp[FILENAMELENGTH];    for(k=1; k<=nlstate; k++) ll[k]=0.;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  
   int firstobs=1, lastobs=10;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int sdeb, sfin; /* Status at beginning and end */      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int c,  h , cpt,l;      for(mi=1; mi<= wav[i]-1; mi++){
   int ju,jl, mi;        for (ii=1;ii<=nlstate+ndeath;ii++)
   int i1,j1, k1,jk,aa,bb, stepsize;          for (j=1;j<=nlstate+ndeath;j++){
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int hstepm, nhstepm;          }
   double bage, fage, age, agelim, agebase;        for(d=0; d<dh[mi][i]; d++){
   double ftolpl=FTOL;          newm=savm;
   double **prlim;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double *severity;          for (kk=1; kk<=cptcovage;kk++) {
   double ***param; /* Matrix of parameters */            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double  *p;          }
   double **matcov; /* Matrix of covariance */          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double ***delti3; /* Scale */                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double *delti; /* Scale */          savm=oldm;
   double ***eij, ***vareij;          oldm=newm;
   double **varpl; /* Variances of prevalence limits by age */        } /* end mult */
   double *epj, vepp;        
   char version[80]="Imach version 0.64, May 2000, INED-EUROREVES ";        s1=s[mw[mi][i]][i];
   char *alph[]={"a","a","b","c","d","e"}, str[4];        s2=s[mw[mi+1][i]][i];
   char z[1]="c", occ;        bbh=(double)bh[mi][i]/(double)stepm; 
 #include <sys/time.h>        /* bias is positive if real duration
 #include <time.h>         * is higher than the multiple of stepm and negative otherwise.
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];         */
   /* long total_usecs;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   struct timeval start_time, end_time;          lli=log(out[s1][s2] - savm[s1][s2]);
          } else if  (s2==-2) {
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          for (j=1,survp=0. ; j<=nlstate; j++) 
             survp += out[s1][j];
           lli= log(survp);
   printf("\nIMACH, Version 0.64a");        }else if (mle==1){
   printf("\nEnter the parameter file name: ");          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
 #ifdef windows          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 */
   scanf("%s",pathtot);        } else if(mle==3){  /* exponential inter-extrapolation */
   cygwin_split_path(pathtot,path,optionfile);          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 */
      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
      chdir(path);          lli=log(out[s1][s2]); /* Original formula */
          } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   /*size=30;          lli=log(out[s1][s2]); /* Original formula */
   getcwd(pathcd, size);          } /* End of if */
   printf("pathcd=%s, path=%s, optionfile=%s\n",pathcd,path,optionfile);        ipmx +=1;
   cutv(path,optionfile,pathtot,'\\');        sw += weight[i];
   chdir(path);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   replace(pathc,path);  /*       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]); */
   printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);        if(globpr){
   */          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
 #endif   %11.6f %11.6f %11.6f ", \
 #ifdef unix                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   scanf("%s",optionfile);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
 #endif          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             llt +=ll[k]*gipmx/gsw;
 /*-------- arguments in the command line --------*/            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
   strcpy(fileres,"r");          fprintf(ficresilk," %10.6f\n", -llt);
   strcat(fileres, optionfile);        }
       } /* end of wave */
   /*---------arguments file --------*/    } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     printf("Problem with optionfile %s\n",optionfile);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     goto end;    if(globpr==0){ /* First time we count the contributions and weights */
   }      gipmx=ipmx;
       gsw=sw;
   strcpy(filereso,"o");    }
   strcat(filereso,fileres);    return -l;
   if((ficparo=fopen(filereso,"w"))==NULL) {  }
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  
   }  
   /*************** function likelione ***********/
   /* Reads comments: lines beginning with '#' */  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   while((c=getc(ficpar))=='#' && c!= EOF){  {
     ungetc(c,ficpar);    /* This routine should help understanding what is done with 
     fgets(line, MAXLINE, ficpar);       the selection of individuals/waves and
     puts(line);       to check the exact contribution to the likelihood.
     fputs(line,ficparo);       Plotting could be done.
   }     */
   ungetc(c,ficpar);    int k;
   
   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);    if(*globpri !=0){ /* Just counts and sums, no printings */
   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);      strcpy(fileresilk,"ilk"); 
   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);      strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   covar=matrix(1,NCOVMAX,1,n);            printf("Problem with resultfile: %s\n", fileresilk);
   if (strlen(model)<=1) cptcovn=0;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   else {      }
     j=0;      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");
     j=nbocc(model,'+');      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     cptcovn=j+1;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   }      for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   ncovmodel=2+cptcovn;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    }
    
   /* Read guess parameters */    *fretone=(*funcone)(p);
   /* Reads comments: lines beginning with '#' */    if(*globpri !=0){
   while((c=getc(ficpar))=='#' && c!= EOF){      fclose(ficresilk);
     ungetc(c,ficpar);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     fgets(line, MAXLINE, ficpar);      fflush(fichtm); 
     puts(line);    } 
     fputs(line,ficparo);    return;
   }  }
   ungetc(c,ficpar);  
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  /*********** Maximum Likelihood Estimation ***************/
     for(i=1; i <=nlstate; i++)  
     for(j=1; j <=nlstate+ndeath-1; j++){  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       fscanf(ficpar,"%1d%1d",&i1,&j1);  {
       fprintf(ficparo,"%1d%1d",i1,j1);    int i,j, iter;
       printf("%1d%1d",i,j);    double **xi;
       for(k=1; k<=ncovmodel;k++){    double fret;
         fscanf(ficpar," %lf",&param[i][j][k]);    double fretone; /* Only one call to likelihood */
         printf(" %lf",param[i][j][k]);    /*  char filerespow[FILENAMELENGTH];*/
         fprintf(ficparo," %lf",param[i][j][k]);    xi=matrix(1,npar,1,npar);
       }    for (i=1;i<=npar;i++)
       fscanf(ficpar,"\n");      for (j=1;j<=npar;j++)
       printf("\n");        xi[i][j]=(i==j ? 1.0 : 0.0);
       fprintf(ficparo,"\n");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     }    strcpy(filerespow,"pow"); 
      strcat(filerespow,fileres);
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   p=param[1][1];      printf("Problem with resultfile: %s\n", filerespow);
        fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     ungetc(c,ficpar);    for (i=1;i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);      for(j=1;j<=nlstate+ndeath;j++)
     puts(line);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     fputs(line,ficparo);    fprintf(ficrespow,"\n");
   }  
   ungetc(c,ficpar);    powell(p,xi,npar,ftol,&iter,&fret,func);
   
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    free_matrix(xi,1,npar,1,npar);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    fclose(ficrespow);
   for(i=1; i <=nlstate; i++){    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     for(j=1; j <=nlstate+ndeath-1; j++){    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       fscanf(ficpar,"%1d%1d",&i1,&j1);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);  }
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar,"%le",&delti3[i][j][k]);  /**** Computes Hessian and covariance matrix ***/
         printf(" %le",delti3[i][j][k]);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
         fprintf(ficparo," %le",delti3[i][j][k]);  {
       }    double  **a,**y,*x,pd;
       fscanf(ficpar,"\n");    double **hess;
       printf("\n");    int i, j,jk;
       fprintf(ficparo,"\n");    int *indx;
     }  
   }    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   delti=delti3[1][1];    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
      void lubksb(double **a, int npar, int *indx, double b[]) ;
   /* Reads comments: lines beginning with '#' */    void ludcmp(double **a, int npar, int *indx, double *d) ;
   while((c=getc(ficpar))=='#' && c!= EOF){    double gompertz(double p[]);
     ungetc(c,ficpar);    hess=matrix(1,npar,1,npar);
     fgets(line, MAXLINE, ficpar);  
     puts(line);    printf("\nCalculation of the hessian matrix. Wait...\n");
     fputs(line,ficparo);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   }    for (i=1;i<=npar;i++){
   ungetc(c,ficpar);      printf("%d",i);fflush(stdout);
        fprintf(ficlog,"%d",i);fflush(ficlog);
   matcov=matrix(1,npar,1,npar);     
   for(i=1; i <=npar; i++){       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     fscanf(ficpar,"%s",&str);      
     printf("%s",str);      /*  printf(" %f ",p[i]);
     fprintf(ficparo,"%s",str);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     for(j=1; j <=i; j++){    }
       fscanf(ficpar," %le",&matcov[i][j]);    
       printf(" %.5le",matcov[i][j]);    for (i=1;i<=npar;i++) {
       fprintf(ficparo," %.5le",matcov[i][j]);      for (j=1;j<=npar;j++)  {
     }        if (j>i) { 
     fscanf(ficpar,"\n");          printf(".%d%d",i,j);fflush(stdout);
     printf("\n");          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     fprintf(ficparo,"\n");          hess[i][j]=hessij(p,delti,i,j,func,npar);
   }          
   for(i=1; i <=npar; i++)          hess[j][i]=hess[i][j];    
     for(j=i+1;j<=npar;j++)          /*printf(" %lf ",hess[i][j]);*/
       matcov[i][j]=matcov[j][i];        }
          }
   printf("\n");    }
     printf("\n");
     fprintf(ficlog,"\n");
    if(mle==1){  
     /*-------- data file ----------*/    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     if((ficres =fopen(fileres,"w"))==NULL) {    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       printf("Problem with resultfile: %s\n", fileres);goto end;    
     }    a=matrix(1,npar,1,npar);
     fprintf(ficres,"#%s\n",version);    y=matrix(1,npar,1,npar);
        x=vector(1,npar);
     if((fic=fopen(datafile,"r"))==NULL)    {    indx=ivector(1,npar);
       printf("Problem with datafile: %s\n", datafile);goto end;    for (i=1;i<=npar;i++)
     }      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     ludcmp(a,npar,indx,&pd);
     n= lastobs;  
     severity = vector(1,maxwav);    for (j=1;j<=npar;j++) {
     outcome=imatrix(1,maxwav+1,1,n);      for (i=1;i<=npar;i++) x[i]=0;
     num=ivector(1,n);      x[j]=1;
     moisnais=vector(1,n);      lubksb(a,npar,indx,x);
     annais=vector(1,n);      for (i=1;i<=npar;i++){ 
     moisdc=vector(1,n);        matcov[i][j]=x[i];
     andc=vector(1,n);      }
     agedc=vector(1,n);    }
     cod=ivector(1,n);  
     weight=vector(1,n);    printf("\n#Hessian matrix#\n");
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    fprintf(ficlog,"\n#Hessian matrix#\n");
     mint=matrix(1,maxwav,1,n);    for (i=1;i<=npar;i++) { 
     anint=matrix(1,maxwav,1,n);      for (j=1;j<=npar;j++) { 
     s=imatrix(1,maxwav+1,1,n);        printf("%.3e ",hess[i][j]);
     adl=imatrix(1,maxwav+1,1,n);            fprintf(ficlog,"%.3e ",hess[i][j]);
     tab=ivector(1,NCOVMAX);      }
     ncodemax=ivector(1,8);      printf("\n");
       fprintf(ficlog,"\n");
     i=1;    }
     while (fgets(line, MAXLINE, fic) != NULL)    {  
       if ((i >= firstobs) && (i <=lastobs)) {    /* Recompute Inverse */
            for (i=1;i<=npar;i++)
         for (j=maxwav;j>=1;j--){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    ludcmp(a,npar,indx,&pd);
           strcpy(line,stra);  
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    /*  printf("\n#Hessian matrix recomputed#\n");
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }    for (j=1;j<=npar;j++) {
              for (i=1;i<=npar;i++) x[i]=0;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      x[j]=1;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        y[i][j]=x[i];
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        printf("%.3e ",y[i][j]);
         fprintf(ficlog,"%.3e ",y[i][j]);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      }
         for (j=ncov;j>=1;j--){      printf("\n");
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      fprintf(ficlog,"\n");
         }    }
         num[i]=atol(stra);    */
   
         /*printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.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]),  (mint[5][i]), (anint[5][i]), (s[5][i]),  (mint[6][i]), (anint[6][i]), (s[6][i]));*/    free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
         i=i+1;    free_vector(x,1,npar);
       }    free_ivector(indx,1,npar);
     }    free_matrix(hess,1,npar,1,npar);
   
     /*scanf("%d",i);*/  
   imx=i-1; /* Number of individuals */  }
   
   /* Calculation of the number of parameter from char model*/  /*************** hessian matrix ****************/
   Tvar=ivector(1,8);      double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
      {
   if (strlen(model) >1){    int i;
     j=0;    int l=1, lmax=20;
     j=nbocc(model,'+');    double k1,k2;
     cptcovn=j+1;    double p2[NPARMAX+1];
        double res;
     strcpy(modelsav,model);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     if (j==0) {    double fx;
       cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb);    int k=0,kmax=10;
     }    double l1;
     else {  
       for(i=j; i>=1;i--){    fx=func(x);
         cutv(stra,strb,modelsav,'+');    for (i=1;i<=npar;i++) p2[i]=x[i];
         if (strchr(strb,'*')) {    for(l=0 ; l <=lmax; l++){
           cutv(strd,strc,strb,'*');      l1=pow(10,l);
           cutv(strb,stre,strc,'V');Tvar[i+1]=ncov+1;      delts=delt;
           cutv(strb,strc,strd,'V');      for(k=1 ; k <kmax; k=k+1){
           for (k=1; k<=lastobs;k++)        delt = delta*(l1*k);
             covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        p2[theta]=x[theta] +delt;
         }        k1=func(p2)-fx;
         else {cutv(strd,strc,strb,'V');        p2[theta]=x[theta]-delt;
         Tvar[i+1]=atoi(strc);        k2=func(p2)-fx;
         }        /*res= (k1-2.0*fx+k2)/delt/delt; */
         strcpy(modelsav,stra);          res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       }        
       cutv(strd,strc,stra,'V');  #ifdef DEBUG
       Tvar[1]=atoi(strc);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   }  #endif
   /*printf("tvar=%d ",Tvar[1]);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   scanf("%d ",i);*/        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     fclose(fic);          k=kmax;
         }
     if (weightopt != 1) { /* Maximisation without weights*/        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       for(i=1;i<=n;i++) weight[i]=1.0;          k=kmax; l=lmax*10.;
     }        }
     /*-calculation of age at interview from date of interview and age at death -*/        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     agev=matrix(1,maxwav,1,imx);          delts=delt;
            }
     for (i=1; i<=imx; i++)  {      }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    }
       for(m=1; (m<= maxwav); m++){    delti[theta]=delts;
         if(s[m][i] >0){    return res; 
           if (s[m][i] == nlstate+1) {    
             if(agedc[i]>0)  }
               if(moisdc[i]!=99 && andc[i]!=9999)  
               agev[m][i]=agedc[i];  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
             else{  {
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    int i;
               agev[m][i]=-1;    int l=1, l1, lmax=20;
             }    double k1,k2,k3,k4,res,fx;
           }    double p2[NPARMAX+1];
           else if(s[m][i] !=9){ /* Should no more exist */    int k;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  
             if(mint[m][i]==99 || anint[m][i]==9999)    fx=func(x);
               agev[m][i]=1;    for (k=1; k<=2; k++) {
             else if(agev[m][i] <agemin){      for (i=1;i<=npar;i++) p2[i]=x[i];
               agemin=agev[m][i];      p2[thetai]=x[thetai]+delti[thetai]/k;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
             }      k1=func(p2)-fx;
             else if(agev[m][i] >agemax){    
               agemax=agev[m][i];      p2[thetai]=x[thetai]+delti[thetai]/k;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
             }      k2=func(p2)-fx;
             /*agev[m][i]=anint[m][i]-annais[i];*/    
             /*   agev[m][i] = age[i]+2*m;*/      p2[thetai]=x[thetai]-delti[thetai]/k;
           }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           else { /* =9 */      k3=func(p2)-fx;
             agev[m][i]=1;    
             s[m][i]=-1;      p2[thetai]=x[thetai]-delti[thetai]/k;
           }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         }      k4=func(p2)-fx;
         else /*= 0 Unknown */      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
           agev[m][i]=1;  #ifdef DEBUG
       }      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
          fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     }  #endif
     for (i=1; i<=imx; i++)  {    }
       for(m=1; (m<= maxwav); m++){    return res;
         if (s[m][i] > (nlstate+ndeath)) {  }
           printf("Error: Wrong value in nlstate or ndeath\n");    
           goto end;  /************** Inverse of matrix **************/
         }  void ludcmp(double **a, int n, int *indx, double *d) 
       }  { 
     }    int i,imax,j,k; 
     double big,dum,sum,temp; 
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    double *vv; 
    
     free_vector(severity,1,maxwav);    vv=vector(1,n); 
     free_imatrix(outcome,1,maxwav+1,1,n);    *d=1.0; 
     free_vector(moisnais,1,n);    for (i=1;i<=n;i++) { 
     free_vector(annais,1,n);      big=0.0; 
     free_matrix(mint,1,maxwav,1,n);      for (j=1;j<=n;j++) 
     free_matrix(anint,1,maxwav,1,n);        if ((temp=fabs(a[i][j])) > big) big=temp; 
     free_vector(moisdc,1,n);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     free_vector(andc,1,n);      vv[i]=1.0/big; 
     } 
        for (j=1;j<=n;j++) { 
     wav=ivector(1,imx);      for (i=1;i<j;i++) { 
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        sum=a[i][j]; 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
            a[i][j]=sum; 
     /* Concatenates waves */      } 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      big=0.0; 
       for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
 Tcode=ivector(1,100);        for (k=1;k<j;k++) 
    nbcode=imatrix(1,nvar,1,8);            sum -= a[i][k]*a[k][j]; 
    ncodemax[1]=1;        a[i][j]=sum; 
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
            big=dum; 
    codtab=imatrix(1,100,1,10);          imax=i; 
    h=0;        } 
    m=pow(2,cptcovn);      } 
        if (j != imax) { 
    for(k=1;k<=cptcovn; k++){        for (k=1;k<=n;k++) { 
      for(i=1; i <=(m/pow(2,k));i++){          dum=a[imax][k]; 
        for(j=1; j <= ncodemax[k]; j++){          a[imax][k]=a[j][k]; 
          for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){          a[j][k]=dum; 
            h++;        } 
            if (h>m) h=1;codtab[h][k]=j;        *d = -(*d); 
          }        vv[imax]=vv[j]; 
        }      } 
      }      indx[j]=imax; 
    }      if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
    /*for(i=1; i <=m ;i++){        dum=1.0/(a[j][j]); 
      for(k=1; k <=cptcovn; k++){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
        printf("i=%d k=%d %d ",i,k,codtab[i][k]);      } 
      }    } 
      printf("\n");    free_vector(vv,1,n);  /* Doesn't work */
    }*/  ;
    /*scanf("%d",i);*/  } 
      
    /* Calculates basic frequencies. Computes observed prevalence at single age  void lubksb(double **a, int n, int *indx, double b[]) 
        and prints on file fileres'p'. */  { 
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);    int i,ii=0,ip,j; 
     double sum; 
    
   /*scanf("%d ",i);*/    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
       sum=b[ip]; 
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      b[ip]=b[i]; 
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      if (ii) 
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      else if (sum) ii=i; 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      b[i]=sum; 
        } 
     /* For Powell, parameters are in a vector p[] starting at p[1]    for (i=n;i>=1;i--) { 
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */      sum=b[i]; 
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
          b[i]=sum/a[i][i]; 
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    } 
   } 
      
     /*--------- results files --------------*/  void pstamp(FILE *fichier)
     fprintf(ficres,"\ntitle=%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(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
    jk=1;  }
    fprintf(ficres,"# Parameters\n");  
    printf("# Parameters\n");  /************ Frequencies ********************/
    for(i=1,jk=1; i <=nlstate; i++){  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
      for(k=1; k <=(nlstate+ndeath); k++){  {  /* Some frequencies */
        if (k != i)    
          {    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
            printf("%d%d ",i,k);    int first;
            fprintf(ficres,"%1d%1d ",i,k);    double ***freq; /* Frequencies */
            for(j=1; j <=ncovmodel; j++){    double *pp, **prop;
              printf("%f ",p[jk]);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
              fprintf(ficres,"%f ",p[jk]);    char fileresp[FILENAMELENGTH];
              jk++;    
            }    pp=vector(1,nlstate);
            printf("\n");    prop=matrix(1,nlstate,iagemin,iagemax+3);
            fprintf(ficres,"\n");    strcpy(fileresp,"p");
          }    strcat(fileresp,fileres);
      }    if((ficresp=fopen(fileresp,"w"))==NULL) {
    }      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     /* Computing hessian and covariance matrix */      exit(0);
     ftolhess=ftol; /* Usually correct */    }
     hesscov(matcov, p, npar, delti, ftolhess, func);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     fprintf(ficres,"# Scales\n");    j1=0;
     printf("# Scales\n");    
      for(i=1,jk=1; i <=nlstate; i++){    j=cptcoveff;
       for(j=1; j <=nlstate+ndeath; j++){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         if (j!=i) {  
           fprintf(ficres,"%1d%1d",i,j);    first=1;
           printf("%1d%1d",i,j);  
           for(k=1; k<=ncovmodel;k++){    for(k1=1; k1<=j;k1++){
             printf(" %.5e",delti[jk]);      for(i1=1; i1<=ncodemax[k1];i1++){
             fprintf(ficres," %.5e",delti[jk]);        j1++;
             jk++;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           }          scanf("%d", i);*/
           printf("\n");        for (i=-5; i<=nlstate+ndeath; i++)  
           fprintf(ficres,"\n");          for (jk=-5; jk<=nlstate+ndeath; jk++)  
         }            for(m=iagemin; m <= iagemax+3; m++)
       }              freq[i][jk][m]=0;
       }  
          for (i=1; i<=nlstate; i++)  
     k=1;        for(m=iagemin; m <= iagemax+3; m++)
     fprintf(ficres,"# Covariance\n");          prop[i][m]=0;
     printf("# Covariance\n");        
     for(i=1;i<=npar;i++){        dateintsum=0;
       /*  if (k>nlstate) k=1;        k2cpt=0;
       i1=(i-1)/(ncovmodel*nlstate)+1;        for (i=1; i<=imx; i++) {
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          bool=1;
       printf("%s%d%d",alph[k],i1,tab[i]);*/          if  (cptcovn>0) {
       fprintf(ficres,"%3d",i);            for (z1=1; z1<=cptcoveff; z1++) 
       printf("%3d",i);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       for(j=1; j<=i;j++){                bool=0;
         fprintf(ficres," %.5e",matcov[i][j]);          }
         printf(" %.5e",matcov[i][j]);          if (bool==1){
       }            for(m=firstpass; m<=lastpass; m++){
       fprintf(ficres,"\n");              k2=anint[m][i]+(mint[m][i]/12.);
       printf("\n");              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       k++;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                    if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     while((c=getc(ficpar))=='#' && c!= EOF){                if (m<lastpass) {
       ungetc(c,ficpar);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       fgets(line, MAXLINE, ficpar);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       puts(line);                }
       fputs(line,ficparo);                
     }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     ungetc(c,ficpar);                  dateintsum=dateintsum+k2;
                    k2cpt++;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);                }
                    /*}*/
     if (fage <= 2) {            }
       bage = agemin;          }
       fage = agemax;        }
     }         
         /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");        pstamp(ficresp);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        if  (cptcovn>0) {
 /*------------ gnuplot -------------*/          fprintf(ficresp, "\n#********** Variable "); 
 chdir(pathcd);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if((ficgp=fopen("graph.plt","w"))==NULL) {          fprintf(ficresp, "**********\n#");
     printf("Problem with file graph.plt");goto end;        }
   }        for(i=1; i<=nlstate;i++) 
 #ifdef windows          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   fprintf(ficgp,"cd \"%s\" \n",pathc);        fprintf(ficresp, "\n");
 #endif        
 m=pow(2,cptcovn);        for(i=iagemin; i <= iagemax+3; i++){
            if(i==iagemax+3){
  /* 1eme*/            fprintf(ficlog,"Total");
   for (cpt=1; cpt<= nlstate ; cpt ++) {          }else{
    for (k1=1; k1<= m ; k1 ++) {            if(first==1){
               first=0;
 #ifdef windows              printf("See log file for details...\n");
     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            fprintf(ficlog,"Age %d", i);
 #ifdef unix          }
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);          for(jk=1; jk <=nlstate ; jk++){
 #endif            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
 for (i=1; i<= nlstate ; i ++) {          }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for(jk=1; jk <=nlstate ; jk++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");            for(m=-1, pos=0; m <=0 ; m++)
 }              pos += freq[jk][m][i];
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);            if(pp[jk]>=1.e-10){
     for (i=1; i<= nlstate ; i ++) {              if(first==1){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   else fprintf(ficgp," \%%*lf (\%%*lf)");              }
 }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);            }else{
      for (i=1; i<= nlstate ; i ++) {              if(first==1)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   else fprintf(ficgp," \%%*lf (\%%*lf)");              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 }              }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          }
 #ifdef unix  
 fprintf(ficgp,"\nset ter gif small size 400,300");          for(jk=1; jk <=nlstate ; jk++){
 #endif            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              pp[jk] += freq[jk][m][i];
    }          }       
   }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   /*2 eme*/            pos += pp[jk];
             posprop += prop[jk][i];
   for (k1=1; k1<= m ; k1 ++) {          }
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);          for(jk=1; jk <=nlstate ; jk++){
                if(pos>=1.e-5){
     for (i=1; i<= nlstate+1 ; i ++) {              if(first==1)
       k=2*i;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       for (j=1; j<= nlstate+1 ; j ++) {            }else{
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              if(first==1)
   else fprintf(ficgp," \%%*lf (\%%*lf)");                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 }                fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);            if( i <= iagemax){
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);              if(pos>=1.e-5){
       for (j=1; j<= nlstate+1 ; j ++) {                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                /*probs[i][jk][j1]= pp[jk]/pos;*/
         else fprintf(ficgp," \%%*lf (\%%*lf)");                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
 }                }
       fprintf(ficgp,"\" t\"\" w l 0,");              else
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       for (j=1; j<= nlstate+1 ; j ++) {            }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");          
 }            for(jk=-1; jk <=nlstate+ndeath; jk++)
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");            for(m=-1; m <=nlstate+ndeath; m++)
       else fprintf(ficgp,"\" t\"\" w l 0,");              if(freq[jk][m][i] !=0 ) {
     }              if(first==1)
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                }
   /*3eme*/          if(i <= iagemax)
             fprintf(ficresp,"\n");
    for (k1=1; k1<= m ; k1 ++) {          if(first==1)
     for (cpt=1; cpt<= nlstate ; cpt ++) {            printf("Others in log...\n");
       k=2+nlstate*(cpt-1);          fprintf(ficlog,"\n");
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);        }
       for (i=1; i< 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);    }
       }    dateintmean=dateintsum/k2cpt; 
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);   
     }    fclose(ficresp);
    }    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
      free_vector(pp,1,nlstate);
   /* CV preval stat */    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     for (k1=1; k1<= m ; k1 ++) {    /* End of Freq */
     for (cpt=1; cpt<nlstate ; cpt ++) {  }
       k=3;  
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);  /************ Prevalence ********************/
       for (i=1; i< nlstate ; i ++)  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
         fprintf(ficgp,"+$%d",k+i+1);  {  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    /* 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).
       l=3+(nlstate+ndeath)*cpt;       We still use firstpass and lastpass as another selection.
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    */
       for (i=1; i< nlstate ; i ++) {   
         l=3+(nlstate+ndeath)*cpt;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
         fprintf(ficgp,"+$%d",l+i+1);    double ***freq; /* Frequencies */
       }    double *pp, **prop;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      double pos,posprop; 
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    double  y2; /* in fractional years */
     }    int iagemin, iagemax;
   }  
      iagemin= (int) agemin;
   /* proba elementaires */    iagemax= (int) agemax;
   for(i=1,jk=1; i <=nlstate; i++){    /*pp=vector(1,nlstate);*/
     for(k=1; k <=(nlstate+ndeath); k++){    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       if (k != i) {    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
         /*  fprintf(ficgp,"%1d%1d ",i,k);*/    j1=0;
         for(j=1; j <=ncovmodel; j++){    
           fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);    j=cptcoveff;
           jk++;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           fprintf(ficgp,"\n");    
         }    for(k1=1; k1<=j;k1++){
       }      for(i1=1; i1<=ncodemax[k1];i1++){
     }        j1++;
   }        
   for(jk=1; jk <=m; jk++) {        for (i=1; i<=nlstate; i++)  
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);          for(m=iagemin; m <= iagemax+3; m++)
   for(i=1; i <=nlstate; i++) {            prop[i][m]=0.0;
     for(k=1; k <=(nlstate+ndeath); k++){       
       if (k != i) {        for (i=1; i<=imx; i++) { /* Each individual */
         fprintf(ficgp," exp(a%d%d+b%d%d*x",i,k,i,k);          bool=1;
         for(j=3; j <=ncovmodel; j++)          if  (cptcovn>0) {
           fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            for (z1=1; z1<=cptcoveff; z1++) 
         fprintf(ficgp,")/(1");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         for(k1=1; k1 <=(nlstate+ndeath); k1++)                bool=0;
           if (k1 != i) {          } 
             fprintf(ficgp,"+exp(a%d%d+b%d%d*x",i,k1,i,k1);          if (bool==1) { 
             for(j=3; j <=ncovmodel; j++)            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
               fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
             fprintf(ficgp,")");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
           }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         fprintf(ficgp,") t \"p%d%d\" ", i,k);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       if ((i+k)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                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) { 
     }                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
   }                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
 fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);                    prop[s[m][i]][iagemax+3] += weight[i]; 
   }                } 
                }
  fclose(ficgp);            } /* end selection of waves */
           }
     chdir(path);        }
     free_matrix(agev,1,maxwav,1,imx);        for(i=iagemin; i <= iagemax+3; i++){  
     free_ivector(wav,1,imx);          
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            posprop += prop[jk][i]; 
              } 
     free_imatrix(s,1,maxwav+1,1,n);  
              for(jk=1; jk <=nlstate ; jk++){     
                if( i <=  iagemax){ 
     free_ivector(num,1,n);              if(posprop>=1.e-5){ 
     free_vector(agedc,1,n);                probs[i][jk][j1]= prop[jk][i]/posprop;
     free_vector(weight,1,n);              } 
     /*free_matrix(covar,1,NCOVMAX,1,n);*/            } 
     fclose(ficparo);          }/* end jk */ 
     fclose(ficres);        }/* end i */ 
    }      } /* end i1 */
        } /* end k1 */
    /*________fin mle=1_________*/    
        /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     /*free_vector(pp,1,nlstate);*/
      free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     /* No more information from the sample is required now */  }  /* End of prevalence */
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){  /************* Waves Concatenation ***************/
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  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)
     puts(line);  {
     fputs(line,ficparo);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   }       Death is a valid wave (if date is known).
   ungetc(c,ficpar);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);       */
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);  
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    int i, mi, m;
 /*--------- index.htm --------*/    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        double sum=0., jmean=0.;*/
   if((fichtm=fopen("index.htm","w"))==NULL)    {    int first;
     printf("Problem with index.htm \n");goto end;    int j, k=0,jk, ju, jl;
   }    double sum=0.;
     first=0;
  fprintf(fichtm,"<body><ul> Imach, Version 0.63<hr> <li>Outputs files<br><br>\n    jmin=1e+5;
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    jmax=-1;
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    jmean=0.;
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    for(i=1; i<=imx; i++){
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>      mi=0;
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>      m=firstpass;
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>      while(s[m][i] <= nlstate){
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>          mw[++mi][i]=m;
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);        if(m >=lastpass)
           break;
  fprintf(fichtm," <li>Graphs</li>\n<p>");        else
           m++;
  m=cptcovn;      }/* end while */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      if (s[m][i] > nlstate){
         mi++;     /* Death is another wave */
  j1=0;        /* if(mi==0)  never been interviewed correctly before death */
  for(k1=1; k1<=m;k1++){           /* Only death is a correct wave */
    for(i1=1; i1<=ncodemax[k1];i1++){        mw[mi][i]=m;
        j1++;      }
        if (cptcovn > 0) {  
          fprintf(fichtm,"<hr>************ Results for covariates");      wav[i]=mi;
          for (cpt=1; cpt<=cptcovn;cpt++)      if(mi==0){
            fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);        nbwarn++;
          fprintf(fichtm," ************\n<hr>");        if(first==0){
        }          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          first=1;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            }
        for(cpt=1; cpt<nlstate;cpt++){        if(first==1){
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        }
        }      } /* end mi==0 */
     for(cpt=1; cpt<=nlstate;cpt++) {    } /* End individuals */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  
 interval) in state (%d): v%s%d%d.gif <br>    for(i=1; i<=imx; i++){
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        for(mi=1; mi<wav[i];mi++){
      }        if (stepm <=0)
      for(cpt=1; cpt<=nlstate;cpt++) {          dh[mi][i]=1;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        else{
 <img src=\"ex%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
      }            if (agedc[i] < 2*AGESUP) {
      fprintf(fichtm,"\n<br>- Total life expectancy by age and              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
 health expectancies in states (1) and (2): e%s%d.gif<br>              if(j==0) j=1;  /* Survives at least one month after exam */
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);              else if(j<0){
 fprintf(fichtm,"\n</body>");                nberr++;
    }                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
  }                j=1; /* Temporary Dangerous patch */
 fclose(fichtm);                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]);
   /*--------------- Prevalence limit --------------*/                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);
                }
   strcpy(filerespl,"pl");              k=k+1;
   strcat(filerespl,fileres);              if (j >= jmax){
   if((ficrespl=fopen(filerespl,"w"))==NULL) {                jmax=j;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;                ijmax=i;
   }              }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);              if (j <= jmin){
   fprintf(ficrespl,"#Prevalence limit\n");                jmin=j;
   fprintf(ficrespl,"#Age ");                ijmin=i;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);              }
   fprintf(ficrespl,"\n");              sum=sum+j;
                /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   prlim=matrix(1,nlstate,1,nlstate);              /*    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 */          }
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          else{
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  /*        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]); */
   k=0;  
   agebase=agemin;            k=k+1;
   agelim=agemax;            if (j >= jmax) {
   ftolpl=1.e-10;              jmax=j;
   i1=cptcovn;              ijmax=i;
   if (cptcovn < 1){i1=1;}            }
             else if (j <= jmin){
   for(cptcov=1;cptcov<=i1;cptcov++){              jmin=j;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              ijmin=i;
         k=k+1;            }
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
         fprintf(ficrespl,"\n#****** ");            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
         for(j=1;j<=cptcovn;j++)            if(j<0){
           fprintf(ficrespl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);              nberr++;
         fprintf(ficrespl,"******\n");              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                      fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
         for (age=agebase; age<=agelim; age++){            }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            sum=sum+j;
           fprintf(ficrespl,"%.0f",age );          }
           for(i=1; i<=nlstate;i++)          jk= j/stepm;
           fprintf(ficrespl," %.5f", prlim[i][i]);          jl= j -jk*stepm;
           fprintf(ficrespl,"\n");          ju= j -(jk+1)*stepm;
         }          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       }            if(jl==0){
     }              dh[mi][i]=jk;
   fclose(ficrespl);              bh[mi][i]=0;
   /*------------- h Pij x at various ages ------------*/            }else{ /* We want a negative bias in order to only have interpolation ie
                      * at the price of an extra matrix product in likelihood */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);              dh[mi][i]=jk+1;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {              bh[mi][i]=ju;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;            }
   }          }else{
   printf("Computing pij: result on file '%s' \n", filerespij);            if(jl <= -ju){
                dh[mi][i]=jk;
   stepsize=(int) (stepm+YEARM-1)/YEARM;              bh[mi][i]=jl;       /* bias is positive if real duration
   if (stepm<=24) stepsize=2;                                   * is higher than the multiple of stepm and negative otherwise.
                                    */
   agelim=AGESUP;            }
   hstepm=stepsize*YEARM; /* Every year of age */            else{
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */              dh[mi][i]=jk+1;
                bh[mi][i]=ju;
   k=0;            }
   for(cptcov=1;cptcov<=i1;cptcov++){            if(dh[mi][i]==0){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              dh[mi][i]=1; /* At least one step */
       k=k+1;              bh[mi][i]=ju; /* At least one step */
         fprintf(ficrespij,"\n#****** ");              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
         for(j=1;j<=cptcovn;j++)            }
           fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);          } /* end if mle */
         fprintf(ficrespij,"******\n");        }
              } /* end wave */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    jmean=sum/k;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    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);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    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);
           oldm=oldms;savm=savms;   }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           fprintf(ficrespij,"# Age");  /*********** Tricode ****************************/
           for(i=1; i<=nlstate;i++)  void tricode(int *Tvar, int **nbcode, int imx)
             for(j=1; j<=nlstate+ndeath;j++)  {
               fprintf(ficrespij," %1d-%1d",i,j);    
           fprintf(ficrespij,"\n");    int Ndum[20],ij=1, k, j, i, maxncov=19;
           for (h=0; h<=nhstepm; h++){    int cptcode=0;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    cptcoveff=0; 
             for(i=1; i<=nlstate;i++)   
               for(j=1; j<=nlstate+ndeath;j++)    for (k=0; k<maxncov; k++) Ndum[k]=0;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    for (k=1; k<=7; k++) ncodemax[k]=0;
             fprintf(ficrespij,"\n");  
           }    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
           fprintf(ficrespij,"\n");                                 modality*/ 
         }        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     }        Ndum[ij]++; /*store the modality */
   }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   fclose(ficrespij);                                         Tvar[j]. If V=sex and male is 0 and 
                                          female is 1, then  cptcode=1.*/
   /*---------- Health expectancies and variances ------------*/      }
   
   strcpy(filerest,"t");      for (i=0; i<=cptcode; i++) {
   strcat(filerest,fileres);        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 */
   if((ficrest=fopen(filerest,"w"))==NULL) {      }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  
   }      ij=1; 
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      for (i=1; i<=ncodemax[j]; i++) {
         for (k=0; k<= maxncov; k++) {
           if (Ndum[k] != 0) {
   strcpy(filerese,"e");            nbcode[Tvar[j]][ij]=k; 
   strcat(filerese,fileres);            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   if((ficreseij=fopen(filerese,"w"))==NULL) {            
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);            ij++;
   }          }
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);          if (ij > ncodemax[j]) break; 
         }  
  strcpy(fileresv,"v");      } 
   strcat(fileresv,fileres);    }  
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);   for (k=0; k< maxncov; k++) Ndum[k]=0;
   }  
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);   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.*/
   k=0;     ij=Tvar[i];
   for(cptcov=1;cptcov<=i1;cptcov++){     Ndum[ij]++;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   }
       k=k+1;  
       fprintf(ficrest,"\n#****** ");   ij=1;
       for(j=1;j<=cptcovn;j++)   for (i=1; i<= maxncov; i++) {
         fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);     if((Ndum[i]!=0) && (i<=ncovcol)){
       fprintf(ficrest,"******\n");       Tvaraff[ij]=i; /*For printing */
        ij++;
       fprintf(ficreseij,"\n#****** ");     }
       for(j=1;j<=cptcovn;j++)   }
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);   
       fprintf(ficreseij,"******\n");   cptcoveff=ij-1; /*Number of simple covariates*/
   }
       fprintf(ficresvij,"\n#****** ");  
       for(j=1;j<=cptcovn;j++)  /*********** Health Expectancies ****************/
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  
       fprintf(ficresvij,"******\n");  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[] )
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  {
       oldm=oldms;savm=savms;    /* Health expectancies, no variances */
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    double age, agelim, hf;
       oldm=oldms;savm=savms;    double ***p3mat;
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    double eip;
        
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    pstamp(ficreseij);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
       fprintf(ficrest,"\n");    fprintf(ficreseij,"# Age");
            for(i=1; i<=nlstate;i++){
       hf=1;      for(j=1; j<=nlstate;j++){
       if (stepm >= YEARM) hf=stepm/YEARM;        fprintf(ficreseij," e%1d%1d ",i,j);
       epj=vector(1,nlstate+1);      }
       for(age=bage; age <=fage ;age++){      fprintf(ficreseij," e%1d. ",i);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    }
         fprintf(ficrest," %.0f",age);    fprintf(ficreseij,"\n");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    if(estepm < stepm){
           }      printf ("Problem %d lower than %d\n",estepm, stepm);
           epj[nlstate+1] +=epj[j];    }
         }    else  hstepm=estepm;   
         for(i=1, vepp=0.;i <=nlstate;i++)    /* We compute the life expectancy from trapezoids spaced every estepm months
           for(j=1;j <=nlstate;j++)     * This is mainly to measure the difference between two models: for example
             vepp += vareij[i][j][(int)age];     * if stepm=24 months pijx are given only every 2 years and by summing them
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));     * we are calculating an estimate of the Life Expectancy assuming a linear 
         for(j=1;j <=nlstate;j++){     * progression in between and thus overestimating or underestimating according
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));     * 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
         fprintf(ficrest,"\n");     * to compare the new estimate of Life expectancy with the same linear 
       }     * hypothesis. A more precise result, taking into account a more precise
     }     * curvature will be obtained if estepm is as small as stepm. */
   }  
            /* For example we decided to compute the life expectancy with the smallest unit */
  fclose(ficreseij);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
  fclose(ficresvij);       nhstepm is the number of hstepm from age to agelim 
   fclose(ficrest);       nstepm is the number of stepm from age to agelin. 
   fclose(ficpar);       Look at hpijx to understand the reason of that which relies in memory size
   free_vector(epj,1,nlstate+1);       and note for a fixed period like estepm months */
   /*scanf("%d ",i); */    /* 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
   /*------- Variance limit prevalence------*/         means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 strcpy(fileresvpl,"vpl");       results. So we changed our mind and took the option of the best precision.
   strcat(fileresvpl,fileres);    */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  
     exit(0);    agelim=AGESUP;
   }    /* nhstepm age range expressed in number of stepm */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
  k=0;    /* if (stepm >= YEARM) hstepm=1;*/
  for(cptcov=1;cptcov<=i1;cptcov++){    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      k=k+1;  
      fprintf(ficresvpl,"\n#****** ");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
      for(j=1;j<=cptcovn;j++)      /* Computed by stepm unit matrices, product of hstepm matrices, stored
        fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
      fprintf(ficresvpl,"******\n");      
            hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
      varpl=matrix(1,nlstate,(int) bage, (int) fage);      
      oldm=oldms;savm=savms;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      
    }      printf("%d|",(int)age);fflush(stdout);
  }      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       
   fclose(ficresvpl);      /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
   /*---------- End : free ----------------*/        for(j=1; j<=nlstate;j++)
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
              eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);            
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
    
            }
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      fprintf(ficreseij,"%3.0f",age );
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      for(i=1; i<=nlstate;i++){
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        eip=0;
          for(j=1; j<=nlstate;j++){
   free_matrix(matcov,1,npar,1,npar);          eip +=eij[i][j][(int)age];
   free_vector(delti,1,npar);          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
          }
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        fprintf(ficreseij,"%9.4f", eip );
       }
   printf("End of Imach\n");      fprintf(ficreseij,"\n");
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      
      }
   /* 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);*/    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*printf("Total time was %d uSec.\n", total_usecs);*/    printf("\n");
   /*------ End -----------*/    fprintf(ficlog,"\n");
     
  end:  }
 #ifdef windows  
  chdir(pathcd);  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[] )
 #endif  
  system("wgnuplot graph.plt");  {
     /* Covariances of health expectancies eij and of total life expectancies according
 #ifdef windows     to initial status i, ei. .
   while (z[0] != 'q') {    */
     chdir(pathcd);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    double age, agelim, hf;
     scanf("%s",z);    double ***p3matp, ***p3matm, ***varhe;
     if (z[0] == 'c') system("./imach");    double **dnewm,**doldm;
     else if (z[0] == 'e') {    double *xp, *xm;
       chdir(path);    double **gp, **gm;
       system("index.htm");    double ***gradg, ***trgradg;
     }    int theta;
     else if (z[0] == 'q') exit(0);  
   }    double eip, vip;
 #endif  
 }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
     xm=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
     pstamp(ficresstdeij);
     fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficresstdeij,"# Age");
     for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++)
         fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficresstdeij," e%1d. ",i);
     }
     fprintf(ficresstdeij,"\n");
   
     pstamp(ficrescveij);
     fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
         for(i2=1; i2<=nlstate;i2++)
           for(j2=1; j2<=nlstate;j2++){
             cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
               fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           }
       }
     fprintf(ficrescveij,"\n");
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
      * 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
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     /* 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
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
     for (age=bage; age<=fage; age ++){ 
   
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
    
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
       /* Computing  Variances of health expectancies */
       /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
         }
         hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
         for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
               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.;
             }
           }
         }
        
         for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
       }/* End theta */
       
       
       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
       
   
        for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
   
        printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(ij=1;ij<=nlstate*nlstate;ij++)
             for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
       }
       /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficresstdeij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0.;
         vip=0.;
         for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
       fprintf(ficresstdeij,"\n");
   
       fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       fprintf(ficrescveij,"\n");
      
     }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
   
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   
   /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k, cptcode;
     double *xp;
     double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     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(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     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);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
     /* 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
        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 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         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 ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   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));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ 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[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     int k, cptcode;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     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 (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);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem 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;
       lval=strtol(strb,&endptr,10); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight.  Exiting.\n",lval, i,line,linei);
         exit(1);
       }
       weight[i]=(double)(lval); 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self).  Exiting.\n",lval,linei, i,line,j);
           exit(1);
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       } 
       lstra=strlen(stra);
       
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - 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",\
             fileres,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("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,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>",strstart, strtend);
     fclose(fichtm);
     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);
     }
   }
   
   
   

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  Added in v.1.119


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